Patent Publication Number: US-2022235101-A1

Title: Compositions and Methods for Regulation of Chronic Toxoplasma Infection

Description:
RELATED APPLICATION(S) 
     This application claims the benefit of U.S. Provisional Application No. 62/855,659, filed on May 31, 2019. The entire teachings of the above application are incorporated herein by reference. 
    
    
     GOVERNMENT SUPPORT 
     This invention was made with government support under Grant No. 1DP5OD017892 awarded by the National Institutes of Health. The government has certain rights in the invention. 
    
    
     BACKGROUND 
       Toxoplasma gondii  chronically infects approximately a quarter of the world&#39;s population.  Toxoplasma  is a pathogen of humans and many domesticated animals. Recrudescence of latent infections can cause life-threatening disease in the immunocompromised and recurrent ocular lesions in the immunocompetent. Chronic infection is established when rapidly replicating tachyzoites differentiate into slow-growing bradyzoites, which form tissue cysts resistant to immune clearance and current therapeutics. 
     Treatments against  Toxoplasma  fail to clear chronic infections and are often poorly tolerated. Evidence suggests a high rate of congenital transmission in the absence of treatments. Thus, there is a need for new strategies to control  Toxoplasma  infection, particularly chronic infection. 
     SUMMARY OF THE INVENTION 
     In one aspect, the present invention provides genetically altered protozoan parasites comprising a mutation in a bradyzoite formation deficient 1 (BFD1) gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the parasite is an apicomplexan parasite, such as, e.g., a  Toxoplasma  parasite, a  Plasmodium  parasite, a  Hammondia  parasite, a  Neospora  parasite or a  Sarcocystis  parasite. 
     In some embodiments, the mutation is a deletion of all or a portion of the coding sequence of the BFD1 gene. In some embodiments, the mutation is a deletion of the entire coding sequence of the BFD1 gene. 
     In some embodiments, the mutation is a loss-of-function mutation. In some embodiments, the loss-of-function mutation is a null mutation. 
     In some embodiments, the mutation is a dominant negative mutation. 
     In some embodiments, the apicomplexan parasite is  Toxoplasma gondii.    
     In some embodiments, the apicomplexan parasite is  Neospora caninum.    
     In some embodiments, the apicomplexan parasite is  Sarcocystis neurona.    
     In some embodiments, the apicomplexan parasite is  Hammondia hammondi.    
     In some embodiments, the apicomplexan parasite is  Hammondia pardalis.    
     In another aspect, the present invention provides compositions (e.g., vaccine compositions or pharmaceutical compositions) comprising (1) genetically altered protozoan parasites comprising a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite; and (2) a pharmaceutically-acceptable carrier. 
     In some embodiments, the composition is a vaccine composition. 
     In certain embodiments, the composition is a pharmaceutical composition. 
     In some embodiments, the vaccine composition further comprises an adjuvant. 
     In some embodiments, the vaccine composition comprises a live vaccine. 
     In some embodiments, the parasite expresses a heterologous antigen. For example, the heterologous antigen can be a cancer antigen. In some embodiments, the parasite expresses a therapeutic agent, such as, e.g., a peptide or a protein. 
     In another aspect, the present invention provides recombinant nucleic acid vectors comprising a nucleotide sequence encoding a BFD1 protein. 
     In some embodiments, the recombinant nucleic acid vector is an expression vector. 
     In a further aspect, the present invention provides host cells comprising recombinant nucleic acid vectors comprising a nucleotide sequence encoding a BFD1 protein. 
     In some embodiments, the host cell is  Toxoplasma gondii.    
     In another aspect, the present invention provides methods of inducing an immune response to an apicomplexan parasite in a subject in need thereof, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the apicomplexan parasite is  Toxoplasma gondii.    
     In some embodiments, the subject is a human. 
     In some embodiments, the subject is a non-human mammal. 
     In some embodiments, the subject has an acute or chronic apicomplexan parasite infection. 
     In another aspect, the present invention provides methods of inhibiting (e.g., preventing or reducing likelihood of) a chronic apicomplexan parasite infection in a subject, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. 
     In another aspect, the present invention provides methods of treating a chronic infection by an apicomplexan parasite in a subject in need thereof, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. 
     In an additional aspect, the present invention provides methods for inoculating a subject in need thereof with an apicomplexan parasite, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. 
     In a further aspect, the present invention provides methods of administering an antigen to a subject in need thereof comprising administering to the subject a composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite, and wherein the parasite comprises an antigen. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. 
     In some embodiments, the parasite is genetically altered to comprise the antigen. 
     In certain embodiments, the antigen is a cancer antigen. 
     The methods and compositions herein described can be used in pharmaceutical, medical, and veterinary applications, as well as fundamental scientific research and methodologies, as would be identifiable by a skilled person upon reading of the present disclosure. Other features and advantages of the invention will be understood by reference to the drawings, detailed description and examples that follow. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee. 
       The foregoing will be apparent from the following more particular description of example embodiments, as illustrated in the accompanying drawings in which like reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating embodiments. 
         FIGS. 1A-1H  show that a forward genetic screen identifies a putative regulator of  T gondii  differentiation.  FIG. 1A . Construction of a differentiation reporter strain constitutively expressing RFP and Cas9. Following alkaline stress, the strain expresses mNeonGreen (mNG) under the regulation of a bradyzoite promoter, along with another marker of differentiation (SAG2Y). Images taken after 48 h of alkaline stress. Scale bar is 10 μm.  FIG. 1B . Efficient gene disruption is mediated by constitutive Cas9 expression. Transfection and selection for a gRNA targeting the surface antigen SAG1 resulted in gene disruption in 98% of the resulting population. n=3 biological replicates. 92-102 vacuoles were scored for each replicate.  FIG. 1C . Percent of alkaline stressed reporter parasites expressing mNG, quantification by FACS. n=2-4 biological replicates, Mean±SD plotted. 
         FIG. 1D . RNA-sequencing and differential expression (DE) analysis identifies 1311 genes significantly upregulated and 933 genes significantly downregulated in bradyzoites (adjusted p&lt;0.001). Parasites were allowed to invade host cells for 24 h, and then switched to either unstressed or stressed conditions. After 24 h of unstressed growth or 48 h of stressed growth, 100,000 tachyzoites (unstressed, mNG −  parasites) or bradyzoites (stressed, mNG +  parasites) were isolated by FACS. n=3 independent experiments.  FIG. 1E . Screening and analysis workflow. Libraries assembled from proteins containing nucleic acid-binding domains, and sub-divided based on differential expression (L1) or the presence of DNA-binding domains commonly found in transcription factors (L2). Libraries contain 5 gRNAs against each gene, control gRNAs against essential/non-essential genes, noncutting gRNAs, and gRNAs targeting the differentiation reporter. Following transfection, parasites were passaged four times in selective media, then split into alkaline (stressed) or standard culture conditions (unstressed). After 10 days, gRNAs were sequenced from bulk populations, FACS-sorted mNG +  parasites from the stressed population, and from the input library. The log 2  fold-changes from the input library to the final unstressed or stressed mNG +  timepoints are defined as the fitness or differentiation scores, respectively. Candidate genes will be depleted specifically from the mNG +  stressed population (low differentiation score relative to their fitness score).  FIGS. 1F and 1G  show results for the screen with L1 ( FIG. 1F ) and L2 ( FIG. 1G ) show that in addition to the control (mNG), only TGME49_200385 (bradyzoite formation deficient 1; BFD1) displays a low differentiation score compared to its fitness score.  FIG. 1H . Fitness and differentiation scores for individual gRNAs in L2. 
         FIGS. 2A-2I  show that BFD1 is a nuclear factor necessary for differentiation.  FIG. 2A . Neighbor-joining tree showing the phylogenetic relationship of the concatenated SANT domains from BFD1 and its closest homologs in other apicomplexans and humans. BFD1 forms a Glade with human c-Myb (green), distinct from CDCl 5 L-like sequences (blue). Bootstrap values for 1000 trials are displayed.  FIG. 2B . Diagram of BFD1 and human c-Myb highlighting the SANT domains (green). The DNA-binding repeats of BFD1 are similar to the second and third repeats of c-Myb.  FIG. 2C . Wild-type parasites transfected with a C-terminally Ty-tagged BFD1 cDNA, driven by the TUB1 promoter, show nuclear localization of the transgene. DNA stained with Hoechst (blue) and Ty1 immunostained with BB2 (red). Scale bar is 3 μm.  FIG. 2D . Generation of a BFD1 knockout through homologous recombination in ME49ΔKU80. The entire coding sequence of BFD1 was replaced with an mNeonGreen-expression cassette using gRNAs against the 5′ and 3′ ends. The locus was fully sequenced to confirm complete deletion of BFD1.  FIG. 2E . Plaque assay of parental ME49ΔKU80 (WT) or ME49ΔKU80ΔBFD1 (ΔBFD1) shows no defect in growth under unstressed conditions. Images taken 14 days post plaquing.  FIG. 2F . BFD1 parasites fail to differentiate. Differentiated parasites were stained with FITC-labeled  Dolichos biflorus  lectin (DBL). Images taken after 48 h of alkaline stress. Scale bar is 10 μm.  FIGS. 2G-2I  show quantification of differentiation in the parental strain and ΔBFD1 parasites following 48 hours of alkaline stress ( FIG. 2G ), 48 hours of Compound 1 treatment ( FIG. 2H ) or occurring spontaneously ( FIG. 2I ). Mean±SD of n=3-4 biological replicates. % DBL positive vacuoles calculated from at least 100 vacuoles counted for each replicate. 
         FIGS. 3A-3J  show that BFD1 is required for initiation of differentiation and expression of bradyzoite genes.  FIG. 3A . Workflow for single-cell RNA-sequencing with Seq-Well. Parasites were allowed to invade host cells for 4 hours, and then shifted to unstressed or stressed conditions. After 24, 48, or 72 additional hours of growth, parasites were mechanically released and filtered, and approximately 12,000 parasites were loaded per Seq-Well array (1 array per strain under unstressed conditions, 2 arrays per strain under stressed conditions).  FIG. 3B . Clustering of unstressed parasites of both genotypes after 72 h of growth. Clustering performed by shared nearest neighbor (SNN) using principal components 1-6. Visualization by t-distributed stochastic neighbor embedding (t-SNE), each dot is a single cell. Arrow represents imputed direction of cell cycle.  FIG. 3C . Six of seven clusters differentially express known cell cycle-regulated genes. Expression profiles for differentially expressed genes within each cluster in B) based on a microarray dataset of synchronized tachyzoites 1 . Expression profiles were scaled, mean-centered and averaged for each cluster. Differential expression determined by Wilcoxon rank test. Central cluster in gray does not have any differentially expressed genes.  FIG. 3D . Proportion of cells in G1 or S/M clusters match the previously determined 60:40 ratio.  FIG. 3E . The canonical stage-specific genes SAG1 and BAG1 show mutually exclusive expression. t-SNE projection of parasites from all timepoints, genotypes and growth conditions. Visualization downsampled to 500 cells per timepoint/genotype/growth condition (6,000 cells total).  FIG. 3F . t-SNE projection as in E), separated by sample of origin. WT and BFD1 parasites cluster similarly under unstressed conditions, while stressed parasites cluster differently by genotype. Unstressed parasites of both genotypes are found primarily in SAG1+ clusters. Under stressed conditions, only WT parasites are found in BAG1+ clusters.  FIG. 3G . Clustering of WT and BFD1 parasites from unstressed and stressed cultures at 72 h timepoint. Clustering performed using principal components 1-18, visualized by t-SNE, and colored according to similarity to the tachyzoite clusters in B).  FIG. 3H . Stressed BFD1 parasites fail to upregulate canonical bradyzoite markers, and express tachyzoite markers weakly. Average scaled expression of the top 20 highly expressed up and downregulated genes identified by bulk RNA-sequencing. Each column is a single cell. Data downsampled to 1,000 cells per genotype/growth condition (4,000 cells total).  FIG. 3I . Plotting cells in stressed, non-tachyzoite clusters according to the major cell-cycle varying principal components 1 and 3 reveals that only WT parasites are dividing in stressed conditions. Cells colored according to clustering in G).  FIG. 3J . Under unstressed conditions, WT and BFD1 replicate similarly as tachyzoites. Following alkaline stress induction, only WT parasites are able to differentiate into bradyzoites and continue dividing, while BFD1 parasites seem to exit the cell cycle and stop replicating. 
         FIGS. 4A and 4B  show that overexpression of BFD1 is sufficient to induce differentiation.  FIG. 4A . Constructs and experimental workflow for transient overexpression of BFD1. cDNA of BFD1 (BFD1 WT ) or BFD1 lacking its DNA-binding domain (BFD1 ΔDBD ) is regulated by the strong constitutive TUB1 promoter. WT or BFD1 parasites were transfected with either BFD1 WT  or BFD1 ΔDBD  and fixed after 48 hours of growth under unstressed conditions. Parasites were immunostained for Ty1 (magenta) and for differentiation with FITC-conjugated DBL (green).  FIG. 4B . Transient overexpression of BFD1 WT  (WT), but not BFD1 ΔDBD , is sufficient to induce differentiation in a majority of WT and BFD1 parasites expressing the transgene. Ty′ vacuoles were identified and then scored for DBL positivity. Examples shown of vacuoles scored as DBL + , DBL +/− , and DBL − . Scale bar is 10 μm. n=2 independent replicates, 17-61 vacuoles counted per replicate. Mean±SD plotted. 
         FIGS. 5A-5D  show stage-specific RNA-sequencing of  Toxoplasma .  FIG. 5A . Sample FACS plots of the C16-B3 reporter strain at 24 or 48 h growth under unstressed or stressed conditions. 10,000 events per plot.  FIG. 5B . Principal component analysis suggests the majority (98%) of variance observed in gene expression is due to growth condition.  FIG. 5C . Comparing differential expression in this study to existing datasets shows good agreement among highly regulated genes, but only moderate correlation (spearman r 2 ˜0.54) overall.  FIG. 5D . The majority of genes called as differentially expressed exclusively in the data set are more lowly expressed. Colors assigned by rank of baseMean expression as calculated by DESeq2. 
         FIG. 6  shows that integration rates in a non-laboratory-attenuated strain of  Toxoplasma  are low. Cas9-expressing ME49 parasites were selected for integration of a gRNA targeting SAG1. Plaquing efficiency post-selection was compared to pre-transfection viability rates to obtain a viability normalized integration rate. n=3 independent experiments. Mean±SD plotted. 
         FIG. 7  shows generation of a ΔBFD1 reporter strain through Cas9-mediated frameshift. Transfection of single gRNA targeting the first exon of TGME49_200385 (BFD1) into the C16-B3 reporter strain allowed isolation of a strain with a frameshift mutation, resulting in a premature stop codon at amino acid 251. 
         FIG. 8  shows updated gene model and protein sequence of TGME49_200385. cDNA sequencing suggests the 5th, 6th, and 7th exons as annotated on ToxoDB v. 42 are a single exon, resulting in a change of reading frame of the final exon. DNA-binding domains (SM00717) highlighted in blue. 
         FIG. 9  shows phylogenetic analysis of  Toxoplasma  SANT/myb-like domains. Neighbor-joining phylogenetic tree of SANT/Myb-like DNA-binding domains (SM00717) present in representative Apicomplexan genomes, along with human c-Myb and CDCSL. Alignment performed using ClustalW. Scale bar is substitutions per site. 
         FIG. 10  shows a schematic for generation of an early passage ME49ΔKu80. Two gRNAs were designed against both the 5′ and 3′ of the KU80 locus. Transfection all four gRNAs into an early passage ME49 strain followed by immediate subcloning allowed recovery of a clone that had deleted the intervening sequence. 
         FIGS. 11A-11C  show gene detection is maximized and rRNA content minimized at the 72 hour timepoint.  FIG. 11A . Distribution of UMIs across single cells from indicated samples and timepoints. Pre-processing quality control cutoffs required a minimum of 200 and maximum of 10,000 UMIs.  FIG. 11B . As in  FIG. 11A , but collapsed to unique genes detected.  FIG. 11C . Proportion of UMIs corresponding to ribosomal genes. Pre-processing quality control cutoffs allowed a maximum of 40% rRNA reads. 
         FIGS. 12A-12B  show TGME49_312330 and TGME49_208740 are novel cyst wall proteins robustly expressed earlier than canonical bradyzoite markers.  FIG. 12A . Violin plots of expression of indicated genes in wildtype parasites after 24, 48 or 72 h growth under unstressed or stressed conditions.  FIG. 12B . Endogenous tagging of TGME49_312330 and TGME49_208740 localizes both to the cyst wall. Pictures taken 72 h post alkaline stress. Scale bar is 10 μm. 
         FIGS. 13A-13C  show that ΔBFD1 parasites do not overlap with BAG1+ clusters.  FIG. 13A . Mutually exclusive expression of the tachyzoite-specific SAG1 and the bradyzoite-specific BAG1 demonstrate strong separation of these two stages. Visualization by t-SNE, colored by normalized log-scale UMIs per cell.  FIG. 13B . Coloring cells by genotype of origin shows distinct localization of wildtype and ΔBFD1 parasites under stressed, but not unstressed, conditions. Notably, only wildtype parasites overlap with BAG1+ clusters.  FIG. 13C . BFD1 is expressed more highly in BAG1+ clusters. 
         FIGS. 14A-14D  show that the majority of variance is driven by cell-cycle and stage-specific genes.  FIG. 14A . Plotting the 18 principal components determined to be statistically significant by permutation analysis shows the first three explain the majority (66.4%) of variance seen at the 72 h timepoint. Statistical significance determined by JackStraw( ) as implemented by Seurat, p-value &lt;0.001.  FIG. 14B . PC1 is driven by cell-cycle regulated genes, including previously known mid-S/M-specific markers of  Toxoplasma , such as members of the ROP/RON and IMC genes families. Top 2000 cells for each loading, with expression shown for the top 30 gene loadings for each component.  FIG. 14C . PC2 is driven by strongly tachyzoite-specific (e.g. SAG1, AMA1) or bradyzoite-specific (BAG1, LDH2, ENO1) genes.  FIG. 14D . PC3 is driven cell-cycle regulated genes, particularly by genes associated with later events in the S/M phase, such as GAP45 and IMC8. 
         FIG. 15  shows that single-cell RNA-sequencing identifies markers specific to replicating bradyzoites. t-SNE visualization of selected markers specific to replicating bradyzoites. Colored by normalized log-scale UMIs per cell. 
         FIG. 16  shows stressed ΔBFD1 parasites show aberrant morphology at later timepoints. Under alkaline stress conditions, ΔBFD1 vacuoles frequently present disordered or bloated appearances, suggesting loss of viability. Pictures taken 72 h post alkaline stress. GAP45 is a marker for the inner membrane complex. Scale bar is 10 μm. 
         FIGS. 17A-17D  show BFD1 is a nuclear factor necessary for differentiation in cell culture.  FIG. 17A . Generation of ΔBFD1 and BFD1 WT  or BFD1 ΔMYB  complemented parasites. To create ΔBFD1 parasites, the endogenous coding sequence was replaced with a fluorescent cassette. The knockout was complemented with a wild-type (WT) (BFD1WT) or DNA-binding deficient (BFD1 ΔMYB ) Ty-tagged allele at the endogenous locus.  FIG. 17B . Plaque assays of indicated strains grown under unstressed conditions for 14 days. Scale bar is 1 cm.  FIG. 17C . Representative vacuoles after 48 h of alkaline stress. FITC-labeled  Dolichos biflorus  lectin (DBL) specifically stains differentiated vacuoles. Ty was stained with BB2 (magenta), and DNA was stained with Hoechst (blue). Scale bar is 10 mm.  FIG. 17D . Quantification of differentiation in WT, knockout, and complemented parasites following 48 h of alkaline stress, 48 h of compound 1 treatment, or occurring spontaneously under unstressed conditions in the same time frame. The mean±SD was plotted for n=3-8 biological replicates, with percentage of DBL positive vacuoles calculated from at least 100 vacuoles per replicate. ****p&lt;0.0001, *p&lt;0.05, Student&#39;s one-tailed t test. 
         FIGS. 18A-E  show that BFD1 is necessary for formation of brain cysts in mice.  FIG. 18A . Timeline of mouse infections. Groups of CD-1 female mice were inoculated i.p. with 500 tachyzoites per animal from each strain or mock inoculated with PBS. Cyst formation was assayed in moribund animals starting 2 weeks post-infection and in all surviving animals at 5 weeks post-infection.  FIG. 18B . Mean normalized weights of animals in each group. Graph represents mean±SEM for all surviving animals at a given time point. Graphs are for n=5 mock-inoculated mice and n=15 for each parasite strain.  FIG. 18C . Survival curve of animals in  FIG. 18B .  FIG. 18D . Representative cysts from WT and ΔBFD1::BFD1 WT -infected animals. The cyst wall was stained with DBL (green) and individual parasites with anti-CDPK1 (magenta). Scale bar is 20 mm.  FIG. 18E . Cyst burden per animal, denoting those sacrificed before (open circles) or after (closed circles) 5 weeks of infection. Cysts per brain were estimated from counting four blinded replicates, with a limit of detection of 56-71 cysts per brain, depending on the volume of the sample analyzed. Mean is plotted for each group. **p&lt;0.01, Student&#39;s one-tailed t test. See also  FIGS. 19A-19E . 
         FIGS. 19A-E  (related to  FIGS. 18A-E ) show virulence and brain cyst formation by ΔBFD1 parasites in CBA/J Mice:  FIGS. 19A, 19B . In groups of 5, female CBA/J mice were inoculated with 100 or 2,000 tachyzoites i.p. of WT, ΔBFD1, or ΔBFD1::BFD1 WT  and surviving animals were sacrificed 2 weeks post-infection to assay brain cyst formation ( FIG. 19A ). Cyst burdens were estimated by counting 4 blinded samples from each animal. Mean±SD is plotted with each dot representing an animal; ****p&lt;0.0001, Student&#39;s one-tailed t test ( FIG. 19B ).  FIGS. 19C-19E . In groups of 5, female CBA/J mice were inoculated with 500 or 10,000 tachyzoites i.p of WT, ΔBFD1, or ΔBFD1::BFD1 WT . Starting at 3 weeks post-infection, brains were isolated from moribund animals, and at 5 weeks post-infection all surviving animals were sacrificed ( FIG. 19C ). Survival curve of animals infected with 10,000 (dotted lines) or 500 (solid lines) tachyzoites ( FIG. 19D ). Brain cyst burden of moribund or sacrificed animals, estimated by counting 4 blinded samples from each animal. Mean±SD is plotted with each dot representing an animal ( FIG. 19E ). 
     
    
    
     DETAILED DESCRIPTION 
     A description of example embodiments follows. 
     Several aspects of the invention are described below, with reference to examples for illustrative purposes only. It should be understood that numerous specific details, relationships, and methods are set forth to provide a full understanding of the invention. One having ordinary skill in the relevant art, however, will readily recognize that the invention can be practiced without one or more of the specific details or practiced with other methods, protocols, reagents, cell lines and animals. The present invention is not limited by the illustrated ordering of acts or events, as some acts may occur in different orders and/or concurrently with other acts or events. Furthermore, not all illustrated acts, steps or events are required to implement a methodology in accordance with the present invention. Many of the techniques and procedures described, or referenced herein, are well understood and commonly employed using conventional methodology by those skilled in the art. 
     Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. It will be further understood that terms, such as those defined in commonly-used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the relevant art and/or as otherwise defined herein. 
     The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. As used herein, the indefinite articles “a”, “an” and “the” should be understood to include plural reference unless the context clearly indicates otherwise. 
       Toxoplasma gondii  chronically infects approximately a quarter of the world&#39;s population. Recrudescence of latent infections can cause life-threatening disease in the immunocompromised and recurrent ocular lesions in the immunocompetent. Chronic infection is established when rapidly replicating tachyzoites differentiate into slow-growing bradyzoites, which form tissue cysts resistant to immune clearance and current therapeutics. Despite its central role in the  Toxoplasma  life cycle, the molecular basis of differentiation is not understood. 
     The length of infection is a critical parameter in the evolutionary fitness of infectious diseases. Pathogens can extend the period of infection by establishing a latent or chronic state, avoiding clearance through slow replication, altered immunogenicity, and a diminished impact on the host. Oftentimes, these reservoirs are resistant to chemotherapy due to decreased metabolic rates. Such persistent stages can recrudesce or contribute to transmission, and are important barriers to curing and eradicating infectious diseases. 
     The life cycles of single-celled protist parasites are marked by distinct developmental stages adapted to the specific stages of their complex life cycles. Within the phylum Apicomplexa, several examples of chronic stages play important roles in the life cycles of these pathogens.  Plasmodium vivax  hypnozoites in the liver are resistant to most antimalarial therapies, leading to long periods of latency, and complicating eradication efforts 2   . Toxoplasma gondii  tachyzoites are capable of invading any nucleated cell in any warm-blooded animal, disseminating throughout the body and causing pathology through lysis of host cells. A proportion of tachyzoites differentiate into slower-growing bradyzoites, forming intracellular cysts with a tropism for brain and muscle tissue. Tissue cysts cannot be cleared by the immune system or by current therapies, and as a result up to ¼ of the world&#39;s population is thought to be chronically infected with  Toxoplasma   3 . Tissue cysts are orally infectious to both the definitive felid host and to other intermediate hosts, providing flexibility in route of transmission. Approximately 2% of infections result in ocular lesions—a leading cause of infectious blindness—with high rates of reactivation from chronic stages that persist after treatment.  Toxoplasma  infection is life threatening in immunocompromised individuals, and a majority of these cases result from recrudescent infections 4 . 
     Major changes accompany differentiation of  Toxoplasma  from rapidly proliferating tachyzoites to cyst-forming bradyzoites. The parasitophorous vacuole  Toxoplasma  replicates within is modified into a heavily glycosylated cyst wall, containing many stage-specific protein products of unknown function 5-8 . Parasite metabolism changes drastically, relying on anaerobic glycolysis instead of aerobic respiration and accumulating cytoplasmic starch granules 9-11 . Underpinning these dramatic changes in lifestyle, between several hundred and several thousand genes have been identified as differentially regulated between tachyzoites and in vitro or in vivo bradyzoites 12-21 . Although differentiation can be induced in vitro through a variety of methods, including alkaline pH, heat shock, small molecules, and nutrient starvation, the molecular mechanisms driving bradyzoite differentiation remain poorly understood 22-25 . 
     Attempts to enrich for mutants no longer able to differentiate have generated strains with decreased rates of stage conversion, though linking these phenotypes to inactivation of individual genes has proven challenging 26,27 . Deletion or chemical inhibition of histone modifying proteins has resulted in differentiation defects 17,28-31 . Interference with translational control through deletion of RNA-binding proteins or chemical modulation of eIF2α phosphorylation also impairs differentiation 32-35 . A single validated class of Apicomplexan transcription factors, the AP2 DNA-binding proteins (ApiAP2s), has been extensively investigated for potential regulators of differentiation. Knockouts of individual ApiAP2s modulate, but ultimately fail to completely ablate, bradyzoite differentiation, leading to the view that no master transcriptional regulator of this process exists in  Toxoplasma   36-41 . 
     Differentiation from tachyzoites to bradyzoites establishes chronic  Toxoplasma  infection; however, the molecular pathways regulating this transition have remained unclear, despite evidence that disparate inputs—heat shock, alkaline stress, and nutrient starvation converge on a common transcriptional program. 
     Using bulk and single-cell RNA sequencing, differentiation is characterized in unprecedented detail. To functionally investigate this transition, over 200 putative DNA-binding proteins were screened, identifying a single factor, BFD1, as indispensable for differentiation. BFD1 knockout parasites are normal under standard conditions but fail to differentiate under all induction conditions tested. Overexpression of BFD1 is sufficient to induce differentiation under standard conditions in both wildtype and knockout parasites, demonstrating its role as a master regulator of bradyzoite formation in  Toxoplasma.    
     By profiling enriched differentiated populations, transcriptional differences between tachyzoites and bradyzoites were captured with greater sensitivity and dynamic range than achieved by previous datasets 15-18,20,21,42 . These changes likely reflect a combination of factors including altered replication, nutrient availability, and general stress responses, in addition to the bradyzoite differentiation program. The genetic handle afforded by BFD1 on differentiation will help disentangle the contributions of these variables. 
     A single family of DNA-binding proteins—the ApiAP2s—has been investigated for their role as  T gondii  transcription factors and mediators of differentiation. While the phenotypes associated with many ApiAP2 mutants are striking, no single gene knockout has resulted in a complete block in differentiation, leading to the assumption that no single factor regulates bradyzoite development in  T gondii   36-41 . By screening a wider range of putative nucleic-acid binding proteins, especially those containing well-conserved DNA-binding motifs such as zinc finger and Myb-like domains, it was observed that inactivation of BFD1 completely ablates bradyzoite formation. This does not preclude important roles for ApiAP2 proteins as downstream mediators of the differentiation program.  Toxoplasma  encodes 13 other proteins containing SANT/Myb-like domains, suggesting the existence of a second extensive transcription factor family. Myb domain—containing proteins are widespread among eukaryotes, and have been implicated in the regulation of encystation in  Entamoeba  and Giardia, along with a wide variety of stress responses in plants 43-47 . In humans, c-Myb is thought to function as a pioneer transcription factor, binding to chromatin and recruiting histone acetyltransferases to commit cells to specific hematopoietic lineages 48,49 . Among apicomplexan parasites, a Myb domain—containing protein has been identified as important for erythrocytic growth of  P. falciparum   50,51  suggesting that other family members will likely play important roles throughout the phylum. 
     Single-cell RNA-sequencing enables profiling of thousands of cells across asynchronous processes, and has been successfully used to examine commitment to sexual differentiation in  Plasmodium  spp. 52,53  Implementing these approaches in  Toxoplasma  retained information about cell-cycle residency and timing of gene expression that is lost in bulk analyses. Single-cell sequencing allowed identification of novel markers specific to actively replicating bradyzoites and genes expressed during the earliest stages of differentiation. This detailed view of differentiation revealed that BFD1 knockout parasites progress normally throughout the tachyzoite cycle but completely fail to initiate bradyzoite differentiation. BFD1 therefore stands out from other genes known to influence differentiation for its complete essentiality during the process. 
     As a necessary and sufficient regulator of differentiation, BFD1 provides a focal point for the molecular mechanisms underlying differentiation. In  Plasmodium , identification of AP2-G as the master transcriptional regulator of gametogenesis has permitted placement of multiple genes observed to affect sexual differentiation into a unified regulatory framework, and allowed directed investigation into their mechanisms of action 54-60  The ability to induce synchronized sexual differentiation through conditional overexpression of AP2-G has allowed for finer temporal mapping of the gene expression changes accompanying gametogenesis, and application of a similar approach in  Toxoplasma  is now possible using BFD1 61 . 
     The transcriptional profiling reveals that BFD1 is expressed in the 75th percentile in tachyzoites, and expression at this level or higher is corroborated by many other RNA-sequencing datasets 19-21,62-65 . BFD1 expression therefore does not appear to be stage specific despite a modest 1.5- to 3.6-fold upregulation in bradyzoites observed by bulk or single-cell RNA sequencing—the former below the cutoff for significance. These results suggest that regulation of BFD1 is post-transcriptional. Preferential translation of some transcripts under stress conditions has been reported, and mutations in RNA-binding proteins have resulted in severe defects that suggest an important role for translational control during differentiation 29 ′ 32 . Post-translational modifications, such as phosphorylation or acylation may provide additional layers of regulation by influencing BFD1 stability or function. 
     Mutations resulting in decreased rates of differentiation in cell culture generally display more profound defects in mice; however, the specificity of the BFD1 phenotype will help define the role of bradyzoites in pathogenesis and immunological memory during  Toxoplasma  infection 36,40,66,67 . The presence of BFD1 orthologs in other agriculturally significant parasites, such as  Neospora caninum  and  Sarcocystis neurona , suggests ΔBFD1 parasites are an ideal attenuated vaccine strain—capable of proliferating robustly yet unable to enter a chronic state. Moreover, modulation of BFD1 holds clinical and biotechnological potential, since chronic infections represent a major barrier to both the treatment of  Toxoplasma  and its use in delivery of heterologous antigens and protein-based therapeutics. 
     The present invention is directed to compositions and methods for the treatment of apicomplexan parasite infection, such as  Toxoplasma  infection. 
     The present invention incorporates new approaches to investigate the tachyzoite to bradyzoite transition. A differentiation reporter strain compatible with Cas9-mediated forward genetic screens was generated, and bulk and single-cell methods to characterize the transcriptional changes that underlie  Toxoplasma  differentiation were developed. The present disclosure provides a single factor necessary and sufficient for the initiation of the differentiation program. Characterization of this master regulator of bradyzoite formation represents an important step in the understanding of the establishment and maintenance of chronic  Toxoplasma  infection. 
     In one aspect, the present invention provides genetically altered protozoan parasites comprising a mutation in a bradyzoite formation deficient 1 (BFD1) gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. As such, attenuated parasites are provided. In some embodiments, the parasite is an apicomplexan parasite, such as e.g., a  Toxoplasma  parasite, a  Plasmodium  parasite, a  Hammondia  parasite, a  Neospora  parasite or a  Sarcocystis  parasite. 
     In some embodiments, the mutation is a deletion of all or a portion of the coding sequence of the BFD1 gene (the sequence of the BFD1 gene is provided in SEQ ID NO: 1). In some embodiments, the mutation is a deletion of the entire coding sequence of the BFD1 gene. In other embodiments, the mutation is a deletion of a portion of the coding sequence of the BFD1 gene. For example, the deletion can be a deletion of a portion of the BFD1 gene comprising at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more of the BFD1 gene. 
     As described herein, the BFD1 protein contains two tandem SANT/myb-like DNA-binding domains (SMART accession 00717), flanked by large extensions lacking identifiable motifs. Collectively, the two tandem SANT/myb-like DNA-binding domains are referred to herein as the “BFD1 DNA binding domain.” Individually, the SANT/myb-like DNA-binding domains are referred to herein as a “Myb-like DNA binding domain,” “Myb-like domain” or “Myb domain.” Accordingly, in some embodiments, the mutation is a deletion of a portion of the BFD1 gene that encodes the BFD1 DNA binding domain (e.g., a deletion of a portion encoding both Myb-like DNA binding domains, a deletion of a portion encoding both Myb-like DNA binding domains along with the flanking extensions). In certain embodiments, the deletion encompasses a portion of the BFD1 gene encoding amino acids 921-1019 of the BFD1 protein. 
     In other embodiments, the mutation is a deletion of a portion of the BFD1 gene encoding one Myb-like DNA binding domain (e.g., a deletion of a portion encoding one of the Myb-like domains while leaving the other Myb-like domain intact, a deletion of a portion encoding one Myb-like domain and a portion of the second Myb-like domain). An example of a mutation comprising a deletion of a portion of the BFD1 gene encoding the BFD1 DNA binding domain is described in the Examples herein, and is referred to interchangeably as the ΔMYB or ΔDBD. 
     In further embodiments, the mutation can be one or more nucleotide base substitutions, one or more nucleotide base deletions, or one or more insertion (of one or more nucleotide bases or constructs (e.g., reporter genes)). In some embodiments, the insertion or deletion results in a frame-shift that changes the reading of subsequent codons, altering the entire amino acid sequence that follows the mutation. In some embodiments, the mutation can introduce a premature stop codon. In some embodiments, a nucleotide sequence of the BFD1 gene comprises a nucleic acid sequence having at least 70% sequence identity to the sequence of SEQ ID NO: 1. In some embodiments, a nucleotide sequence of the BFD1 gene comprises a nucleic acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the nucleic acid sequence of SEQ ID NO: 1. 
     In some embodiments, the mutation is a loss-of-function mutation. As used herein, a “loss-of-function” mutation refers to a mutation that results in the altered gene product&#39;s loss of a specific biological function in which it is involved, such as, e.g., differentiation. Loss-of-function mutations can elicit a complete loss of function of the altered gene product (a “null mutation”) or a partial loss of function. In certain embodiments, the loss-of-function mutation is a null mutation. 
     In some embodiments, the mutation is a dominant negative mutation. As used herein, a “dominant negative” mutation results in an altered gene product that acts antagonistically to the wild-type allele. 
     As used herein, a “coding sequence” of a gene consists of the nucleotide residues of the coding strand of the gene and the nucleotides of the non-coding strand of the gene which are homologous with or complementary to, respectively, the coding region of an mRNA molecule which is produced by transcription of the gene. 
     A “coding region” of an mRNA molecule also consists of the nucleotide residues of the mRNA molecule which are matched with an anti-codon region of a transfer RNA molecule during translation of the mRNA molecule or which encode a stop codon. The coding region may thus include nucleotide residues corresponding to amino acid residues which are not present in the mature protein encoded by the mRNA molecule (e.g., amino acid residues in a protein export signal sequence). 
     “Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (e.g., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA. Unless otherwise specified, a nucleotide sequence encoding an amino acid sequence includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. Nucleotide sequences that encode proteins and RNA may include introns. 
     In some embodiments, the apicomplexan parasite is  Toxoplasma gondii.    
     In some embodiments, the apicomplexan parasite is  Neospora caninum.    
     In some embodiments, the apicomplexan parasite is  Sarcocystis neurona.    
     In another aspect, the present invention provides compositions (e.g., vaccine compositions or pharmaceutical compositions) comprising (1) genetically altered protozoan parasites comprising a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite; and (2) a pharmaceutically-acceptable carrier. 
     As used herein, “vaccine composition” refers to a composition comprising a microbial immunogen (e.g., antigen or collection of antigens) that is capable of eliciting an adaptive immune response and/or immune memory against the microbe. The vaccine composition can further comprise a pharmaceutically acceptable carrier. 
     “Pharmaceutically acceptable” refers to those properties and/or substances which are acceptable to the patient from a pharmacological/toxicological point of view and to the manufacturing pharmaceutical chemist from a physical/chemical point of view regarding composition, formulation, stability, patient acceptance and bioavailability. “Pharmaceutically acceptable carrier” refers to a medium that does not interfere with the effectiveness of the biological activity of the active ingredient(s) and is not toxic to the host to which it is administered. 
     As used herein, the term “antigen” refers to any molecule capable of generating an immune response, such as a peptide, polypeptide, protein, polysaccharide, lipid, cell, cancer cell (such as a self-antigen associated with a cancer cell), live-attenuated pathogen (e.g., microbe), or heat-killed pathogen that has the potential to stimulate an immune response. Additionally, a “pathogen” refers to any organism capable of eliciting an immune response from a subject upon infection of the subject with pathogen. A nonlimiting example includes the pathogen  Toxoplasma gondii . A given pathogen can be comprised of multiple antigens to which the subject&#39;s immune response may respond. 
     In some embodiments, the microbial immunogen comprises a live, genetically altered protozoan parasite that results in attenuation of the parasite. Thus, a vaccine composition refers to any composition that is administered to a subject with the goal of establishing an immune response and/or immune memory to a particular antigen or antigens. The vaccine compositions can comprise other substances designed to increase the ability of the vaccine to generate an immune response. For example, a live-attenuated vaccine can comprise the live-attenuated parasite plus an adjuvant. 
     Adjuvants can be any substance that enhances the immune response to the antigens in the vaccine composition. Non-limiting examples of adjuvants suitable for use in the present invention include Freund&#39;s adjuvant, incomplete Freund&#39;s adjuvant, saponin, surfactants such as hexadecylamine, octadecylamine, lysolecithin, demethyldioactadecyl ammonium bromide, N,N-dioctadecyl-N′-N-bis (2-hydroxyethylpropane diamine), methoxyhexa-decyl-glycerol, pluronic polyols, polyanions such as pyran, diethylaminoethyl (DEAE) dextran, dextran sulfate, polybrene, poly IC, polyacrylic acid, carbopol, ethylene maleic acid, aluminum hydroxide, and aluminum phosphate peptides, oil or hydrocarbon emulsions, and the like. 
     It is also contemplated that the vaccine compositions disclosed herein can be therapeutic or prophylactic. Thus, for example, the vaccine compositions disclosed herein can be used to prevent or reduce the likelihood of an infection such as, but not limited to,  Toxoplasma . Alternatively, the vaccine compositions disclosed herein can be used therapeutically to treat one or more symptoms of an infection in an individual with a chronic infection. 
     The term “treating” as used within the context of the present invention is meant to include therapeutic treatment as well as prophylactic, or suppressive measures for the disease or disorder. Thus, for example, the term treatment includes the administration of an agent prior to or following the onset of a disease or disorder thereby preventing or removing all signs of the disease or disorder. As another example, administration of the agent after clinical manifestation of the disease to combat the symptoms of the disease comprises “treatment” of the disease. This includes for instance, prevention of parasite propagation to uninfected cells of an organism. 
     Additionally, the present invention provides additional antigens in combination with the live, attenuated parasite in the vaccine compositions herein disclosed. The antigens provided in the mixture for vaccine compositions or immunization protocols can come from the same, different or unrelated targets. Thus, the antigens may be the same antigen, or the antigens may be heterologous antigens. For example, a vaccine composition can comprise a heterologous antigen, such as, e.g., a peptide of a protein of a target. In certain embodiments, the heterologous antigen is a peptide having a length of at least 5 amino acids (e.g., 5, 6, 7, 8, 9, 10, 11, 12, 15, 20, 25, 50, 75, 100 or more amino acids). The heterologous antigen can be, for example, a cancer antigen. In some embodiments, the parasite expresses the heterologous antigen. 
     The heterologous antigen can be an antigen found in various pathogens (e.g., viral, bacterial, fungal, protozoal, helminth) that may infect the subject. For example, the heterologous antigen may be derived from a different protozoan parasite (e.g., if the parasite is  T gondii , the antigen may be from a  Plasmodium  species). Alternatively, the heterologous antigen may be derived from a viral pathogen, such as a coronavirus (e.g., a SARS-CoV-2 virus). Examples of suitable antigens may include antigens derived from viral envelope or capsid proteins, proteins present at the cell surface (e.g., the cell surface of protozoan cells, bacterial cells, cancer cells), or secreted proteins. In some embodiments, the antigen is a coronavirus antigen, such as a spike protein or portion thereof (e.g., a SARS-CoV-2 spike protein or portion thereof, such as the S1 subunit or S2 subunit of the SARS-CoV-2 spike protein). 
     In some embodiments, the parasite that is genetically altered to have a mutation in the BFD1 gene may be genetically altered to express the heterologous antigen. In specific embodiments, a coding sequence for the heterologous antigen can be inserted into the genome of the parasite at a location that is non-essential for parasite viability, e.g., into a non-essential gene. For example, the heterologous antigen can be inserted into a gene that is dispensable (see Example 2). In some embodiments, the coding sequence may be inserted into the BFD1 locus. The coding sequence can be operably linked to a promoter. The promoter can be, for example, the SAG1 or TUB1 promoter. In some embodiments, the heterologous antigen can be expressed as a fusion protein containing the heterologous antigen and all or a portion of an endogenous protein. In some embodiments, the endogenous protein, or portion thereof, is expressed at the cell surface (e.g., a SAG1 protein or a portion thereof), and the resulting fusion protein is expressed at the cell surface (e.g., of the parasite). In other embodiments, the endogenous protein, or portion thereof, is a secreted protein, and the resulting fusion protein is secreted (e.g., by the parasite). 
     The antigen(s) can be coupled to a carrier protein. Non-limiting examples of suitable carrier proteins include albumin, ovalbumin,  Pseudomonas  exotoxin, tetanus toxin, ricin toxin, diphtheria toxin, cholera toxin, heat labile enterotoxin, keyhole lympet hemocyanin, epidermal growth factor, fibroblast growth factor, transferrin, platelet-derived growth factor, poly-L-lysine, poly-L-glutamine, mannose-6-phosphate, as well as various cell surface and membrane proteins, and the like. 
     Vaccine compositions can be formulated in aqueous solutions (carriers) such as water or alcohol, or in physiologically compatible buffers such as Hanks&#39; solution, Ringer&#39;s solution, or physiological saline buffer, including PBS. Vaccine compositions can also be prepared as solid form preparations which are intended to be converted, shortly before use, to liquid form preparations suitable for administration to a subject, for example, by constitution with a suitable vehicle, such as sterile water, saline solution, or alcohol, before use. 
     The vaccine compositions can also be formulated using sustained release vehicles (carriers) or depot preparations. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the vaccines may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt. Liposomes and emulsions can be used as delivery vehicles suitable for use with hydrophobic formulations. Sustained-release vehicles may, depending on their chemical nature, release the antigens over a range of several hours to several days to several weeks to several months. 
     The vaccine compositions may further include one or more antioxidants. Exemplary reducing agents include mercaptopropionyl glycine, N-acetylcysteine, (3-mercaptoethylamine, glutathione, ascorbic acid and its salts, sulfite, or sodium metabisulfite, or similar species. In addition, antioxidants can also include natural antioxidants such as vitamin E, C, leutein, xanthine, beta carotene and minerals such as zinc and selenium. 
     Vaccine compositions may further incorporate additional substances to function as stabilizing agents, preservatives, buffers, wetting agents, emulsifying agents, dispersing agents, and monosaccharides, polysaccharides, and salts for varying the osmotic balance. The vaccine compositions can further comprise immunostimulatory molecules to enhance vaccine efficacy. Such molecules can potentiate the immune response, can induce inflammation, and can be any lymphokine or cytokine. Nonlimiting examples of cytokines include interleukin (IL)-1, IL-2, IL-3, IL-4, IL-12, IL-13, granulocyte-macrophage colony stimulating factor (GMCSF), macrophage inflammatory factor, and the like. In some embodiments, the parasite may be genetically altered to express an immunostimulatory molecule such as any one or more of the aforementioned cytokines. 
     In some embodiments, the parasite utilized in a vaccine composition can express a therapeutic agent, such as e.g., a peptide or protein. In some embodiments, expression of a therapeutic agent or heterologous antigen in a tachyzoite can be under control of a promotor. In some embodiments, the promoter can be a constitutive promoter. In some embodiments, the promoter can be a promoter of a gene that encodes a protein that is expressed during the tachyzoite stage. For example, in some embodiments, the promoter can be the SAG1 or TUB1 promoter, in the case of  T gondii . Further, expression of a heterologous antigen by the parasite, e.g., a cancer antigen or antigen from a different pathogen can be under control of such promoters. A coding sequence of a heterologous polypeptide, e.g., a heterologous antigen or therapeutic agent, may be a codon optimized for expression by the parasite, e.g.,  T gondii.    
     In the context of the present invention, the terms “peptide,” “polypeptide” and “protein” are used herein. They refer to an amino acid chain, and include any post-translational modifications thereto (for example phosphorylation or glycosylation). Typically, the term protein is utilized when referring to a full-length product of a gene; and, the use of the term peptide and/or polypeptide is utilized when describing a fragment of a protein. 
     In some aspects, the present invention provides methods of treating cancer in a subject in need thereof, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite, and wherein the parasite expresses a cancer antigen. 
     In another aspect, the present invention provides methods of inhibiting development or progression of cancer in a subject, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite, and wherein the parasite expresses a cancer antigen. 
     In another aspect, the present invention provides recombinant nucleic acid vectors comprising a nucleotide sequence encoding a BFD1 protein. In some embodiments, the nucleotide sequence encoding the amino acid sequence of a BFD1 protein comprises SEQ ID NO:1. In some embodiments, a nucleotide sequence encoding the amino acid sequence of the BFD1 protein comprises a nucleic acid sequence having at least 70% sequence identity to the sequence of SEQ ID NO: 1. In some embodiments, a nucleotide sequence encoding the amino acid sequence of a BFD1 protein comprises a nucleic acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the nucleic acid sequence of SEQ ID NO: 1. 
     In some embodiments, the amino acid sequence of a BFD1 protein comprises the sequence of SEQ ID NO:2. 
     In some embodiments, the recombinant nucleic acid vector is an expression vector. “Expression vector” refers to a vector comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide. The expression vectors can have cis-acting elements such as promoter sequences and non-promoter regulatory elements. As used herein, a “non-promoter regulatory element” refers to non-promoter sequence(s) of a nucleic acid molecule that are capable of increasing or decreasing the expression of specific genes within the recombinant vector. Such non-promoter regulatory elements include but are not limited to, e.g., enhancer elements, inducer elements, silencer elements, 5′ untranslated regions (UTRs), 3′UTRs, terminator elements, CAAT boxes, CCAAT boxes, Pribnow boxes, SECIS elements, polyadenylation signals, A-boxes, Z-boxes, C-boxes, E-boxes, G-boxes, and Cis-regulatory elements (CREs). 
     In some embodiments, the vector is a viral vector. Non-limiting examples of viral vectors that can be utilized by the present invention include DNA or RNA viral vectors including but not limited to retroviral vectors, herpes virus vectors, adenovirus vectors, lentivirus vectors, rabies virus vectors, lentiviral vectors, VSV vectors, vaccinia virus vectors, reovirus vectors, semliki forest virus, and sindbis virus vectors. 
     In some embodiments, the vector is a non-viral vector. Non-viral vectors can be plasmid DNA, liposome-DNA complexes (lipoplexes), and polymer-DNA complexes (polyplexes). Non-viral vectors can be plasmid RNA, liposome-RNA complexes (lipoplexes), and polymer-RNA complexes (polyplexes). 
     In some embodiments, the recombinant nucleic acid vector further comprises a selectable marker element. A “selectable marker element” is an element that confers a trait suitable for artificial selection. Examples of selectable marker elements useful in the present invention include, but are not limited to, Chloramphenicol acetyltransferase, Hypoxanthine-guanine phosphoribosyltransferase, bleomycin binding protein, beta-lactamase, neomycin resistance genes, mutant Fabl genes conferring triclosan resistance, URA3 elements, fluorescent gene products, affinity tags such as GST, His, CBP, MBP, and epitope tags such as Myc HA, FLAG. Selectable marker elements can be negative or positive selection markers. 
     In a further aspect, the present invention provides host cells comprising recombinant nucleic acid vectors comprising a nucleotide sequence encoding a BFD1 protein. 
     In some embodiments, the host cell is from an apicomplexan parasite. In some embodiments, the host cell is  Toxoplasma gondii.    
     In another aspect, the present invention provides methods of inducing an immune response to an apicomplexan parasite in a subject in need thereof, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the apicomplexan parasite is  Toxoplasma gondii.    
     As used herein, the term, “subject,” refers to an animal. Typically, the terms “subject” and “patient” may be used interchangeably herein in reference to a subject. As such, a “subject” includes an animal that is being treated for a disease, being immunized, or the recipient of a mixture of components as described here, such as a vaccine composition. The term “animal,” includes, but is not limited to, mouse, rat, dog, guinea pig, cow, horse, sheep, chicken, cat, rabbit, pig, monkey, chimpanzee, and human. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. In some embodiments, the subject is a bird. 
     The vaccine compositions described herein can be formulated for and administered by infusion or injection (intravenously, intraarterially, intramuscularly, intracutaneously, subcutaneously, intrathecally, intraduodenally, intraperitoneally, and the like). The vaccine compositions can also be administered intranasally, vaginally, rectally, orally, topically, buccally, transmucosally, or transdermally. 
     An effective antigen dosage to treat against apicomplexan parasite infection can be determined empirically, by means that are well established in the art. The effective dose of the vaccine composition may depend on any number of variables, including without limitation, the size, height, weight, age, sex, overall health of the subject, the type of formulation, the mode or manner or administration, whether the parasite is active or attenuated, whether the patient is suffering from secondary infections, or other related conditions. 
     As an example, a suitable dose of genetically altered apicomplexan parasites, such as  Toxoplasma gondii , per inoculation can be between about 1,000 to about 10 million tachyzoites, or between about 1,000 and 1 million tachyzoites, or between 5,000 and 50,000 tachyzoites, or between 10,000 and 50,000 tachyzoites. In some embodiments, a dose of at least about 1,000 genetically altered tachyzoites are administered to a subject, e.g., a human subject, per inoculation. In some embodiments, a dose of at between about 1,000 and 10,000 genetically altered tachyzoites are administered to a subject, e.g., a human subject. In some embodiments of the invention, a dose of at between about 10,000 and 100,000 genetically altered tachyzoites are administered to a subject, e.g., a human subject. 
     Vaccine regimens can also be based on the above-described factors. Vaccination can occur at any time during the lifetime of the subject, including development of the fetus through adulthood. Supplemental administrations, or boosters, may be required for full protection. To determine whether adequate immune protection has been achieved, seroconversion and antibody titers can be monitored in the patient following vaccination. 
     As used herein, “immune response,” refers to an acquired and enhanced degree of protective immunity, preferably complete or sterile protection, against subsequent exposure to the parasites disclosed herein. In some embodiments, the protective immunity achieved after administration of the genetically altered protozoan parasites will not be complete but will reduce the severity of the infection symptoms after exposure to wild-type apicomplexan parasites (i.e., partial protection). 
     It is generally contemplated that inoculating a subject according to the methods described herein with genetically altered apicomplexan parasite will induce protective immunity against challenge with wildtype apicomplexan parasites of the same species. However, it is also contemplated by the present disclosure that immunization with one apicomplexan parasite can protect against challenge with another apicomplexan parasite of a different species, and eliciting cross-species protection in this manner is also within the scope of the invention. 
     As used herein, “immunization” or “vaccination” is intended for prophylactic or therapeutic immunization or vaccination. “Therapeutic vaccination” is meant for vaccination of a patient with apicomplexan parasitic infection and/or for vaccination of a subject suffering from cancer, wherein the parasite expresses a cancer antigen. 
     Also, the disclosed methods can comprise the simultaneous or separate administration of multiple vaccine compositions. Thus, the present invention may further include the administration of a second, third, fourth, etc. antigen, wherein the second, third, fourth, etc. antigen is administered in a separate vaccine composition for administration at the same time as or 1, 2, 3, 4, 5, 6, 10, 14, 18, 21, 30, 60, 90, 120, 180, 360 days (or any number of days in between) after the first antigen. 
     In some embodiments, the parasite can be genetically altered to encode two or more antigens. In some embodiments, two or more antigens may be encoded as part of a single polypeptide. In some embodiments, two or more antigens may be encoded as separate polypeptides. In some embodiments, at least two of the antigens are from different proteins. In some embodiments, the two or more antigens include two or more different cancer antigens. 
     In some embodiments, the subject has an acute or chronic apicomplexan parasite infection. 
     In another aspect, the present invention provides methods of inhibiting or preventing a chronic apicomplexan parasite infection in a subject, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. 
     In another aspect, the present invention provides methods of treating a chronic infection by an apicomplexan parasite in a subject in need thereof, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. 
     In another aspect, the present invention provides methods for inoculating a subject in need thereof with an apicomplexan parasite, comprising administering to the subject a vaccine composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. 
     In another aspect, the present invention provides methods of administering an antigen to a subject in need thereof comprising administering to the subject a composition comprising a genetically altered protozoan parasite, wherein the parasite comprises a mutation in a BFD1 gene, wherein the mutation inhibits differentiation of the parasite into a bradyzoite, and wherein the parasite comprises an antigen. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. 
     In some embodiments, the parasite is genetically altered to comprise additional antigen(s). 
     In certain embodiments, the antigen is a cancer/tumor antigen. Non-limiting examples of possible cancer/tumor antigens that can be utilized in the present invention include alpha-fetoprotein (AFP), cancer antigen 125 (CA125), cancer antigen 15-3 (CA15-3), carbohydrate antigen 19-9 (CA19-9), carcinoembryonic antigen (CEA), HE4, chromogranin A (CgA), CD20, human chorionic gonadotropin (hCG or beta-hCG), lactate dehydrogenase, beta-2-microglobulin (B2M), calcitonin, neuron-specific enolase (NSE), programmed death ligand 1 (PD-L1), nuclear matrix protein 22, thyroglobulin, and prostate-specific antigen (PSA). 
     The present invention also provides for methods of generating genetically altered protozoan parasites comprising one or more mutations in the BFD1 gene. As would be understood by those skilled in the art, routine molecular biology techniques, including but not limited to, gene knockouts, etc. can be utilized in generation of the genetically altered parasites described herein. For example, targeted mutation of a BFD1 gene can be carried out in a lab setting by routine methods, such as homologous recombination techniques. In certain embodiments, the genetically altered protozoan parasites of the present invention are lab strains. Alternatively, the genetically altered protozoan parasites can be natural isolates. 
     In some embodiments, a targeted mutation of a BFD1 gene may be generated using CRISPR methodology. 
     In some embodiments, the genetically altered protozoan parasite generated by the methods described herein is an apicomplexan parasite. 
     In certain embodiments, the genetically altered protozoan parasite generated by the methods described herein is  Toxoplasma gondii.    
     In certain embodiments, the genetically altered protozoan parasite generated by the methods described herein is  Neospora caninum.    
     In certain embodiments, the genetically altered protozoan parasite generated by the methods described herein is  Sarcocystis neurona.    
     In certain embodiments, the genetically altered protozoan parasite generated by the methods described herein is  Hammondia hammondi.    
     In certain embodiments, the genetically altered protozoan parasite generated by the methods described herein is  Hammondia pardalis.    
     In a further aspect, the present invention provides for methods of identifying a candidate anti-parasitic compound comprising identifying a compound (small or large molecule compounds) that inhibits expression or activity of BFD1. The invention features methods for screening compounds that inhibit the expression or activity of the BFD1 gene. In some embodiments, the screening assays involve contacting a proliferating tachyzoite with a test compound, and determining whether the test compound inhibits the tachyzoite from differentiation into a cyst-forming bradyzoite. In some embodiments, the screening assays involve contacting a proliferating tachyzoite with a test compound, and determining whether the test compound inhibits expression of the BFD1 gene. In some embodiments, determining whether the test compound inhibits expression of the BFD1 gene comprises measuring the level of mRNA encoding BFD1 and/or measuring the level of BFD1 protein in tachyzoites contacted with the test compound and comparing the level of BFD1 mRNA or protein with a suitable control, e.g., the level of BFD1 mRNA or protein found in tachyzoites not contacted with the test compound. In some embodiments, the screening assays involve contacting a proliferating tachyzoite with a test compound, and determining whether the test compound inhibits expression of one or more bradyzoite specific genes. 
     BFD1 may be necessary to maintain the differentiated state; therefore, interfering with its expression or activity (e.g., using compounds identified using screening methods described herein) may reactivate latent stages, which could subsequently be cleared with available anti-parasitic drugs (e.g., the subject could be treated with an anti-BRD1 compound and an anti-parasite drug). 
     In some embodiments, reporter assays can be utilized to screen for compounds that inhibit expression of a reporter gene operably linked to a BFD1-responsive promoter or promoter of any gene that is selectively expressed in the bradyzoite stage. The reporter gene may, for example, encode a reporter protein such as a fluorescent protein or an enzyme such as luciferase or beta-galactosidase, etc. 
     Compounds to be tested by the methods of the present invention include purified molecules, substantially purified molecules, molecules that are one or more components of a mixture of compounds, or a mixture of a compound with any other material. Test compounds can be organic or inorganic chemicals, or biomolecules, and all fragments, analogs, homologs, conjugates, and derivatives thereof. Test compounds can be of natural or synthetic origin, and can be isolated or purified from their naturally occurring sources, or can be synthesized de novo. Test compounds can be defined in terms of structure or composition, or can be undefined. The compound can be an isolated product of unknown structure, a mixture of several known products, or an undefined composition comprising one or more compounds. Examples of undefined compositions include cell and tissue extracts, growth medium in which prokaryotic, eukaryotic, and archaebacterial cells have been cultured, fermentation broths, protein expression libraries, and the like. In some embodiments of this invention, the test compound could be a small peptide. Small peptides can be from 2 to about 10 amino acids in length, from about 10 to about 20 amino acids in length, from about 20 to about 30 amino acids in length, from about 30 to about 40 amino acids in length, from about 40 to about 50 amino acids in length, from about 50 to about 60 amino acids in length, from about 60 to about 70 amino acids in length, from about 70 to about 80 amino acids in length, from about 80 to about 90 amino acids in length, or from about 90 to about 100 amino acids in length. The peptides can contain naturally occurring amino acids, chemically modified amino acids and/or synthetic derivatives of amino acids. In another embodiment, the test compound is an antibody specific for the BFD1 protein. In some embodiments, the test compound is a small molecule. As used herein, a “small molecule” is a low molecular weight organic compound of about 50 daltons (D) up to about 1 kD or about 2 kD. In some embodiments, the small molecule can be &lt;900 daltons. Most drug active ingredients are small molecules. 
     In some embodiments, the screening assays involve contacting a proliferating tachyzoite with a test compound, and determining whether the test compound inhibits the tachyzoite from differentiation into a cyst-forming bradyzoite by molecular analysis of differentiation-related proteins or RNAs. If such differentiation-related proteins/RNAs show a reduction or elimination in expression, then the test compound is a candidate anti-parasitic compound. Analyses can be performed by methods understood in the art, such as, e.g., Western blot, Northern blot, and microarray analysis. 
     In another embodiment, candidate anti-parasitic compounds shown to affect differentiation of a tachyzoite can be further evaluated for their ability to reduce or inhibit progression of the tachyzoite into bradyzoites. In another embodiment, candidate anti-parasitic compounds shown to affect differentiation of a tachyzoite can be further evaluated for their ability to reduce or inhibit progression of acute infection to chronic infection in a subject. 
     
       
         
           
               
               
            
               
                 BFD1 genomic sequence: 
                   
               
               
                 SEQ ID NO: 1 
                   
               
               
                 ATGGAGGGAGCCAGTACTCAGCCAATGCCGCATTCGCAGCGGGAGCGTCAGGCT 
                   
               
               
                   
               
               
                 CCTGTGCACGCCATCAGTGGCACGTGGGAAAACTGCGACCAGGCGGGTGAATAC 
               
               
                   
               
               
                 AAGGGGACTGCCTGTTGCGTCGTGGAGAGGCAAGTGTATTCTACGGAGACGCAC 
               
               
                   
               
               
                 GCAGTGGAAGGCTGCTGTTCCACGCGATGGAACGGAGTTAAGGAGGAAAAGGGC 
               
               
                   
               
               
                 GGTGGTGAAGTGTCCTCAAGAACTGCTTTAGCAGGGGTTGTCCATCTTTATACAA 
               
               
                   
               
               
                 ATTCAGACGGAAACGCATATACGCACATTTCTGACCAAGGAATGAGACAGGATG 
               
               
                   
               
               
                 AAGCTGTGGCGGGACAGGAGCAGCGTCACCTTAACTGTGAGGGGGAACACGAGA 
               
               
                   
               
               
                 AGAAAGGGAACGTGGCAGCAGGAGGTGGTACCCTCATGGTGACAAAATCGGAG 
               
               
                   
               
               
                 ATTGAACCGTGCGACGACTACTACTCCGTGCAGAGAGGACAGTCGTGCGCGGGA 
               
               
                   
               
               
                 GAGAGAGCGCCGCGTGACGGATGCTGTAGACTCCTTGATGGCAGCCGTGTCGAC 
               
               
                   
               
               
                 CCGGCAGAAGGAGGTTCGGAGGAAGATGAAAACTGTTATACACATGTGCTTCAG 
               
               
                   
               
               
                 AAGCATCTGGGTCAGATGCCGACGGCACCGTACCAAGGCGACGACCGCTTACAG 
               
               
                   
               
               
                 ACTGACTTACGACTGGGAGACTTCCAGTCCGGTCCTTCGGATGCCTTGTCCGGAC 
               
               
                   
               
               
                 ACCATGTAACACGGACACCAATTCTTTCGCCTCATGGCAGGTACTCTGAATACAT 
               
               
                   
               
               
                 CAGCGAACGTCTTGCGTGGCAGTATGCTGAGAGACCGGGGCATGGTATTGCTGC 
               
               
                   
               
               
                 GGAGAATACCGTTGTGATGCACAGCCATACTGGTGAGGCAACCGGATCATTGCG 
               
               
                   
               
               
                 AGCGGATGCGCCTTCGCAGTGGTCCACAGAGAGCCGCCTTCAGTTTCACGTCGGG 
               
               
                   
               
               
                 TCTCAATTTACCACCGAGAATCCGGAACTGTTCGCTGGCATTGTGGGATTAGACA 
               
               
                   
               
               
                 CAGAGCAATTCGACGCGAGAAATGCAGAAGCGCTGCACTGGAGACAACAGGGA 
               
               
                   
               
               
                 GAGGCTCGCTCAACGGAGACCGAATGCATCGCTGACATAACACCAGAGCGAGGC 
               
               
                   
               
               
                 AACCGGAGTACAATACGGCAATGGAATAAACCAGAAGCGGCGCGACAGGAATA 
               
               
                   
               
               
                 TCACCGTGCGTCAGgtgagagtggggctgcagtagtttgtctaacaggatgaacactaccagcacactagtcgcctgtaa 
               
               
                   
               
               
                 gactcgtgtgttttgtccggagtgtgattccaagatacaaggcgaccaagagctatttttgccagatgtgttgtgtccaacagCCTCT 
               
               
                   
               
               
                 GCTCGAGGGCCAGAGGAGACCAATATCATCACTCGGGGAGCACACTCCGACGAC 
               
               
                   
               
               
                 CAAAGTATAGACGCTGCTGCTCCAGGCTGCTGGGCTGCGCGCCATCTCACGTCTC 
               
               
                   
               
               
                 GACAGCATCCTAACCCGCGACCGAGGATGAAGGAGGAACATTGCGGTCGGGAAA 
               
               
                   
               
               
                 GGGAAGTCTTGTCTTCGGAGCAGCCCTCAGACTGTGGCGAAACACAGAAAACAC 
               
               
                   
               
               
                 CGgttagctgctagaactaaaaaatacatcaacatggctgatatccttcgagcgtacccacttagcctagcgtgaactgttgtgctcgc 
               
               
                   
               
               
                 gtggtaggcgaaaattggtgctgagcactgcccggcgagttgaaagaagtgacccgcaactcgcactcactaacactgcaccatggc 
               
               
                   
               
               
                 ggaatccgtttaccgattgfficcgtgttccacccacagcgtgatgacttcgctgtggagggagcctcatttcaattgctgcgtcgatgtgt 
               
               
                   
               
               
                 gtcctggttcctgtgcagGCGTCTCATTCACTTGTCTTGGATTCCAAGAGTCGAGCAGACGC 
               
               
                   
               
               
                 GAGTCAAACATCACCGTATACGCGTAACGACGAAATTCAAACGATTCGAGCATT 
               
               
                   
               
               
                 TGAGGAACAATGTCTTGAGGTGCAACTTCCTCAATCACGCTTAAGGCGTGGCATT 
               
               
                   
               
               
                 GACTATGAAGCTGGCATGTCACAGCTGGCTCCCACAACGCAAGAGTTGAAGGCC 
               
               
                   
               
               
                 AAAGTGTTGACAACGGGACTGTCCCCTTCGTGTCCAAACGCAGCCGTTCTTCGAG 
               
               
                   
               
               
                 CTAGTGTACCCTTGTCTATGGATACAACAGTTACGGTTCACCTTGCTGATGTCGA 
               
               
                   
               
               
                 GGATCCGAGTTCGAAGCGTCACACGCCTATCGAAAACTCTATTTCCAGCGGGCAT 
               
               
                   
               
               
                 TGTGATCCTCCGTGCTCGAGCCCGGGGGGAATGATGGAGCCCCGTGTATCCGTTT 
               
               
                   
               
               
                 CGGGTTTAGGCAGTCCTCACAACTGCGTGGAGGACAGAGAGATTGCGCGACACG 
               
               
                   
               
               
                 GAGACGGTATTGGAAGGGACATACTGGAAAGGCGTCCGCTACCATTCTCTCCTGC 
               
               
                   
               
               
                 TGCACTCCTGACGGGCTGCTCTAGCACGGCAGCCTCATCCGTTGTGTCTGGTGAC 
               
               
                   
               
               
                 GTGTTCACTTCGGTAGCAGCCTCTGCTCGCGCTAACGCGTGTAGATCGAGTACTG 
               
               
                   
               
               
                 ATACCCAGGAAGAGAGTGGCTGTGGCGACGCGCCGCGGTATGTACTACTGTTCC 
               
               
                   
               
               
                 CTGACGAACAAGACGAGAGATTAGGACATGCGCAAACCAGCATTGCCACGCCGT 
               
               
                   
               
               
                 CTGGATCAGGCCAATCAAAATGCATGTTTAAGGGCGACGGAAATGCAGAGGCCA 
               
               
                   
               
               
                 CATTCAGGGAGGAGGTAAAGAGTTCAGAACTTCGGACGCCCTCGAGGATACAAA 
               
               
                   
               
               
                 CACGGCGTTTGCTTCCCGGGGTACAGCTTCAAGGCATGGACTGTGACGGATGCGG 
               
               
                   
               
               
                 TGCCTCCGATCCCCAGAAAGGGAGACCTGCGCCAGAGACAGGTTTTTTGCCTGAG 
               
               
                   
               
               
                 ATTTGCCATTTCTCACCTCAGCATCCATGGCAACCGGGATCGGAAGTCAACCAGG 
               
               
                   
               
               
                 GGTACCGGGCGGGCGCTGACTACGGGACCTCTCGGGTACAGCAGAGTCTTGAAA 
               
               
                   
               
               
                 ATTGTTCATGGGAAGAGTCAGTGGATGAGGGTGAACAACCACGCACCACATCGT 
               
               
                   
               
               
                 CCTCCTCATACGGACAAGACACGCAGAAACGGGATTCCTTCCTCCAGTCAATCGA 
               
               
                   
               
               
                 TAACAGAATAGCAAGCGAACCGGTTGACCCCACAGGTACATGCGGATATAACTC 
               
               
                   
               
               
                 AACGCCTGAAACCTTTCGTAGTGGATGCATTATGCGTGATCAGATGCTCGGTGTC 
               
               
                   
               
               
                 AAGCCACATCTGTCTCATGTATCTTTAACGCGCGAGGGCAAGCATCGGGGACAG 
               
               
                   
               
               
                 CAAACGCACCTACGGAAAACTGGAGTGCCAACATGGAGCGCTGAGGAGGATGCG 
               
               
                   
               
               
                 AGTCTCGCAGAGTTGGTGTCTAGAAAGGGCTTCAAGTGGGCACTGATCTCTTCAC 
               
               
                   
               
               
                 AACTTACTGGCGCCTTTGGGATCCCACGGACTGgtaagcgtggatttgagtataccaagagagggtcat 
               
               
                   
               
               
                 ctgagcaagccaaacaccagatggcacgacggtacgagatttcccaagtgtgaaatcactgatgtttttggtgattctcgactgtgcgt 
               
               
                   
               
               
                 gtgttctgattgtagGTAAACAATGTCGGGAACGATGGTTTAATCATGTGAATCCCGAGGT 
               
               
                   
               
               
                 TAAGAAAGGCGACTGGTCAGCCGAGGAGGATGCCATGATACTGATGCTTCAGAA 
               
               
                   
               
               
                 TGAACTGgtgagtggttgtatctegggtggtcgatttgtttcacaatggcgttagacctctcaaaagtcagtgattgatgttgeggtg 
               
               
                   
               
               
                 ttgtccgaaaaagaaggttettctctctgtgtttcgactctgcacgtgagtacccgtacaaggcaggctcacccagtatttttcctgctccat 
               
               
                   
               
               
                 gggctagtgcagacgagtgaattttcgtctgtctgcattcttatggaggtcacgaagatccacactgtgcaagcacgcgacgcgtgtga 
               
               
                   
               
               
                 gacttacgcagaaatgaggccgttgtttgccatgtttttgttatgatgcagGGAAATCGCTGGGCGACTATCGCA 
               
               
                   
               
               
                 AAGAAGTTGCGGGGCCGCACAGAGAATGCCGTGAAGAACCGCTTTATTTCTCTC 
               
               
                   
               
               
                 AGCAATGCCCGCCTAGGTTATGGTCGTCCAAAGCGCGATGGCTCGAGCGCGGAC 
               
               
                   
               
               
                 TGCTTCAGTAACAGACGTACCGGTAGTGGGAAGTCGTCAGGCATAACAGGGATG 
               
               
                   
               
               
                 CCGAATCTATGTCAGTCTGTATGTTCCGCTGGCACAACGAAGAAGGACTCGTCTG 
               
               
                   
               
               
                 AATCGGGTAACCATTTCGTTATGTCCGTTGCCACGAAAGTTTTTGAATTTTCGGAC 
               
               
                   
               
               
                 GTGGCAGTGGATTCTGGGGTGAGCCGACCGAGACAGTGCACTGGCACGTCACCC 
               
               
                   
               
               
                 AGTTGTGGGCATCCGTCGGCAGGTGAGGGGGATCCATCTCATTTAAAGAACACT 
               
               
                   
               
               
                 GACGTTGTCGGCCGGGAACAACCCATACAGCGGAACAACAACGAATCAGGCAAA 
               
               
                   
               
               
                 GCTGCAGAGCAAACTGCGTTTTCAGGCGTGAAGACAGGGACACTATCGGTTTCA 
               
               
                   
               
               
                 CAGGATGCTGTCCCTGTCGGTCGTCTAGTCGTAGCAAGTGTAGGGCCTCAGCACA 
               
               
                   
               
               
                 TTCGTAGGAGCTTCCCGACTGACGAAACATTACCAAAATTCGCTGCTAAAGAGCA 
               
               
                   
               
               
                 TAACAACCAACAGCTGAACGACGAGAGAGAACATCTCGAACAAAGCAACTCCAC 
               
               
                   
               
               
                 GTCAGAGGGGAGCTTTCTGGCATCAGCTCATGAACATGCAGACATCGCGCGAAG 
               
               
                   
               
               
                 TGATCCTGATGAGGACACGCTGGAGCCCCATCAAAAACGACGACGCAAGCGATG 
               
               
                   
               
               
                 TGCAATAGCATACCAGGGCGAGGAACGTGGTGACAGCAACGGTCTTGATTCAAT 
               
               
                   
               
               
                 TGCGGATCGTGCAGAGCAAGCAGGGAACTTCCAGGCAATGAGGAAAGCTAACAC 
               
               
                   
               
               
                 GGACAACGGAAAAGTCGATTACTTGGAGCCTCATCGCTACGAAAAGTTGTCACC 
               
               
                   
               
               
                 ATGCGAGCAGGTGATCCAGCCGTCCTTGCGGCCAGCATGTGACCATCGTGGTGCA 
               
               
                   
               
               
                 CCCCAAAACTCAGTCGAGAGTGGTGAGCAGTCTCCCGATGCACAGCGACAGTTG 
               
               
                   
               
               
                 TGTAATCAAGGCTGTCGGACTTCCAACCGAACAGTACACAGCTCTGTTTACAGCA 
               
               
                   
               
               
                 ACGAAGTGGAGTCAAATGAGCTGCGCGGTGTGTTTCGGCTGGCGGAACAATCGC 
               
               
                   
               
               
                 TGCCTTCCCAGAGCGGGGATCCTGCGTGGTCGACAGCAGGATTTCAGTTGTCTAT 
               
               
                   
               
               
                 CCTGCCTCAGAAGGTGGAAGTACACTCCAGGAACAAATGCGATGGTCAAAATGT 
               
               
                   
               
               
                 GATGTATCGGTGTTCGCCCGGTTCTTTGCCGACTACCCATCAGCAGACAGTGTTT 
               
               
                   
               
               
                 CATTACGATAGAGATTCAAGCAGGTTCCCTTGCGCGGCCAAGCCTGCCGCAGCA 
               
               
                   
               
               
                 AGTGGAGCCCAGGGGACGATCGAGGAGAACGACGGATTAGTTAAAGAAGGACC 
               
               
                   
               
               
                 GAGCATGATTGTTACCGGGAGCAGTGTGGAAGTAGTACACTGCTGTTCAGTGTCC 
               
               
                   
               
               
                 CTTCGCAGGCGTGACCGGTCGTTACCAAGCGCTCAGTTGTGGACTTCACAAGAGA 
               
               
                   
               
               
                 CTGAGTCTGACACGAATCCATCACCGAACCAGCAGCATGAGAGTTGCCACCAAT 
               
               
                   
               
               
                 ACTGTAAGCGCCACGCTGCTTGGTGTGGGAAGACGGACCAGTTTTCCAAGCTGAC 
               
               
                   
               
               
                 TTCTTCGCATCAAGAGAACAGTAGTGGTAAAGATGCATGTCTTGTGTCTGTGTCT 
               
               
                   
               
               
                 CCAACAGTAACGCTAGATGATCTTCAGAAACAATCCCGAGGCACAGTTCTGTCA 
               
               
                   
               
               
                 GCGAAAGAAGAAATCGGCAAGCCGGAGACGTGGTCTCACGTTGTTGACAACACT 
               
               
                   
               
               
                 TACTCGAAGACAGACCACCAGCGTGCGTCGCTGTGTGCAGAGAATTCGTCAGGA 
               
               
                   
               
               
                 TGCGCCGAAGGAAGCACGGAACTCGTCAGATTCTCGGGAGGCTCTGTAAAATCA 
               
               
                   
               
               
                 GGGAGCAGTATGAGCGTCGACTGCGGAAATGGAAACCCAGATGACTGCCAGGAT 
               
               
                   
               
               
                 TGCAAAGCTGAGGAGATATGGCGAGGCGAGCAACGATATGCCGAAAGGGGCCA 
               
               
                   
               
               
                 CTCGGTTGAATCCAGGGGTGCTGGTTCAGTAGGTAGGAGCACGGATCTAACTATC 
               
               
                   
               
               
                 ACCGACTCTGGATCGATGCCGCTGTGTGCCAGCCCAATCGGTAGACCTCCTGCAG 
               
               
                   
               
               
                 ACAACGACACGCTGTTTTTAAGTGATGCCAGGTGCAACGTAGTGGCACAACTTAA 
               
               
                   
               
               
                 CCATCAAGATAACAGCAGGATTTCCCGATTAGCAAGCTGTGAAGAGGAATTCTT 
               
               
                   
               
               
                 GGCATGCGGAGGTGAGCGTCTGATTAATGCTTCCGGCGGTTTTAAGCCGGATGGT 
               
               
                   
               
               
                 GGATGCTTGTATCGCATGCAGCAAGCTGGTGCATGCAACACAAAACTTCACCGA 
               
               
                   
               
               
                 CCAGTGCATAGTTGCTCCACGATTGACTCGGAACAGCTTGAAGATCTTCCTTCTG 
               
               
                   
               
               
                 TGGAGAAGGCAGTTGGCGACCGAAGCTTCTCCAGCAAACGAAAAGGAGACATCC 
               
               
                   
               
               
                 CACCTTTCGCTGAATGGAAAAAAAATGACGAACTACGTGAGTTATACCGCGGCG 
               
               
                   
               
               
                 TGTCAGAAGCAGTTTCCCACGGTCAACCTGGCGACTGGAACGGCAGCTGGCCCG 
               
               
                   
               
               
                 GTATCTCAGGGCGCGCTCATCAAACGTCTTCGTGTTTCCCTGATAGGGTTAATGC 
               
               
                   
               
               
                 AAGCGACCGTAGAGAGCTGAATAGTTGGCGGCTCCACGTCTCCGCCGCCGCCGA 
               
               
                   
               
               
                 GCTAGGGTCAAGTCACATCTGGAACTCGCAATCATACGCTTCGGCCTCTGTGAGT 
               
               
                   
               
               
                 CGGGATAAACAACGGGAGCCACCTAAAAATGGGCTCACTGGCTGTGACGTGCCA 
               
               
                   
               
               
                 GAGTATCTGGGGACCAGTCAAAGTGCAGGACTACCTGCAGCAAACGCGCACGAA 
               
               
                   
               
               
                 CGCGGCAACTTCTATGGACATGATAGATGCCGACCACGTGAAGGAGAGCGGGTC 
               
               
                   
               
               
                 CGTTGGGTGGGCCTACAGCGAAATCGAAAACCCGAGGCATCGGTATCCTCTGGA 
               
               
                   
               
               
                 GCGAGCAACAGTGCGACAACAGCGAGACCGAAGGACAGCACGGAACCTGACGA 
               
               
                   
               
               
                 AGGCAACAGTGAAGGAGTGAGCACGAGGCGAAAAGACTCTGGTTCCACTGCAGC 
               
               
                   
               
               
                 GACTATCAGTCGGGCTGTTTCCCTGGGTATGGTGACACCGAGTGCTGCTTGTGAG 
               
               
                   
               
               
                 AATTCTTCTTCACTAACAGATACGTCTCCTCCTCTGAGCCATCGGCCCTCCTTCAG 
               
               
                   
               
               
                 CTTTACTCATTGCTGCGAGGAGACTTTGAGCAGGTGTAACTCCTCTAATTATTTGT 
               
               
                   
               
               
                 GTCCTCCAGCAACGTGTCATACGTCGGATGATGGTAGGTCTTTAGGGCCGTCGCG 
               
               
                   
               
               
                 AGAGGCACAAGCTCTCCGGTCATTGAGCCTAGCTTCCGGCTATGGTTACCCGGGG 
               
               
                   
               
               
                 ATACCTGCCGAGGCAACGTCCTTCTGGCAGGGCAGCTCACTGGAGCACTCAATA 
               
               
                   
               
               
                 ATGGAACCGCAGATGGTGCCATCCGATGATGAACTTCGATTGTGGGTCCATCCTC 
               
               
                   
               
               
                 GTGACGCAGCGAATTGGTCGCAGAGCACGTTGAAACCCGTTGCTGTCGTAAGCG 
               
               
                   
               
               
                 GGACCGACGCTGGTGACGATCAACATAAGACGCCAGAGAACTTGACTCCCGAAA 
               
               
                   
               
               
                 GCGGGCAGGCCCATCGCCGGGACGGCCACGACATGCAGCGTGTGCAACGGTGCG 
               
               
                   
               
               
                 ATGACGAGGGGGAGTGCCCCCCTACAACAGTCGAACTGACTTTTCCGCATTCACA 
               
               
                   
               
               
                 CTCTAGTGATGAAATGCAGGACTTGCCGTCGAAGGTACAAGGAAATTTTCTCTTG 
               
               
                   
               
               
                 CGAAGAGAGCTCTCGGACTCACTGCAACATGAGACTGCCGAAAGCGTTGCTGGT 
               
               
                   
               
               
                 TACGGGTGGATGCGTATACGGAATGCTGGAGATATTCCAAACTCGAAGGTACCTT 
               
               
                   
               
               
                 GTGCTTGGGAACAGTGCATGCCAGCATCGGAGAGAGAACGGGGAGTGAACGACC 
               
               
                   
               
               
                 ACATGAGTAGTGAAGCCTCACGAATGTCGAAGGCAGCAAGTTCAAGCTTCGTTC 
               
               
                   
               
               
                 CTAGCTCATGCACAGATGCGCCGGTGGTCAGAGTAGGTGAGGACACTACCAAGT 
               
               
                   
               
               
                 CGGTCTGTGAGGAGCAACAGCTGTGCGAAGGAGGTAATCGTGGTTCCTTGTCCCC 
               
               
                   
               
               
                 GGAAGCCACAGGCTTTGAGAGCTTGGGCCCACCGCTCCAGTTGTTGCTTGTTGAC 
               
               
                   
               
               
                 GGATACACTCCATTCGAGCCCGTAGTGGAAAAGGTCTCTCAAACAATGGAGCAG 
               
               
                   
               
               
                 ACTTTATTTCCTGTGCCAGGTCAGGAGACTGATACAAGAGATGAGGATGGACGA 
               
               
                   
               
               
                 TACAACTGgtaagaaaaacaatacactcaggcaaggccagggtgcgtgaaagagaagtgtatgctgtcccagtgtaggtagc 
               
               
                   
               
               
                 agtgctatttgtaggccttcgaaagaaagaaagtggaacagaaggctacttcgatgcggtagttccacagggtggcagggcagcccc 
               
               
                   
               
               
                 gccttgaggtgatctggcacgaagtcagtgttcaaatgctcaggcaccgattcaagccatatatccatatgtggccaacatagagaaaa 
               
               
                   
               
               
                 tggtgaatcaccacatttatttaagcacacataaaacagtatcagtaactatcagtgtgcaagaggeggctataggcgtccggagccaa 
               
               
                   
               
               
                 gtgtaatggattatgtccctcttcccacacggcagccgtgagatggtctggtgtacaatagccacggacttaaagctgtttccgggaga 
               
               
                   
               
               
                 cacagctggagactacacaacgttgtcaccgaagcctggtacgcgatgagtacacgcccgacctgtttcttgcctttctcctgtgttctca 
               
               
                   
               
               
                 gCGAGTGCTTACAAAACCGCCAGCCACCTTTGCATTCGGGGGGCTTGATG 
               
               
                   
               
               
                 BED 1 amino acid sequence: 
               
               
                 SEQ ID NO: 2 
                   
               
               
                 MEGASTQPMPHSQRERQAPVHAISGTWENCDQAGEYKGTACCVVERQVYSTETHA 
                   
               
               
                   
               
               
                 VEGCCSTRWNGVKEEKGGGEVSSRTALAGVVHLYTNSDGNAYTHISDQGMRQDEA 
               
               
                   
               
               
                 VAGQEQRHLNCEGEHEKKGNVAAGGGTLMVTKSEIEPCDDYYSVQRGQSCAGERA 
               
               
                   
               
               
                 PRDGCCRLLDGSRVDPAEGGSEEDENCYTHVLQKHLGQMPTAPYQGDDRLQTDLRL 
               
               
                   
               
               
                 GDFQSGPSDALSGHHVTRTPILSPHGRYSEYISERLAWQYAERPGHGIAAENTVVMH 
               
               
                   
               
               
                 SHTGEATGSLRADAPSQWSTESRLQFHVGSQFTTENPELFAGIVGLDTEQFDARNAE 
               
               
                   
               
               
                 ALHWRQQGEARSTETECIADITPERGNRSTIRQWNKPEAARQEYHRASASARGPEET 
               
               
                   
               
               
                 NIITRGAHSDDQSIDAAAPGCWAARHLTSRQHPNPRPRMKEEHCGREREVLSSEQPS 
               
               
                   
               
               
                 DCGETQKTPASHSLVLDSKSRADASQTSPYTRNDEIQTIRAFEEQCLEVQLPQSRLRR 
               
               
                   
               
               
                 GIDYEAGMSQLAPTTQELKAKVLTTGLSPSCPNAAVLRASVPLSMDTTVTVHLADVE 
               
               
                   
               
               
                 DPSSKRHTPIENSISSGHCDPPCSSPGGMMEPRVSVSGLGSPHNCVEDREIARHGDGIG 
               
               
                   
               
               
                 RDILERRPLPFSPAALLTGCSSTAASSVVSGDVFTSVAASARANACRSSTDTQEESGC 
               
               
                   
               
               
                 GDAPRYVLLFPDEQDERLGHAQTSIATPSGSGQSKCMFKGDGNAEATFREEVKSSEL 
               
               
                   
               
               
                 RTPSRIQTRRLLPGVQLQGMDCDGCGASDPQKGRPAPETGELPEICHFSPQHPWQPGS 
               
               
                   
               
               
                 EVNQGYRAGADYGTSRVQQSLENCSWEESVDEGEQPRTTSSSSYGQDTQKRDSFLQ 
               
               
                   
               
               
                 SIDNRIASEPVDPTGTCGYNSTPETERSGOIVIRDQMLGVKPHLSHVSLTREGKHRGQQ 
               
               
                   
               
               
                 THLRKTGVPTWSAEEDASLAELVSRKGFKWALISSQLTGAFGIPRTGKQCRERWFNH 
               
               
                   
               
               
                 VNPEVKKGDWSAEEDAMILMLQNELGNRWATIAKKLRGRTENAVKNRFISLSNARL 
               
               
                   
               
               
                 GYGRPKRDGSSADCFSNRRTGSGKSSGITGMPNLCQSVCSAGTTKKDSSESGNHFVM 
               
               
                   
               
               
                 SVATKVFEFSDVAVDSGVSRPRQCTGTSPSCGHPSAGEGDPSHLKNTDVVGREQPIQ 
               
               
                   
               
               
                 RNNNESGKAAEQTAFSGVKTGTLSVSQDAVPVGRLVVASVGPQHIRRSFPTDETLPK 
               
               
                   
               
               
                 FAAKEHNNQQLNDEREHLEQSNSTSEGSFLASAHEHADIARSDPDEDTLEPHQKRRR 
               
               
                   
               
               
                 KRCAIAYQGEERGDSNGLDSIADRAEQAGNFQAMRKANTDNGKVDYLEPHRYEKL 
               
               
                   
               
               
                 SPCEQVIQPSLRPACDHRGAPQNSVESGEQSPDAQRQLCNQGCRTSNRTVHSSVYSN 
               
               
                   
               
               
                 EVESNELRGVFRLAEQSLPSQSGDPAWSTAGFQLSILPQKVEVHSRNKCDGQNVMY 
               
               
                   
               
               
                 RCSPGSLPTTHQQTVFHYDRDSSRFPCAAKPAAASGAQGTIEENDGLVKEGPSMIVT 
               
               
                   
               
               
                 GSSVEVVHCCSVSLRRRDRSLPSAQLWTSQETESDTNPSPNQQHESCHQYCKRHAA 
               
               
                   
               
               
                 WCGKTDQFSKLTSSHQENSSGKDACLVSVSPTVTLDDLQKQSRGTVLSAKEEIGKPE 
               
               
                   
               
               
                 TWSHVVDNTYSKTDHQRASLCAENSSGCAEGSTELVRFSGGSVKSGSSMSVDCGNG 
               
               
                   
               
               
                 NPDDCQDCKAEEIWRGEQRYAERGHSVESRGAGSVGRSTDLTITDSGSMPLCASPIG 
               
               
                   
               
               
                 RPPADNDTLFLSDARCNVVAQLNHQDNSRISRLASCEEEFLACGGERLINASGGFKPD 
               
               
                   
               
               
                 GGCLYRMQQAGACNTKLHRPVHSCSTIDSEQLEDLPSVEKAVGDRSFSSKRKGDIPP 
               
               
                   
               
               
                 FAEWKKNDELRELYRGVSEAVSHGQPGDWNGSWPGISGRAHQTSSCFPDRVNASDR 
               
               
                   
               
               
                 RELNSWRLHVSAAAELGSSHIWNSQSYASASVSRDKQREPPKNGLTGCDVPEYLGTS 
               
               
                   
               
               
                 QSAGLPAANAHERGNFYGHDRCRPREGERVRWVGLQRNRKPEASVSSGASNSATTA 
               
               
                   
               
               
                 RPKDSTEPDEGNSEGVSTRRKDSGSTAATISRAVSLGMVTPSAACENSSSLTDTSPPLS 
               
               
                   
               
               
                 HRPSFSFTHCCEETLSRCNSSNYLCPPATCHTSDDGRSLGPSREAQALRSLSLASGYG 
               
               
                   
               
               
                 YPGIPAEATSFWQGSSLEHSIMEPQMVPSDDELRLWVHPRDAANWSQSTLKPVAVV 
               
               
                   
               
               
                 SGTDAGDDQUKTPENLTPESGQAHRRDGHDMQRVQRCDDEGECPPTTVELTEPHSH 
               
               
                   
               
               
                 SSDEMQDLPSKVQGNFLLRRELSDSLQHETAESVAGYGWMRIRNAGDIPNSKVPCA 
               
               
                   
               
               
                 WEQCMPASERERGVNDHMSSEASRMSKAASSSFVPSSCTDAPVVRVGEDTTKSVCE 
               
               
                   
               
               
                 EQQLCEGGNRGSLSPEATGFESLGPPLQLLLVDGYTPFEPVVEKVSQTMEQTLFPVPG 
               
               
                   
               
               
                 QETDTRDEDGRYNCECLQNRQPPLHSGGLM 
               
            
           
         
       
     
     The following examples are provided to describe the invention in more detail. They are intended to illustrate, not to limit, the invention. 
     Materials and Methods 
     Strains and Cell Culture 
     Human foreskin fibroblasts were maintained in DMEM (Gibco) supplemented with 3% inactivated fetal serum (IFS) and 10 μg/mL gentamicin, referred to as standard media. If HFFs were to be used in bradyzoite experiments, host cells were maintained exclusively in DMEM supplemented with 10% IFS and 10 μg/mL gentamicin prior to infection. Alkaline stress media consists of RPMI 1640 (Sigma), supplemented with 1% IFS and 10 μg/mL gentamicin, and buffered with 50 mM HEPES adjusted to pH 8.1 with 10N NaOH. 
     Plasmids and Primers 
     Oligos were ordered from IDT. All cloning was performed with Q5 2× master mix (NEB) unless otherwise noted. Primers and plasmids used or generated are found in Tables 1 and 2. 
     
       
         
           
               
             
               
                 TABLE 1  
               
             
            
               
                   
               
               
                 Plasmids utilized in present disclosure. 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 SEQ 
                   
               
               
                   
                   
                 ID 
                   
               
               
                 Vector 
                 Description 
                 NO 
                 Sequence 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 pU6_Library_ 
                 generic gRNA 
                 3 
                 ccagatggtaagccctcccgtatcgtagttatctacacgacggggagtcaggcaactat 
               
               
                 DHFR 
                 expression + 
                   
                 ggatgaacgaaatagacagatcgctgagataggtgcctcactgattaagcattggtaa 
               
               
                   
                 pyrimethamine 
                   
                 ctgtcagaccaagtttactcatatatactttagattgatttaaaacttcatttttaatttaaaag 
               
               
                   
                 resistance. 
                   
                 gatctaggtgaagatcattttgataatctcatgaccaaaatcccttaacgtgagttttcgtt 
               
               
                   
                 Library 
                   
                 ccactgagcgtcagaccccgtagaaaagatcaaaggatcttcttgagatcctattttctg 
               
               
                   
                 backbone. 
                   
                 cgcgtaatctgctgcttgcaaacaaaaaaaccaccgctaccagcggtggtttgtttgcc 
               
               
                   
                   
                   
                 ggatcaagagctaccaactattttccgaaggtaactggcttcagcagagcgcagatac 
               
               
                   
                   
                   
                 caaatactgtccttctagtgtagccgtagttaggccaccacttcaagaactctgtagcac 
               
               
                   
                   
                   
                 cgcctacatacctcgctctgctaatcctgttaccagtggctgctgccagtggcgataagt 
               
               
                   
                   
                   
                 cgtgtcttaccgggttggactcaagacgatagttaccggataaggcgcagcggtcgg 
               
               
                   
                   
                   
                 gctgaacggggggttcgtgcacacagcccagcttggagcgaacgacctacaccgaa 
               
               
                   
                   
                   
                 ctgagatacctacagcgtgagctatgagaaagcgccacgcttcccgaagggagaaa 
               
               
                   
                   
                   
                 ggcggacaggtatccggtaagcggcagggtcggaacaggagagcgcacgaggga 
               
               
                   
                   
                   
                 gcttccagggggaaacgcctggtatctttatagtcctgtcgggtttcgccacctctgactt 
               
               
                   
                   
                   
                 gagcgtcgatttttgtgatgctcgtcaggggggcggagcctatggaaaaacgccagc 
               
               
                   
                   
                   
                 aacgcggcctttttacggttcctggccttttgctggccttagctcaCATGgGATG 
               
               
                   
                   
                   
                 AGACAAAGTGCGCGAGTTGAAATCGTCGTGGGGAC 
               
               
                   
                   
                   
                 GATTTCACCGCGGCCACATGTTGGAGACACTGAGGG 
               
               
                   
                   
                   
                 CACACGGGAAACGCGAAAGATTTCAAATTAACGTAC 
               
               
                   
                   
                   
                 CCAAACGCGAAAGCTTGCGCAGCATACACTCGAAGC 
               
               
                   
                   
                   
                 GAACATCCCGAACCATCGAGAGGCGGAGAGCGATA 
               
               
                   
                   
                   
                 AGTCTTTCACGCTGCGAAGTGTTGCGACGGCTGCGC 
               
               
                   
                   
                   
                 CGCTGCACTGTGAATTGGGCGCCAATATTGCATCCT 
               
               
                   
                   
                   
                 AGGCCTGACGCGCCTCCTGCAGAACGCGAGACACTG 
               
               
                   
                   
                   
                 GGATATGTAGAGCCAAGGGGGAAACCTTCGAACTCT 
               
               
                   
                   
                   
                 CGAATGTCTTCTCTGACAAGAATCATATTTCCATCAG 
               
               
                   
                   
                   
                 TTCTGTCAGATTTTCAAATGGCGACCTGCAGAGGCC 
               
               
                   
                   
                   
                 TGCTTCCTCCCTGTGCGCTCTTCGAAGGGGCTTTCTG 
               
               
                   
                   
                   
                 TCGCGCAGGGTCACCTCGTCCCCGAAGGGGGTGTTT 
               
               
                   
                   
                   
                 GCCTTCTGGTAAATGGGGATGTCAAGTTAGAGACCG 
               
               
                   
                   
                   
                 GTCTCAGTTTaAGAGCTAtgctgGAAAcagcaTAGCAAGT 
               
               
                   
                   
                   
                 TtAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTG 
               
               
                   
                   
                   
                 GCACCGAGTCGGTGCTTTTTTTTTCTTTTTCtctagaggtac 
               
               
                   
                   
                   
                 CATGCA 
               
               
                   
               
               
                 pBAG1-mNG 
                 pBAG1-mNG 
                 4 
                 gagaaggggcgggccagagcgttcggaaaattatctgcaaagcccaggtcccgtat 
               
               
                   
                 reporter 
                   
                 gatattcaaaaaagatgatggtgagcaagggcgaggaggataacatggcctctctccc 
               
               
                   
                   
                   
                 agcgacacatgagttacacatctttggctccatcaacggtgtggactttgacatggtgg 
               
               
                   
                   
                   
                 gtcagggcaccggcaatccaaatgatggttatgaggagttaaacctgaagtccaccaa 
               
               
                   
                   
                   
                 gggtgacctccagttctccccctggattctggtccctcatatcgggtatggcttccatca 
               
               
                   
                   
                   
                 gtacctgccctaccctgacgggatgtcgcctttccaggccgccatggtagatggctcc 
               
               
                   
                   
                   
                 ggctaccaagtccatcgcacaatgcagtttgaagatggtgcctcccttactgttaactac 
               
               
                   
                   
                   
                 cgctacacctacgagggaagccacatcaaaggagaggcccaggtgaaggggactg 
               
               
                   
                   
                   
                 gtttccctgctgacggtcctgtgatgaccaactcgctgaccgctgcggactggtgcag 
               
               
                   
                   
                   
                 gtcgaagaagacttaccccaacgacaaaaccatcatcagtacctttaagtggagttaca 
               
               
                   
                   
                   
                 ccactggaaatggcaagcgctaccggagcactgcgcggaccacctacacctttgcca 
               
               
                   
                   
                   
                 agccaatggcggctaactatctgaagaaccagccgatgtacgtgttccgtaagacgga 
               
               
                   
                   
                   
                 gctcaagcactccaagaccgagctcaacttcaaggagtggcaaaaggcctttaccgat 
               
               
                   
                   
                   
                 gtgatgggcatggacgagctgtacaagtaagcgcgcccagcccacagaagctgccc 
               
               
                   
                   
                   
                 gtctctcgttttcctctcttttcggagggatcagggagagtgcctcgggtcggagagag 
               
               
                   
                   
                   
                 ctgacgagggggtgccagagacccctgtgtcctttatcgaagaaaagggatgactctt 
               
               
                   
                   
                   
                 catgtggcatttcacacagtctcacctcgccttgttttctttttgtcaatcagaacgaaagc 
               
               
                   
                   
                   
                 gagttgcgggtgacgcagatgtgcgtgtatccactcggaatgcgttatcgttctgtatgc 
               
               
                   
                   
                   
                 cgctagagtgctggactgttgctgtctgcccacgacagcagacaactttccttctatgca 
               
               
                   
                   
                   
                 cttgcaggatggtgcagcgcaaacgacggagagaaaggagcaccctctcagtttccc 
               
               
                   
                   
                   
                 tacgatgtgctgtcagtttcgactcttcaccgcgaacgattggcgatacgtctctgttgac 
               
               
                   
                   
                   
                 ttgttaggctccgaccacgaagctcccttaactagataagccgcgacacctaagtgtac 
               
               
                   
                   
                   
                 accatttgcagatcgataatctgcgaccgctgaatccgtccagatcagtaaaaccgcac 
               
               
                   
                   
                   
                 cacctaagtgtaaaccttgtttaggtcgataaaatgctaccaacccccacccacaatcg 
               
               
                   
                   
                   
                 agccttgagcgtttctgcgcacgcgttggcctacgtgacttgctgatgcctgcctctggc 
               
               
                   
                   
                   
                 cattcatgccagtcagtgcgcataaaaatgtggacacagtcggttgacaagtgttctgg 
               
               
                   
                   
                   
                 caggctacagtgacaccgcggtggagggggatccactagttctactcgagggtcgac 
               
               
                   
                   
                   
                 ggtatcgat 
               
               
                   
               
               
                 pSAG1-mNG 
                 pSAG1-mNG 
                 5 
                 ctcccagcgacacatgagttacacatctttggctccatcaacggtgtggactttgacatg 
               
               
                   
                 reporter (used 
                   
                 gtgggtcagggcaccggcaatccaaatgatggttatgaggagttaaacctgaagtcca 
               
               
                   
                 as ternplate 
                   
                 ccaagggtgacctccagttctccccctggattctggtccctcatatcgggtatggcttcc 
               
               
                   
                 only) 
                   
                 atcagtacctgccctaccctgacgggatgtcgcattccaggccgccatggtagatgg 
               
               
                   
                   
                   
                 ctccggctaccaagtccatcgcacaatgcagtttgaagatggtgcctcccttactgttaa 
               
               
                   
                   
                   
                 ctaccgctacacctacgagggaagccacatcaaaggagaggcccaggtgaagggg 
               
               
                   
                   
                   
                 actggtttccctgctgacggtcctgtgatgaccaactcgctgaccgctgcggactggtg 
               
               
                   
                   
                   
                 caggtcgaagaagacttaccccaacgacaaaaccatcatcagtacctttaagtggagtt 
               
               
                   
                   
                   
                 acaccactggaaatggcaagcgctaccggagcactgcgcggaccacctacacctttg 
               
               
                   
                   
                   
                 ccaagccaatggcggctaactatctgaagaaccagccgatgtacgtgttccgtaagac 
               
               
                   
                   
                   
                 ggagctcaagcactccaagaccgagctcaacttcaaggagtggcaaaaggcctttac 
               
               
                   
                   
                   
                 cgatgtgatggGCATGGACGAGCTGTACAAGTAAgcgcgccca 
               
               
                   
                   
                   
                 gcccacagaagctgcccgtctctcgttttcctctatttcggagggatcagggagagtg 
               
               
                   
                   
                   
                 cctcgggtcggagagagctgacgagggggtgccagagacccctgtgtcctttatcga 
               
               
                   
                   
                   
                 agaaaagggatgactcttcatgtggcatttcacacagtctcacctcgccttgttttctUttg 
               
               
                   
                   
                   
                 tcaatcagaacgaaagcgagttgcgggtgacgcagatgtgcgtgtatccactcggaat 
               
               
                   
                   
                   
                 gcgttatcgttctgtatgccgctagagtgctggactgttgctgtctgcccacgacagcag 
               
               
                   
                   
                   
                 acaactttccttctatgcacttgcaggatggtgcagcgcaaacgacggagagaaagga 
               
               
                   
                   
                   
                 gcaccctctcagtttccctacgatgtgctgtcagtttcgactcttcaccgcgaacgattgg 
               
               
                   
                   
                   
                 cgatacgtctctgttgacttgttaggctccgaccacgaagctcccttaactagataagcc 
               
               
                   
                   
                   
                 gcgacacctaagtgtacaccatttgcagatcgataatctgcgaccgctgaatccgtcca 
               
               
                   
                   
                   
                 gatcagtaaaaccgcaccacctaagtgtaaaccttgtttaggtcgataaaatgctaccaa 
               
               
                   
                   
                   
                 cccccacccacaatcgagccttgagcgtttctgcgcacgcgttggcctacgtgacttgc 
               
               
                   
                   
                   
                 tgatgcctgcctctggccattcatgccagtcagtgcgcataaaaatgtggacacagtcg 
               
               
                   
                   
                   
                 gttgacaagtgttctggcaggctacagtgacaccgcggtggagggggatccactagtt 
               
               
                   
                   
                   
                 ctactcgagggtcgacggtatcgat 
               
               
                   
               
               
                 pTLJB1- 
                 Overexpression 
                 6 
                 gtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggatt 
               
               
                 BFD1_wt-Ty 
                 of BFD1 
                   
                 agcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacg 
               
               
                   
                   
                   
                 gctacactagaaggacagtatttggtatctgcgctctgctgaagccagttaccttcggaa 
               
               
                   
                   
                   
                 aaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttg 
               
               
                   
                   
                   
                 tttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatctttt 
               
               
                   
                   
                   
                 ctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgaga 
               
               
                   
                   
                   
                 ttatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaa 
               
               
                   
                   
                   
                 agtatatatgagtaaacttggtctgacagttaccaatgcttaatcagtgaggcacctatct 
               
               
                   
                   
                   
                 cagcgatctgtctatttcgttcatccatagttgcctgactccccgtcgtgtagataactacg 
               
               
                   
                   
                   
                 atacgggagggcttaccatctggccccagtgctgcaatgataccgcgagacccacgc 
               
               
                   
                   
                   
                 tcaccggctccagatttatcagcaataaaccagccagccggaagggccgagcgcag 
               
               
                   
                   
                   
                 aagtggtcctgcaactttatccgcctccatccagtctattaattgttgccgggaagctaga 
               
               
                   
                   
                   
                 gtaagtagttcgccagttaatagtttgcgcaacgttgttgccattgctacaggcatcgtgg 
               
               
                   
                   
                   
                 tgtcacgctcgtcgtttggtatggcttcattcagctccggttcccaacgatcaaggcgag 
               
               
                   
                   
                   
                 ttacatgatcccccatgttgtgcaaaaaagcggttagctccttcggtcctccgatcgttgt 
               
               
                   
                   
                   
                 cagaagtaagttggccgcagtgttatcactcatggttatggcagcactgcataattctctt 
               
               
                   
                   
                   
                 actgtcatgccatccgtaagatgctifictgtgactggtgagtactcaaccaagtcattct 
               
               
                   
                   
                   
                 gagaatagtgtatgcggcgaccgagttgctcttgcccggcgtcaatacgggataatac 
               
               
                   
                   
                   
                 cgcgccacatagcagaactttaaaagtgctcatcattggaaaacgttcttcggggcgaa 
               
               
                   
                   
                   
                 aactctcaaggatcttaccgctgttgagatccagttcgatgtaacccactcgtgcaccca 
               
               
                   
                   
                   
                 actgatcttcagcatcttttactttcaccagcgtttctgggtgagcaaaaacaggaaggc 
               
               
                   
                   
                   
                 aaaatgccgcaaaaaagggaataagggcgacacggaaatgagaatactcatactctt 
               
               
                   
                   
                   
                 cattttcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaa 
               
               
                   
                   
                   
                 tgtatttagaaaaataaacaaataggggttccgcgcacataccccgaaaagtgccac 
               
               
                   
               
               
                 pTUB1-BFD1_ 
                 Overexpression 
                 7 
                 gcgaggtatgtaggcggtgctacagagacttgaagtggtggcctaactacggctaca 
               
               
                 ΔDBD-Ty 
                 of BFD1ΔDBD 
                   
                 ctagaaggacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaaga 
               
               
                   
                   
                   
                 gttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgca 
               
               
                   
                   
                   
                 agcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatctatctacg 
               
               
                   
                   
                   
                 gggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatc 
               
               
                   
                   
                   
                 aaaaaggatcttcacctagatcatttaaattaaaaatgaagttttaaatcaatctaaagtat 
               
               
                   
                   
                   
                 atatgagtaaacttggtctgacagttaccaatgcttaatcagtgaggcacctatctcagc 
               
               
                   
                   
                   
                 gatctgtctatttcgttcatccatagagcctgactccccgtcgtgtagataactacgatac 
               
               
                   
                   
                   
                 gggagggcttaccatctggccccagtgctgcaatgataccgcgagacccacgctcac 
               
               
                   
                   
                   
                 cggctccagatttatcagcaataaaccagccagccggaagggccgagcgcagaagt 
               
               
                   
                   
                   
                 ggtcctgcaactttatccgcctccatccagtctattaattgagccgggaagctagagtaa 
               
               
                   
                   
                   
                 gtagttcgccagttaatagtttgcgcaacgttgttgccattgctacaggcatcgtggtgtc 
               
               
                   
                   
                   
                 acgctcgtcgtttggtatggcttcattcagctccggttcccaacgatcaaggcgagttac 
               
               
                   
                   
                   
                 atgatcccccatgttgtgcaaaaaagcggttagctccttcggtcctccgatcgttgtcag 
               
               
                   
                   
                   
                 aagtaagaggccgcagtgttatcactcatggttatggcagcactgcataattctcttact 
               
               
                   
                   
                   
                 gtcatgccatccgtaagatgcttactgtgactggtgagtactcaaccaagtcattctgag 
               
               
                   
                   
                   
                 aatagtgtatgcggcgaccgagttgctcttgcccggcgtcaatacgggataataccgc 
               
               
                   
                   
                   
                 gccacatagcagaactttaaaagtgctcatcattggaaaacgacttcggggcgaaaac 
               
               
                   
                   
                   
                 tctcaaggatcttaccgctgagagatccagttcgatgtaacccactcgtgcacccaact 
               
               
                   
                   
                   
                 gatcttcagcatatttactttcaccagcgtttctgggtgagcaaaaacaggaaggcaaa 
               
               
                   
                   
                   
                 atgccgcaaaaaagggaataagggcgacacggaaatgttgaatactcatactcttcctt 
               
               
                   
                   
                   
                 tttcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaatgta 
               
               
                   
                   
                   
                 tttagaaaaataaacaaataggggaccgcgcacatttccccgaaaagtgccac 
               
               
                   
               
               
                 p312330-Ty 
                 Endogenous Ty 
                 8 
                 gGCATGGACGAGCTGTACAAGTGAtcaccgagtgctcacttctc 
               
               
                   
                 tagging vector 
                   
                 aaatcgacaaaggaaacacacttcgtgcagcatgtgccccattataaagaaactgagtt 
               
               
                   
                 for 312330.  
                   
                 gttccgctgtggcttgcaggtgtcacatccacaaaaaccggccgactctaaataggagt 
               
               
                   
                 Co-transfect  
                   
                 gtacgcagcaagcagcgaaagtttatgactgggtccgaatctctgaacggatgtgtgg 
               
               
                   
                 with 
                   
                 cggacctggctgatgagatcgccgtcgacacacgcgccacatgggtcaatacacaa 
               
               
                   
                 pCas9-CAT 
                   
                 gacagctatcagttgttttagtcgaaccggttaacacaattcttgcccccccgaTGAct 
               
               
                   
                   
                   
                 agaggtacCATGCATctagcatgtcattcgattttcaccccccgcgtagacctgt 
               
               
                   
                   
                   
                 gtgtcattcgttgtcgagacaactctgtcccgccccggtgctgttccatatgcgtgacttt 
               
               
                   
                   
                   
                 cccgcaattttttcagactttcaggaaagacaggctccggaacgatctcgtccatgactg 
               
               
                   
                   
                   
                 gtaaatccacgacaccgcaatggcccccagcacctctatctctcgtgccaggggacta 
               
               
                   
                   
                   
                 acgttgtatgcgtctgcgtcttgtctttttgcattcgctttccaaaaaagagagccatccgtt 
               
               
                   
                   
                   
                 cccccgcacattcaacgccgcgagtgcggtttttgtcttttttgagtggtaggacgctttt 
               
               
                   
                   
                   
                 catgcgcgaactacgtggacattaagaccattctattttcgacagcacgaaaccttgca 
               
               
                   
                   
                   
                 ttcaaacccgcccgcggaagatccgatcttgctgctgacgcagtcccagtagcgtcct 
               
               
                   
                   
                   
                 gtcggccgcgccgtctctGttggtgggcagccgctacacctgttatCtgactgccgtg 
               
               
                   
                   
                   
                 cgcgaaaatgacgccatttttgggaaaatcggggaacttcattctttaaaagtatgcgga 
               
               
                   
                   
                   
                 ggtttcctttttcttctgttcgtttctttttctcgggtttgataaccgtgttcgatgtaagcacttt 
               
               
                   
                   
                   
                 ccgtctctcctccgtgctttgttcgacatcgagaGcaggtgtgcagatccttcgcttgtc 
               
               
                   
                   
                   
                 gatccggagacgcgtgtctcgtagaaccttttcattttaccacacggcagtgcggagca 
               
               
                   
                   
                   
                 ctgctctgagtgcagcagggacgggtgaagtttcgctttagtagtgcgtttctgctctac 
               
               
                   
                   
                   
                 ggggcgttgtcgtgtctgggaag 
               
               
                   
               
               
                 p208740-Ty 
                 Endogenous Ty 
                 9 
                 gagttgttccgctgtggcttgcaggtgtcacatccacaaaaaccggccgactctaaata 
               
               
                   
                 tagging vector 
                   
                 ggagtgtttcgcagcaagcagcgaaagtttatgactgggtccgaatctctgaacggat 
               
               
                   
                 for 208740. 
                   
                 gtgtggcggacctggctgatgttgatcgccgtcgacacacgcgccacatgggtcaata 
               
               
                   
                 Co-transfect 
                   
                 cacaagacagctatcagttgttttagtcgaaccggttaacacaattcttgcccccccgaT 
               
               
                   
                 with pCas9-CAT 
                   
                 GActagaggtacCATGCATctagcatgtcattcgattttcaccccccgcgtagtt 
               
               
                   
                   
                   
                 cctgtgtgtcattcgttgtcgagacaactctgtcccgccccggtgctgttccatatgcgtg 
               
               
                   
                   
                   
                 actttcccgcaattttttcagactttcaggaaagacaggctccggaacgatctcgtccat 
               
               
                   
                   
                   
                 gactggtaaatccacgacaccgcaatggcccccagcacctctatctctcgtgccaggg 
               
               
                   
                   
                   
                 gactaacgttgtatgcgtctgcgtcttgtctttttgcattcgctttccaaaaaagagagcca 
               
               
                   
                   
                   
                 tccgttcccccgcacattcaacgccgcgagtgcggtttttgtcttttttgagtggtaggac 
               
               
                   
                   
                   
                 gcttttcatgcgcgaactacgtggacattaagttccattctctttttcgacagcacgaaac 
               
               
                   
                   
                   
                 cttgcattcaaacccgcccgcggaagatccgatcttgctgctgttcgcagtcccagtag 
               
               
                   
                   
                   
                 cgtcctgtcggccgcgccgtctctGttggtgggcagccgctacacctgttatCtgact 
               
               
                   
                   
                   
                 gccgtgcgcgaaaatgacgccatttttgggaaaatcggggaacttcattctttaaaagta 
               
               
                   
                   
                   
                 tgcggaggtttcctttttcttctgttcgtttctttttctcgggtttgataaccgtgttcgatgtaa 
               
               
                   
                   
                   
                 gcactttccgtctctcctccgtgctttgttcgacatcgagaGcaggtgtgcagatccttc 
               
               
                   
                   
                   
                 gcttgtcgatccggagacgcgtgtctcgtagaaccttttcattttaccacacggcagtgc 
               
               
                   
                   
                   
                 ggagcactgctctgagtgcagcagggacgggtgaagtttcgctttagtagtgcgtttct 
               
               
                   
                   
                   
                 gctctacggggcgttgtcgtgtctgggaag 
               
               
                   
               
               
                 pU6-BFD1- 
                 anti-BFD1 gRNA + 
                 10 
                 cggacaggtatccggtaagcggcagggtcggaacaggagagcgcacgagggagc 
               
               
                 DHFR 
                 pyrimethamine 
                   
                 ttccagggggaaacgcctggtatctttatagtcctgtcgggtttcgccacctctgacttga 
               
               
                   
                 resistance, 
                   
                 gcgtcgatttttgtgatgctcgtcaggggggcggagcctatggaaaaacgccagcaac 
               
               
                   
                 used to  
                   
                 gcggcctttttacggttcctggccttttgctggccttttgctcaCATGgGATGAG 
               
               
                   
                 generated 
                   
                 ACAAAGTGCGCGAGTTGAAATCGTCGTGGGGACGAT 
               
               
                   
                 BFD1 frameshift 
                   
                 TTCACCGCGGCCACATGTTGGAGACACTGAGGGCAC 
               
               
                   
                   
                   
                 ACGGGAAACGCGAAAGATTTCAAATTAACGTACCCA 
               
               
                   
                   
                   
                 AACGCGAAAGCTTGCGCAGCATACACTCGAAGCGA 
               
               
                   
                   
                   
                 ACATCCCGAACCATCGAGAGGCGGAGAGCGATAAG 
               
               
                   
                   
                   
                 TCTTTCACGCTGCGAAGTGTTGCGACGGCTGCGCCG 
               
               
                   
                   
                   
                 CTGCACTGTGAATTGGGCGCCAATATTGCATCCTAG 
               
               
                   
                   
                   
                 GCCTGACGCGCCTCCTGCAGAACGCGAGACACTGGG 
               
               
                   
                   
                   
                 ATATGTAGAGCCAAGGGGGAAACCTTCGAACTCTCG 
               
               
                   
                   
                   
                 AATGTCTTCTCTGACAAGAATCATATTTCCATCAGTT 
               
               
                   
                   
                   
                 CTGTCAGATTTTCAAATGGCGACCTGCAGAGGCCTG 
               
               
                   
                   
                   
                 CTTCCTCCCTGTGCGCTCTTCGAAGGGGCTTTCTGTC 
               
               
                   
                   
                   
                 GCGCAGGGTCACCTCGTCCCCGAAGGGGGTGTTTGC 
               
               
                   
                   
                   
                 CTTCTGGTAAATGGGGATGTCAAGTTGTGTCCGGAC 
               
               
                   
                   
                   
                 ACCATGTAACAgttttagagctagaaatagcaagttaaaataaggctagtcc 
               
               
                   
                   
                   
                 gttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTTTTTCTTTTTC 
               
               
                   
                   
                   
                 t 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2  
               
             
            
               
                   
               
               
                 Primers utilized in present disclosure. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                   
                 SEQ 
               
               
                   
                   
                   
                   
                 ID 
               
               
                 Oliqo 
                 Sequence 
                 Description 
                   
                 NO 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 P1 
                 AAGTTGACAAAATCCTCCTCCCTGGG 
                 gRNA against exon 3 of 
                   
                 11 
               
               
                   
                   
                 HXGPRT 
                   
                   
               
               
                   
               
               
                 P2 
                 AAAACCCAGGGAGGAGGATTTTGTCA 
                 gRNA against exon 3 of 
                   
                 12 
               
               
                   
                   
                 HXGPRT 
                   
                   
               
               
                   
                   
                 gRNA against exon 5 of 
                   
                 13 
               
               
                   
               
               
                 P3 
                 AAGTTGGACATAGTGCTCGAAGAAGG 
                 HXGPRT 
                   
                   
               
               
                   
                   
                 gRNA against exon 5 of 
                   
                 14 
               
               
                   
               
               
                 P4 
                 AAAACCTTCTTCGAGCACTATGTCCA 
                 HXGPRT 
                   
                   
               
               
                   
               
               
                 P5 
                 AAGTTCCACAGAACTTACTTCGGCGG 
                 gRNA against exon 4 of 
                   
                 15 
               
               
                   
                   
                 HXGPRT 
                   
                   
               
               
                   
               
               
                 P6 
                 AAAACCGCCGAAGTAAGTTCTGTGGA 
                 gRNA against exon 4 of 
                   
                 16 
               
               
                   
                   
                 HXGPRT 
                   
                   
               
               
                   
               
               
                 P7 
                 ATGGCGTCCAAACCCATTGA 
                 screening for HXGPRT 
                   
                 17 
               
               
                   
                   
                 deletions 
                   
                   
               
               
                   
               
               
                 P8 
                 TCGTTGAAGTCGTAGCAGCA 
                 screening for HXGPRT 
                   
                 18 
               
               
                   
                   
                 deletions 
                   
                   
               
               
                   
               
               
                 P9 
                 acttccaatccaatttaatTATCCAGTTGCCCGGCTC 
                 amplification of pBAG1 
                   
                 19 
               
               
                   
               
               
                 P10 
                 ctcaccatCATCTTTTTTGAATATCATACGGGACC 
                 amplification of pBAG1 
                   
                 20 
               
               
                   
               
               
                 P11 
                 tggggatgtcaagttGACTGTGGGTTGAGTTACAAGg 
                 first gRNA upstream of 
                   
                 21 
               
               
                   
                 ttttagagctagaa 
                 Ku80 
                   
                   
               
               
                   
               
               
                 P12 
                 ttctagctctaaaacCTTGTAACTCAACCCACAGTCaa 
                 first gRNA upstream of 
                   
                 22 
               
               
                   
                 cttgacatcccca 
                 Ku80 
                   
                   
               
               
                   
               
               
                 P13 
                 tggggatgtcaagttGAACAGAGACATCATAGACGTg 
                 second gRNA upstream 
                   
                 23 
               
               
                   
                 ttttagagctagaa 
                 of Ku80 
                   
                   
               
               
                   
               
               
                 P14 
                 ttctagctctaaaacACGTCTATGATGTCTCTGTTCaa 
                 second gRNA upstream 
                   
                 24 
               
               
                   
                 cttgacatcccca 
                 of Ku80 
                   
                   
               
               
                   
               
               
                 P15 
                 tggggatgtcaagttGTTTTGTCAAAGACCGCCTGAgt 
                 first gRNA downstream 
                   
                 25 
               
               
                   
                 tttagagctagaa 
                 of Ku80 
                   
                   
               
               
                   
               
               
                 P16 
                 ttctagctctaaaacTCAGGCGGTOTTTGACAAAACa 
                 first gRNA downstream 
                   
                 26 
               
               
                   
                 acttgacatcccca 
                 of Ku80 
                   
                   
               
               
                   
               
               
                 P17 
                 tggggatgtcaagttGGTOTTTGACAAAACGGGAGgtt 
                 second gRNA 
                   
                 27 
               
               
                   
                 ttagagctagaa 
                 downsream of Ku80 
                   
                   
               
               
                   
               
               
                 P18 
                 ttctagctctaaaacCTCCCGTTTTGTCAAAGACCaac 
                 second gRNA 
                   
                 28 
               
               
                   
                 ttgacatcccca 
                 downsream of Ku80 
                   
                   
               
               
                   
               
               
                 P19 
                 CTGCAGAACGCGAGACACTG 
                 for sequence verification 
                   
                 29 
               
               
                   
                   
                 of gRNA constructs 
                   
                   
               
               
                   
               
               
                 P20 
                 ccgacggttcgatcctgagt 
                 screening for Ku80 
                   
                 30 
               
               
                   
                   
                 deletion 
                   
                   
               
               
                   
               
               
                 P21 
                 ggactttccgaccagccctc 
                 screening for Ku80 
                   
                 31 
               
               
                   
                   
                 deletion 
                   
                   
               
               
                   
               
               
                 P22 
                 GTACCGACTCTTCGCAAGCG 
                 amplifies internal to 
                   
                 32 
               
               
                   
                   
                 Ku80, exon 3 
                   
                   
               
               
                   
               
               
                 P23 
                 TACTATCGCGCCTCGTCACG 
                 amplifies internal to 
                   
                 33 
               
               
                   
                   
                 Ku80, exon 3 
                   
                   
               
               
                   
               
               
                 P24 
                 tggggatgtcaagttGTTGAGTCCAAGCAGAGCTCgtt 
                 gRNA upstream of 
                   
                 34 
               
               
                   
                 ttagagctagaa 
                 BFD1 
                   
                   
               
               
                   
               
               
                 P25 
                 ttctagctctaaaacGAGCTCTGCTTGGACTCAACaac 
                 gRNA upstream of 
                   
                 35 
               
               
                   
                 ttgacatcccca 
                 BFD1 
                   
                   
               
               
                   
               
               
                 P26 
                 tggggatgtcaagttGTGTAGAGTCGTGGAAGGAGgtt 
                 gRNA downstream of 
                   
                 36 
               
               
                   
                 ttagagctagaa 
                 BFD1 
                   
                   
               
               
                   
               
               
                 P27 
                 ttctagctctaaaacCTCCTTCCACGACTCTACACaac 
                 gRNA downstream of 
                   
                 37 
               
               
                   
                 ttgacatcccca 
                 BFD1 
                   
                   
               
               
                   
               
               
                 P28 
                 cgtcacccactcacatcgtgtgagttgagtccaagcagagGCTT 
                 amplification of pSAG1- 
                   
                 38 
               
               
                   
                 TTACATCCGTTGcctt 
                 mNG with homology to 
                   
                   
               
               
                   
                   
                 BFD1 
                   
                   
               
               
                   
               
               
                 P29 
                 tcatactgccgttgcgcgctccactttcagcaccccactcTTACTT 
                 amplification of pSAG1- 
                   
                 39 
               
               
                   
                 GTACAGCTCGTCCA 
                 mNG with homology to 
                   
                   
               
               
                   
                   
                 BFD1 
                   
                   
               
               
                   
               
               
                 P30 
                 acattaatgcgtgcgccgca 
                 sequencing across 
                   
                 40 
               
               
                   
                   
                 BFD1 locus 
                   
                   
               
               
                   
               
               
                 P31 
                 tgcttcgggcaggcgactat 
                 sequencing across 
                   
                 41 
               
               
                   
                   
                 BFD1 locus 
                   
                   
               
               
                   
               
               
                 P32 
                 atggagggagccagtactcag 
                 BFD1 cDNA 
                   
                   
               
               
                   
                   
                 amplification, forward 
                   
                 42 
               
               
                   
               
               
                 P33 
                 CAATCGAGCGGGTCCTGGTTCGTGTGGACCT 
                 BFD1 cDNA 
                   
                 43 
               
               
                   
                 CcaTCAAGCCCCCCGAATGCAAAGGT 
                 amplification, reverse 
                   
                   
               
               
                   
               
               
                 P34 
                 ACCATAACCTAGGCGGGCATTTGTTGGCACTC 
                 BFD1 dDBD cDNA 
                   
                 44 
               
               
                   
                 CAGTTTTCCGT 
                 amplification, reverse 
                   
                   
               
               
                   
               
               
                 P35 
                 AATGCCCGCCTAGGTTATGGT 
                 BFD1 dDBD cDNA 
                   
                 45 
               
               
                   
                   
                 amplification, forward 
                   
                   
               
               
                   
               
               
                 P36 
                 CTGAGTACTGGCTCCCTCCATTGTCGAAAAAG 
                 TUB1 promoter 
                   
                 46 
               
               
                   
                 GGAATTCAAGaaaaaatgcc 
                   
                   
                   
               
               
                   
               
               
                 P37 
                 ctcgaggtcgacggtatcgatattaattaaCCCCCCACTGC 
                 TUB1 promoter 
                   
                 47 
               
               
                   
                 AAGCCCTACATTGACAAAATCCTCCTCCCCAT 
                   
                   
                   
               
               
                   
                 GCATGTCCCGCGTTCG 
                   
                   
                   
               
               
                   
               
               
                 P38 
                 GAGGTCCACACGAACCAGGACCCGCTCGATT 
                 BFD1 3 UTR 
                   
                 48 
               
               
                   
                 GAtgtaacagatggaagagggt 
                   
                   
                   
               
               
                   
               
               
                 P39 
                 aaagggaacaaaagctggagctGCGGCCGCacttacCAA 
                 BFD1 3&#39; UTR 
                   
                 49 
               
               
                   
                 CTTCTCAACTCTGTCCTTGACCAATCCACCAtg 
                 amplification of L1 from 
                   
                   
               
               
                   
                 actcgcaagcgtagcacg 
                   
                   
                   
               
               
                   
               
               
                 P40 
                 TTAGACGAGCAGGTTTCTTGCCTAT 
                 oligonucleotide pool 
                   
                 50 
               
               
                   
                   
                 amplification of L1 from 
                   
                   
               
               
                   
               
               
                 P41 
                 AAGTAAGCTCGCGATGTAGACGTTT 
                 oligonucleotide pool 
                   
                 51 
               
               
                   
                   
                 amplification of L2 from 
                   
                   
               
               
                   
               
               
                 P42 
                 GCCGATTACACCGTTAAATAACCTG 
                 oligonucleotide pool 
                   
                 52 
               
               
                   
               
               
                 P43 
                 TGGCGTGACTATGTTCGGTTACTAC 
                 amplification of L2 from 
                   
                 53 
               
               
                   
                   
                 oligonucleotide pool 
                   
                   
               
               
                   
               
               
                 P44 
                 TTCTGGTAAATGGGGATGTCAAGTT 
                 to make compatible with 
                   
                 54 
               
               
                   
                   
                 Gibson assembly 
                   
                   
               
               
                   
               
               
                 P45 
                 gctgTTTCcagcaTAGCTCTtAAAC 
                 to make compatible with 
                   
                 55 
               
               
                   
                   
                 Gibson assembly 
                   
                   
               
               
                   
               
               
                 P46 
                 GTAAATGGGGATGTCAAGTTGGACTTTGACAT 
                 first gRNA against mNG 
                   
                 56 
               
               
                   
                 GGTGGGTCGTTTaAGAGCTAtgctgGAA 
                   
                   
                   
               
               
                   
               
               
                 P47 
                 TTCcagcaTAGCTCTtAAACGACCCACCATGTCA 
                 first gRNA against mNG 
                   
                 57 
               
               
                   
                 AAGTCCAACTTGACATCCCCATTTAC 
                   
                   
                   
               
               
                   
               
               
                 P48 
                 GTAAATGGGGATGTCAAGTTGGCACCGGCAA 
                 second gRNA against 
                   
                 58 
               
               
                   
                 TCCAAATGAGTTTaAGAGCTAtgctgGAA 
                 mNG 
                   
                   
               
               
                   
               
               
                 P49 
                 TTCcagcaTAGCTCTtAAACTCATTTGGATTGCC 
                 second gRNA against 
                   
                 59 
               
               
                   
                 GGTGCCAACTTGACATCCCCATTTAC 
                 mNG 
                   
                   
               
               
                   
               
               
                 P50 
                 GTAAATGGGGATGTCAAGTTGGATTCTGGTCC 
                 third gRNA against 
                   
                 60 
               
               
                   
                 CTCATATCGTTTaAGAGCTAtgctgGAA 
                 mNG 
                   
                   
               
               
                   
               
               
                 P51 
                 TTCcagcaTAGCTCTtAAACGATATGAGGGACCA 
                 third gRNA against 
                   
                 61 
               
               
                   
                 GAATCCAACTTGACATCCCCATTTAC 
                 mNG 
                   
                   
               
               
                   
               
               
                 P52 
                 GTAAATGGGGATGTCAAGTTGGAAGCCATAC 
                 fourth gRNA against 
                   
                 62 
               
               
                   
                 CCGATATGAGTTTaAGAGCTAtgctgGAA 
                 mNG 
                   
                   
               
               
                   
               
               
                 P53 
                 TTCcagcaTAGCTCTtAAACTCATATCGGGTATG 
                 fourth gRNA against 
                   
                 63 
               
               
                   
                 GCTTCCAACTTGACATCCCCATTTAC 
                 mNG 
                   
                   
               
               
                   
               
               
                 P54 
                 GTAAATGGGGATGTCAAGTTGCGGTAGTTAAC 
                 fifth gRNA against mNG 
                   
                 64 
               
               
                   
                 AGTAAGGGGTTTaAGAGCTAtgctgGAA 
                   
                   
                   
               
               
                   
               
               
                 P55 
                 TTCcagcaTAGCTCTtAAACCCCTTACTGTTAAC 
                 fifth gRNA against mNG 
                   
                 65 
               
               
                   
                 TACCGCAACTTGACATCCCCATTTAC 
                   
                   
                   
               
               
                   
               
               
                 P56 
                 AATGATACGGCGACCACCGAGATCTACACgaat 
                 gRNA amplification + P5 
                   
                 66 
               
               
                   
                 gacacacaggaactacgcg 
                 adapater for Illumina 
                   
                   
               
               
                   
                   
                 sequencing 
                   
                   
               
               
                   
               
               
                 P57 
                 CAAGCAGAAGACGGCATACGAGATTCGCCTT 
                 gRNA amplification + 
                 TAAGGC 
                 67 
               
               
                   
                 Agattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 GA 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P58 
                 CAAGCAGAAGACGGCATACGAGATCTAGTAC 
                 gRNA amplification + 
                 CGTACTA 
                 68 
               
               
                   
                 Ggattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 G 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P59 
                 CAAGCAGAAGACGGCATACGAGATTTCTGCC 
                 gRNA amplification + 
                 AGGCAG 
                 69 
               
               
                   
                 Tgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 AA 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P60 
                 CAAGCAGAAGACGGCATACGAGATGCTCAGG 
                 gRNA amplification +  
                 TCCTGAG 
                 70 
               
               
                   
                 Agattttcaaatggcgacctgc 
                 barcode + P7 adapter  
                 C 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P61 
                 CAAGCAGAAGACGGCATACGAGATAGGAGTC 
                 gRNA amplification + 
                 GGACTC 
                 71 
               
               
                   
                 Cgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 CT 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P62 
                 CAAGCAGAAGACGGCATACGAGATCATGCCT 
                 gRNA amplification + 
                 TAGGCAT 
                 72 
               
               
                   
                 Agattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 G 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P63 
                 CAAGCAGAAGACGGCATACGAGATGTAGAGA 
                 gRNA amplification + 
                 CTCTCTA 
                 73 
               
               
                   
                 Ggattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 C 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P64 
                 CAAGCAGAAGACGGCATACGAGATCAGCCTC 
                 gRNA amplification + 
                 CGAGGC 
                 74 
               
               
                   
                 Ggattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 TG 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P65 
                 CAAGCAGAAGACGGCATACGAGATTGCCTCT 
                 gRNA amplification + 
                 AAGAGG 
                 75 
               
               
                   
                 Tgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 CA 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P66 
                 CAAGCAGAAGACGGCATACGAGATTCCTCTA 
                 gRNA amplification + 
                 GTAGAG 
                 76 
               
               
                   
                 Cgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 GA 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P67 
                 CAAGCAGAAGACGGCATACGAGATTCATGAG 
                 gRNA amplification + 
                 GCTCATG 
                 77 
               
               
                   
                 Cgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 A 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P68 
                 CAAGCAGAAGACGGCATACGAGATCCTGAGA 
                 gRNA amplification + 
                 ATCTCAG 
                 78 
               
               
                   
                 Tgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 G 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P69 
                 CAAGCAGAAGACGGCATACGAGATTAGCGAG 
                 gRNA amplification + 
                 ACTCGCT 
                 79 
               
               
                   
                 Tgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 A 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P70 
                 CAAGCAGAAGACGGCATACGAGATGTAGCTC 
                 gRNA amplification + 
                 GGAGCT 
                 80 
               
               
                   
                 Cgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 AC 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P71 
                 CAAGCAGAAGACGGCATACGAGATTACTACG 
                 gRNA amplification + 
                 GCGTAG 
                 81 
               
               
                   
                 Cgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 TA 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P72 
                 CAAGCAGAAGACGGCATACGAGATAGGCTCC 
                 gRNA amplification + 
                 CGGAGC 
                 82 
               
               
                   
                 Ggattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 CT 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P73 
                 CAAGCAGAAGACGGCATACGAGATGCAGCGT 
                 gRNA amplification + 
                 TACGCTG 
                 83 
               
               
                   
                 Agattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 C 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P74 
                 CAAGCAGAAGACGGCATACGAGATCTGCGCA 
                 gRNA amplification + 
                 ATGCGC 
                 84 
               
               
                   
                 Tgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 AG 
                   
               
               
                   
                   
                 for Illumina sequencing 
                   
                   
               
               
                   
               
               
                 P75 
                 CAAGCAGAAGACGGCATACGAGATGAGCGCT 
                 gRNA amplification + 
                   
                   
               
               
                   
                 Agattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 TAGCGCT 
                 85 
               
               
                   
                   
                 for Illumina sequencing 
                 C 
                   
               
               
                   
               
               
                 P76 
                 CAAGCAGAAGACGGCATACGAGATCGCTCAG 
                 gRNA amplification + 
                   
                   
               
               
                   
                 Tgattttcaaatggcgacctgc 
                 barcode + P7 adapter 
                 ACTGAG 
                 86 
               
               
                   
                   
                 for Illumina sequencing 
                 CG 
                   
               
               
                   
               
               
                 P77 
                 TTTTCAAGTTGATAACGGACTAGCCTTATTTAA 
                 Custom sequencing 
                   
                 87 
               
               
                   
                 ACTTGCTATGCTGTTTCCAGCATAGCTCTTAA 
                 primer 
                   
                   
               
               
                   
                 AC 
                   
                   
                   
               
               
                   
               
               
                 P78 
                 GCGCGACAGAAAGCCCCTTCGAAGAGCGCAC 
                 Custom indexing primer 
                   
                 88 
               
               
                   
                 AGGGAGGAAGCAGGCCTCTGCAGGTCGCCAT 
                   
                   
                   
               
               
                   
                 TTGAAAATC 
                   
                   
                   
               
               
                   
               
               
                 P79 
                 AGACTTCCAGTCCGGTCCTT 
                 200385 cDNA seq1 
                   
                 89 
               
               
                   
               
               
                 P80 
                 TCCTCAATCACGCTTAAGGC 
                 200385 cDNA seq2 
                   
                 90 
               
               
                   
               
               
                 P81 
                 GTACAGCTTCAAGGCATGGA 
                 200385 cDNA seq3 
                   
                 91 
               
               
                   
               
               
                 P82 
                 GCGGATCGTGCAGAGCAAGC 
                 200385 cDNA seq4 
                   
                 92 
               
               
                   
               
               
                 P83 
                 GAGGCACAGTTCTGTCAGCG 
                 200385 cDNA seq5 
                   
                 93 
               
               
                   
               
               
                 P84 
                 ACTACGTGAGTTATACCGCG 
                 200385 cDNA seq6 
                   
                 94 
               
               
                   
               
               
                 P85 
                 CACAAGCTCTCCGGTCATTG 
                 200385 cDNA seq7 
                   
                 95 
               
               
                   
               
               
                 P86 
                 CATGCGTGCGTTACATTGTACCT 
                 312330 forward primer 
                   
                 96 
               
               
                   
               
               
                 P87 
                 TGACGTGCATGATTTTGTTGTGTCTGT 
                 208740 forward primer 
                   
                 97 
               
               
                   
               
               
                 P88 
                 gaccgtcagcagggaaacc 
                 mNeonGreen reverse 
                   
                 98 
               
               
                   
                   
                 primer 
                   
                   
               
               
                   
               
               
                 P89 
                 aagttGTGTCCGGACACCATGTAACAg 
                 gRNA against exon 1 of 
                   
                 99 
               
               
                   
                   
                 BFD1 
                   
                   
               
               
                   
               
               
                 P90 
                 aaaacTGTTACATGGTGTCCGGACACa 
                 gRNA against exon 1 of 
                   
                 100 
               
               
                   
                   
                 BFD1 
                   
                   
               
               
                   
               
            
           
         
       
     
     Strain Generation 
     C16-B3. Starting with a robustly cyst-forming ME49 strain that constitutively expresses RFP (dsRed2.0) under control of the GRA1 promoter 68 , the endogenous selectable marker HXGPRT was inactivated through transfection with three gRNAs targeting the third, fourth and fifth exons. These gRNA expression vectors were assembled by annealing oligos P1/P2, P3/P4, and P5/P6, ligating into BsaI (NEB) digested pU6-Universal 69 , and sequence verifying with P19 69 . Transfected parasites were selected with 300 μg/mL 6-thioxanthine and screened for large deletions with P7/P8 70 . This strain was made constitutively Cas9 + by co-transfection with pCas9-CAT and pU6-Decoy as described previously 71 . The strain was further transfected with ScaI (NEB) linearized pBAG1-mNeonGreen containing the promoter of BAG1 (1.22 kb upstream of the coding sequence ATG), amplified with primers P9/10 driving expression of mNeonGreen and an HXGPRT resistance cassette, and selected for integration with 25 μg/ml mycophenolic acid and 50 μg/ml xanthine 16 ′ 72 . Note this plasmid contains two identical DHFR 3′ UTRs, and care had to be taken to avoid the loss of HXGPRT by recombination during growth in bacteria. 
     BFD1 frameshift . One gRNA was designed targeting the first exon of BFD1. Oligos P89/P90 were annealed, Gibson-assembled into pU6-Universal, and sequenced verified with P19, generating plasmid pU6-BFD1-DHFR. Bradyzoite reporter strain parasites were transfected with 50 μg of AseI (NEB) linearized pU6-BFD1-DHFR, and selected with 3 μM pyrimethamine in standard medium the next day. After stabilization of the population, parasites were subcloned into 96-well plates at 3 parasites per well. Clonal strains isolated from single plaques were screened and sequenced for polymorphisms at the targeted site. 
     ME49ΔKU80. Two gRNAs were designed targeting regions immediately upstream or downstream of the KU80 coding sequence. Oligos P11/12, P13/14, P15/16, P17/18 were annealed, Gibson-assembled into pU6-Universal, and sequence verified with P19. An early passage ME49 strain was transfected with 25 μg of each plasmid, and immediately subcloned into 96-well plates at 20 or 40 parasites per well to account for loss of viability during transfection. Clonal strains isolated from single plaques were screened for deletion of KU80 with P20/21, which amplifies a band of ˜5.9 kb in wildtype parasites or ˜500 bp if KU80 is excised. A single mixed population was identified from 225 strains tested, and further subcloned to isolate ME49ΔKU80. Loss of KU80 was also confirmed by complete sequencing of the locus and failure to amplify an internal fragment using P22/P23. 
     ME49ΔKU80ΔBFD1. Two gRNAs were designed targeting regions immediately upstream or downstream of BFD1. Oligos P24/25 and P26/27 were annealed, Gibson-assembled into pU6-Universal, and sequenced verified with P19. A repair template consisting of the SAG1 promoter driving expression of mNeonGreen was amplified from pSAG1-mNeonGreen using primers P28/29 with 40 bp of homology to regions flanking the targeted sites. ME49ΔKu80 was transfected with 50 μg of each gRNA and 10 μg of repair template. 5 days post-transfection parasites were sorted by green fluorescence and subcloned. Clonal strains isolated from single plaques were further characterized by sequencing the locus using P30/31 to confirm complete deletion of BFD1. 
     Immunofluorescence Assays 
     HFFs were grown on coverslips for 2-3 days before inoculation with  Toxoplasma . Coverslips were fixed with 4% formaldehyde for 20 minutes, permeabilized with 1% Triton-X 100 for 8 minutes, and blocked (5% normal goat serum and 5% IFS in phosphate buffered saline (PBS)) for at least 15 minutes ( FIGS. 1A-1H, 2A-2I, 4A-4B and 16 ). Alternatively, fixation was done using ice-cold 100% methanol for 2 minutes, without further permeabilization, followed by blocking as above ( FIGS. 12A-12B ). All primary and secondary antibody incubations were performed for 1 hour, with coverslips inverted on 50 μL of antibody dilutions in blocking buffer on Parafilm in a humidified chamber. Three washes with PBS were performed after each step. Coverslips were mounted on 5 μL of Prolong Diamond (ThermoFisher) and set for 30 minutes at 37° C. or overnight at room temperature. DBL-488 (Vector Labs) was used at 1:500. Mouse-anti-Ty antibody (BB2) was used at 1:1000 73 . Rabbit-anti-GAP45 was a gift from Dominique Soldati (University of Geneva) and was used at 1:1000 74 . Rabbit-anti-SAG2Y was used at 1:2000 67 . Mouse-anti-SAG1 (DG52) was used at 1:500 75 . Hoechst (Santa Cruz) was used at 1:2000. Secondary antibodies labeled with Alexa Fluor 488, 594 or 647 (ThermoFisher) were used at 1:1000. 
     Quantification of Gene Disruption 
     Cas9-expressing C16-B3 parasites were transfected with 50 μg of AseI (NEB) linearized pU6-SAG1-DHFR 71 , encoding a gRNA targeting SAG1. Selection with 3 μM pyrimethamine in standard media was initiated the next day, and drug-resistant pools were inoculated onto coverslips two passages (five days) after transfection. Coverslips were fixed 24 h later with methanol, and stained for SAG1 to quantify KO rates, relative to an untransfected control. GAP45 was used as a counterstain. Knockout rates were quantified before each forward genetic screen to ensure Cas9 activity. 
     Endogenous Tagging 
     To endogenously tag TGME49_312330 and TGME49_208740, ME49ΔKU80 was co-transfected with 50 μg of pCas9-CAT and 50 μg of BsaI-linearized p312330-Ty or p208740-Ty. Selection with 3 μM pyrimethamine in standard media was initiated the next day. Parasites were subcloned in 96 well plates, and isolated clones screened for successful integration using primers P86/88 or P87/88, respectively, and validated by Sanger sequencing. 
     Overexpression Vectors of BFD1 WT  and BFD1 ΔDBD    
     The sequence of BFD1 was amplified from ME49 cDNA using primers P32/33. To amplify BFD1 lacking the DNA binding domain (removing amino acids 921-1019), primers P32/34 and P35/P33 were used. BFD1 fragments were Gibson assembled together with the TUB1 promoter (amplified with P36/37) and the native BFD1 3′ UTR (˜1.1 kb amplified with P38/39), and sequence-verified by Sanger sequencing with oligos P79-P85. 
     Phylogenetic Analysis of BFD1 
     Protein sequences containing SANT/Myb-like domains were obtained for representative apicomplexan genomes from EupathDB based on their annotation with SMART domain SM00717. Domains from human c-Myb and CDCl5L were used for comparison. Individual domains were extracted from each sequence and aligned using ClustalW and the phylogenetic tree was generated by neighbor-joining ( FIG. 9 ) 76 . Alignments were also prepared for the concatenated domain sequences for a subset of proteins, and Bootstrap values were calculated for 10,000 trials ( FIG. 2A ). 
     Library Assembly 
     The gRNA oligonucleotide library was synthesized by Agilent and resuspended at 1 ng/μL in water. All library amplifications were done using iProof (Bio-Rad), using 2.5 ng of the oligonucleotide pool as template per 50 μL reaction. Sublibraries were amplified using primers P40/41 for library 1 and P42/43 for library 2, and subsequently amplified with primers P44/45 for cloning. Amplified libraries were Gibson assembled into gel-extracted (Zymo) BsaI-digested pU6 Library DHFR, dialyzed against water, and electroporated into E. cloni (Lucigen). Coverage was assessed by dilution plating in comparison to a no-insert negative control. Libraries were maxiprepped (Zymo), and retransformed into chemically competent NEB 5-alpha (NEB) to improve yields. Both E. cloni and NEB 5-alpha libraries were sequenced to ensure diversity. Libraries were linearized with AseI, dialyzed 1 h against water, and divided into 50 μg aliquots. Guide RNAs against mNeonGreen were assembled separately by annealing primer pairs P46/47, P48/49, P50/51, P52/53, or P54/55 and Gibson assembling into gel-extracted, BsaI-digested pU6 Library DHFR. Constructs were verified by sequencing with P19, and spiked into library aliquots at equimolar concentrations. 
     Forward Genetic Screening 
     C16-B3 reporter strain parasites were grown up in ˜10 15-cm dishes per screen. 10 transfections were performed for each library as described previously, with 50 μg of library transfected into approximately 2.6×10 7  parasites in 400 μL cytomix for each reaction 69 . Transfections were pooled and split between four 15-cm dishes. Media was changed the next day to standard media supplemented with 3 μM pyrimethamine and 10 μg/mL DNaseI (Sigma-Aldrich). At each passage of the screen, plates were scraped, parasites were mechanically released with a 27-gauge needle, and passed through a 3 μm filter. For the second passage of screen, all parasites were passed into 4 15-cm plates without counting. All subsequent passages were performed with at a multiplicity of infection (MOI) of 1 (6×10 6  parasites per plate). Plates lysed every 2-3 days under unstressed growth in standard media supplemented with 3 μM pyrimethamine. At fourth passage (14 days post-transfection), parasites were inoculated into seven 15-cm plates, and media was changed after 4 hours to standard media supplemented with 3 μM pyrimethamine (3 plates) or alkaline stress media (4 plates). Unstressed parasites were passaged at an MOI of 1 every 2-3 days into 1-2 15-cm plates, in standard media supplemented with 3 μM pyrimethamine. Parasites under stressed conditions did not lyse out and were not passaged for the duration of the experiment, and media was changed every 2 days to fresh alkaline stress media. At each passage of unstressed parasites, 1-4×10 7  parasites were frozen down. At 10 days post media change, stressed populations were scraped, parasites were mechanically released, passed through a 3 μm filter, and sorted based on green fluorescence. At final timepoints for stressed parasites, both bulk populations (˜2×10 5  parasites) and mNG + -sorted populations (˜7×10 5 ) were frozen. DNA was isolated using the Qiagen Blood and Tissue kit, following the protocol for blood cells. Integrated gRNAs were amplified and barcoded using primers P56 and P57-76 in 50 μL reactions. Each reaction contained 200 ng or a maximum of 20 μL of template DNA. Amplicons were gel extracted (Zymo), eluted in water, and quantified using the QuBit dsDNA HS kit (ThermoFisher). Amplicons were pooled equally at a final concentration of 8 pM each and sequenced using a MiSeq v2 kit. Reads were 40 bp single-end and an 8 bp index. Custom sequencing primer P77 and custom indexing primer P78 were used. Guides were quantified using a custom Perl script. Guides not detected were assigned a pseudocount of 90% of the lowest detected gRNA in that sample. The phenotype or differentiation score for a gene was calculated by determining the mean log e  fold-change of all five gRNAs targeting that gene in the final sample compared to the input library. All analysis done in R (https://www_r-project_org/). 
     Stage-Specific RNA-Sequencing and Analysis 
     Parasites were allowed to invade and replicate inside host cells for 24 h in standard media, and then switched to either standard or alkaline stress media. For FACS, parasites were mechanically released from host cells using a 27- followed by a 30-gauge syringe needle, and passed through a 3 μm filter. At 24 and 48 h post media change, ˜1×10 5  unstressed mNG −  or stressed mNG +  parasites were sorted directly into TRIzol LS and frozen on dry ice. Sorting was done using a BD FACS Aria II, and visualization of events and gates using FCS Express 6. RNA was extracted by TRIzol-chloroform according to manufacturer&#39;s protocol, DNaseI digested, and TRIzol-chloroform extracted again. RNA quality was assessed by BioAnalyzer or Fragment analyzer. When possible, two samples were prepared per replicate and timepoint and treated as technical replicates in downstream processing. Libraries were generated using the SMARTseq low-input v4 kit, and sequenced on two lanes of a HiSeq 2000. Reads were 75 bp, paired-end. Alignment to the ToxoDB v. 36 assembly of the ME49 genome was done using STAR 77 . Differential expression analysis was done using the DESeq2 R package 78 . The cutoff for differential expression was an adjusted p value of 0.001 or lower. 
     Single-Cell RNA-Sequencing and Analysis 
     Seq-Well was performed as previously described, with the following amendments to the protocol 79 . Single cell suspensions of  Toxoplasma  were prepared by syringe release of parasites from host cells with a 27 followed by a 30-gauge needle, followed by filtering through a 5 μm filter and counting on a haemocytometer. Approximately 12,000 parasites were loaded per array, with two arrays per strain and timepoint used for stressed samples, and one array per strain for unstressed. At the 48 h timepoint, one wildtype stressed and one ΔBFD1 stressed array failed to seal correctly, resulting in only one array per strain and growth condition at this timepoint. Sequencing was done on two NovaSeq flowcells. Pre-processing, alignment to the ToxoDB v.41 assembly of the ME49 genome, and downstream processing done following the DropSeq Cookbook (http://mccarrolllab.org/dropseq/) 80 . An estimate of the number of single cells was made using plotCumulativeFractionOfReads (function implemented by the package “Dropbead” (https://github_com/rajewsky-lab/dropbead) that estimates the number of realistic cells sequenced, based on the fraction of cumulative reads assigned to each individual cell) from Dropbead in R with a maximum of 12,000 cells 81 . The corresponding cells were then further parsed and analyzed using the Seurat R package 82 . In the analysis of all timepoints, genotypes and growth conditions, cells were required to contain a minimum of 200 and a maximum of 10,000 non-rRNA mapping UMIs and have 40% or fewer total UMIs originating from rRNA. In the analysis of the final timepoint (72 h), cells were required to contain a minimum of 500 and a maximum of 5,000 non-rRNA mapping UMIs and have 10% or fewer total UMIs originating from rRNA. Cells were log-normalized and scaled to 10,000 UMIs, regressing out the number of UMIs detected. Variable genes were identified through outlier analysis of an average expression/dispersion scatter plot. Principal component analysis was run using these variable genes. The number of principal components (PCs) chosen to use for clustering and t-SNE visualization was based on permutation analysis and visual inspection of standard deviations of PCs. Differential gene expression between clusters or groups of clusters was performed using the Wilcoxon rank sum test, with differentially expressed genes required to be expressed in at least 10 percent of cells in one of the compared groups, have a log-fold change of 0.5 or less, and an adjusted p value of 0.001 or less. 
     Example 1: Generation of a Differentiation Reporter Compatible with Cas9-Mediated Screens 
     To screen for  Toxoplasma  mutants deficient in differentiation, a strain compatible with Cas9-mediated gene disruption and enrichment was developed for differentiated parasites 69  ( FIG. 1A ). Constitutive Cas9 expression was achieved as described previously 71 . Selection for a gRNA targeting the major tachyzoite surface antigen SAG1 resulted in 98% SAG1 −  parasites, confirming robust inactivation of genes in this background ( FIG. 1B ). To facilitate isolation of differentiated parasites, the reporter strain constitutively expresses RFP, and conditionally expresses the bright green fluorescent protein mNeonGreen (mNG) under the promoter of the canonical bradyzoite-specific gene BAG1. Growth of the reporter strain, referred to as C16-B3, under alkaline stress resulted in increasing proportions of parasites expressing mNeonGreen ( FIGS. 1C and 5A ). 
     To characterize transcriptomic differences between tachyzoites and bradyzoites, stage-specific bulk RNA-sequencing was performed using C16-B3. Gene expression of FACS-purified tachyzoites (mNG − , 24 h unstressed growth) was compared to bradyzoites (mNG + , 48 h stressed growth), and 1311 genes identified as upregulated and 933 genes as downregulated in bradyzoites ( FIG. 1D ). Principal component analysis shows 98% of variance is explained by growth condition, with minimal batch effects ( FIG. 5B ). Highly regulated genes show agreement with previous datasets, with the most highly upregulated genes including the canonical bradyzoite-specific genes bradyzoite antigen 1 (BAG1), lactate dehydrogenase 2 (LDH2), and enolase 1 (ENO1) ( FIG. 5C ). One of the most highly downregulated genes is the major tachyzoite surface antigen SAG1. Genes previously missed as differentially regulated tend to be more lowly expressed, suggesting enhanced sensitivity in the dataset ( FIG. 5D ). 
     Example 2: Forward Genetic Screening Identifies a Putative Regulator of  T gondii Differentiation    
     Genome-wide forward screens in  Toxoplasma  have been performed successfully, but performing these screens in a non-lab-attenuated strain presents additional challenges. In particular, the lower viability and integration rates observed suggest the largest number of genes that can be screened to be in the low hundreds ( FIG. 6 ). Therefore, sets of candidate genes small enough to meet these technical limitations were curated. By combining differential expression analysis with domain annotation and gene ontology, two libraries of ˜100 potential nucleic acid-binding proteins were assembled, targeting each gene with 5 guide RNAs (gRNAs). Library 1 (L1) consists of genes identified as differentially regulated in a preliminary RNA-seq experiment. Library 2 (L2) contains genes with DNA-binding domains commonly found in transcription factors, such as zinc finger and Myb-like domains. Across both libraries all 67 members of the ApiAP2 transcription factor family are targeted, along with 151 putative nucleic acid-binding proteins ( FIG. 1E ) 83,84 . As controls, each library additionally contains 10 genes known to be essential, 10 genes known to be dispensable, 10 non-cutting gRNAs, and 5 gRNAs against the mNG reporter itself. The effect inactivation of a gene has upon parasite fitness can be calculated by looking at changes in gRNA abundances over the course of an experiment. It is expected that gRNAs targeting highly essential genes to negatively affect parasite fitness and will be depleted quickly from the population, while gRNAs against non-essential genes or non-existent sequences should be retained. Guide against the mNG reporter should not affect fitness, but will mimic an inability to differentiate. 
     Following transfection of the libraries, parasites were passaged in selective media for four passages before being split between unstressed or stressed conditions for 10 days, passaging unstressed parasites as necessary ( FIG. 1E ). After 10 days, stressed mNG +  parasites were isolated by FACS. Integrated gRNAs from the final unstressed passage or from stressed mNG +  alkaline stress parasites were amplified, sequenced, and compared to the input library. The mean log 2  fold-change of all gRNAs against a gene from input library to final unstressed sample or stressed, mNG +  sample is referred to as a fitness or differentiation score, respectively. Candidate genes should be depleted specifically in the mNG +  population (low differentiation score relative to their fitness score), as should guides against the mNG reporter. In L1, only control mNG gRNAs were depleted in the mNG +  parasite population ( FIG. 1F ). However, in L2, gRNAs targeting a single other gene—TGME49_200385, renamed bradyzoite formation deficient 1 (BFD1)—were depleted along with control mNG gRNAs ( FIGS. 1G-1H ). Failure of a BFD1 mutant to express the mNG reporter following alkaline stress was confirmed by transfecting a single BFD1 targeting gRNA into C16-B3. A frameshifted clone was isolated with a single nucleotide insertion at the cut site ( FIG. 7 ). Under alkaline stress, the wildtype reporter strain shows robust mNG expression, while the frameshifted clone does not. 
     Example 3: BFD1 Contains Conserved DNA-Binding Domains and Localizes to the Nucleus 
     The sequence of the BFD1 open reading frame was defined based on cDNA sequencing, which differed from the annotated gene model and encoded a protein of 2,415 amino acids ( FIG. 8 ). BFD1 contains two tandem SANT/myb-like DNA-binding domains (SMART accession 00717), flanked by large extensions lacking identifiable motifs. The  Toxoplasma  genome encodes 14 proteins with SANT/myb-like domains. Phylogenetic analysis of these proteins reveals BFD1&#39;s two DNA-binding domains have homology to the R2 and R3 repeats of the human c-Myb protein, respectively ( FIGS. 2A-2B  and  FIG. 9 ). BFD1 orthologs can be found in all Apicomplexan species that form tissue cysts, while different patterns of conservation are found for other SANT domain—containing proteins. Transiently expressed, full-length BFD1-Ty localized to the nucleus, and co-localized with a DNA stain ( FIG. 2C ). 
     Example 4: Loss of BFD1 Blocks Parasite Differentiation 
     To provide a clean background for precise genetic manipulation, a low-passage, NHEJ-deficient ME49 strain was generated through deletion of KU80 ( FIG. 10 ). In this background, the entire coding sequence of BFD1 was replaced with an mNG expression cassette ( FIG. 2D ). Deletion of BFD1 caused no defect in tachyzoite growth as assayed by plaque formation ( FIG. 2E ).  Dolichos biflorus  lectin (DBL) recognizes N-acetylgalactosamine on the bradyzoite-specific cyst wall protein CST1, providing a convenient way of distinguishing differentiating vacuoles 6 . The ability of a ΔBFD1 strain to differentiate following 48 h of alkaline stress was tested. Wildtype vacuoles became robustly DBL +  under alkaline stress conditions. By contrast, no ΔBFD1 vacuoles developed DBL positivity ( FIGS. 2F-2G ). ΔBFD1 parasites exhibited a similar defect when differentiation was induced by a small molecule known to induce differentiation in  Toxoplasma  (Compound 1) 2425  or occurred spontaneously ( FIGS. 2H-2I ). 
     Example 5: Single-cell sequencing can be used to analyze  Toxoplasma  cell-cycle Progression 
     To profile cell cycle progression and the asynchronous process of differentiation, the first single-cell RNA-sequencing of  T gondii  was performed using Seq-Well 79 . Wildtype or ΔBFD1 parasites were grown under unstressed or stressed conditions for 24, 48 or 72 h. Following downstream processing and alignment, 26,560 cells passed quality control cutoffs, with an average of 1537 UMIs per cell representing an average of 685 genes per cell. ( FIGS. 3A, 11A-11C ). As cells from the 72 h timepoint were of the highest quality, unstressed parasites from this timepoint were clustered to examine the tachyzoite cell cycle. Seven clusters were identified, with six arranged in a circular pattern ( FIG. 3B ). 1,173 genes were identified as differentially expressed in one or more clusters. The average expression profile for markers from each cluster was determined using an existing dataset of synchronized tachyzoite gene expression 1 . The timing of marker expression indicates a progression through the cell cycle in a counter clock-wise direction through the various clusters ( FIG. 3C ). The proportion of cells identified as being in G1 or S/M matches the 60:40 ratio previously determined ( FIG. 3D ) 85 . 
     Example 6: BFD1 is Necessary for Initiation of Differentiation 
     Clustering cells from all timepoints, growth conditions and genotypes revealed a clear division between tachyzoite (SAG1+) and bradyzoite (BAG1+) containing clusters ( FIG. 3E ). Wildtype and ΔBFD1 parasites respond to alkaline stress very differently over time ( FIG. 3F ). WT parasites quickly exit the tachyzoite cell cycle and begin progressing towards bradyzoite-containing clusters. By contrast, ΔBFD1 parasites continue to replicate as tachyzoites until the 72 h timepoint, when they largely leave and cluster separately from both tachyzoites and bradyzoites. This suggests ΔBFD1 parasites fail to initiate differentiation despite the presence of an inducing signal. Examination of the timing of expression of canonical bradyzoite markers in wildtype cells suggested BAG1 is not among the earliest genes induced ( FIG. 12A ). Endogenous tagging of two strong, early markers of differentiation (TGME49_312330, TGME49_208740) localized both to the cyst wall ( FIG. 12B ). 
     To understand the nature of the clusters parasites end up in, the clustering of unstressed and stressed parasites of both genotypes from the 72 h timepoint were analyzed ( FIG. 3G ). The canonical stage-specific genes SAG1 and BAG1 show high, mutually exclusive expression, demonstrating strong separation of tachyzoites and bradyzoites ( FIG. 13A ). Tachyzoites (high SAG1) are colored in red, while bradyzoites (high BAG1) are in blue, according to expression level of each marker. Clusters with minimal BAG1 expression and weaker SAG1 expression are in gray. Stressed wildtype parasites overlap strongly with BAG1-expressing clusters, while stressed ΔBFD1 parasites either continue replicating as tachyzoites or move to the weakly SAG1 +  clusters ( FIG. 13B ). By contrast to bulk RNA-sequencing, in the single-cell data BFD1 is identified as differentially regulated in bradyzoite-containing clusters ( FIG. 13C ). 
     Examining highly expressed, stage-specific genes identified by the bulk RNA-sequencing showed widespread defects in bradyzoite-specific gene expression by ΔBFD1 parasites, including canonical markers such as LDH2 and ENO1 ( FIG. 3H ). Weaker expression of SAG1 and other normally highly expressed genes in stressed ΔBFD1 parasites made us wonder if these parasites were still actively dividing. Based on the cell-cycle regulation of the genes driving them, the first and third principal components explain the majority of variance due to the cell cycle ( FIGS. 14A-14C ). Wildtype stressed parasites plotted across these components show a clear cyclical pattern, indicating active bradyzoite replication ( FIG. 3I ). Many genes were identified as expressed specifically in replicating bradyzoites, including the previously identified bradyzoite rhoptry protein 1 ( FIG. 15 ) 86 . 19% of bradyzoites are in clusters expressing S/M markers compared to 39.5% of tachyzoites, recapitulating the approximately two-fold slower replication previously observed 87 . Non-tachyzoite ΔBFD1 stressed parasites show no such pattern, suggesting these parasites are no longer replicating ( FIG. 3I ). It has additionally been observed that aberrant morphologies in later timepoints of alkaline stressed ΔBFD1 parasites ( FIG. 16 ). These results suggest that BFD1 is necessary for parasites to initiate differentiation, and that after 72 hours under alkaline stress ΔBFD1 parasites are dying due to their failure to respond to that stress appropriately ( FIG. 3J ). 
     Example 7: Overexpression of BFD1 is Sufficient to Induce Differentiation in the Absence of Stress 
     As BFD1 is necessary for differentiation to occur, it was investigated whether overexpression of BFD1 would be sufficient to induce differentiation. Two constructs expressing epitope-tagged BFD1 under the TUB1 promoter—either full-length BFD1 (BFD1 WT ) or a mutant protein with its DNA-binding domain removed (BFD1ΔDBD) were generated ( FIG. 4A ). Wildtype or ΔBFD1 parasites were transfected with either BFD1 WT  or BFD1ΔDBD, and allowed to grow for 48 h under unstressed conditions. At 48 h, parasites were immunostained for BFD1 (Ty) and differentiation (DBL). Vacuoles containing Ty +  parasites were identified and scored for DBL positivity. Both constructs localized to the nucleus. Transient overexpression of BFD1 WT , but not BFD1ΔDBD, was sufficient to induce differentiation in over 60% of wildtype or ΔBFD1 parasites, demonstrating that the inability of ΔBFD1 parasites to differentiate is due to the specific absence of BFD1 ( FIG. 4B ). The requirement of the DNA-binding domain of BFD1 suggests its activity as a bona fide transcription factor drives differentiation. 
     Example 8: Loss of BFD1 blocks parasite differentiation regardless of induction method 
     ΔBFD1 parasites were complemented by introducing Ty-tagged cDNA copies of BFD1 at the endogenous locus, either full-length (ΔBFD1::BFD1 WT -Ty) or with its Myb-like domains deleted (ΔBFD1::BFD1 ΔMYB -Ty) ( FIG. 17A ). Deletion of BFD1 and subsequent complementation caused no defect in tachyzoite growth as assayed by plaque formation. The complemented strains grew slightly faster, perhaps due to prolonged passaging in cell culture ( FIG. 17B ). Differentiating vacuoles can be identified using  Dolichos biflorus  lectin (DBL) staining, which recognizes N-acetylgalactosamine on the bradyzoite-specific cyst-wall protein CST1 (Tomita et al., 2013). Many cyst wall proteins, including CST1, are robustly detected in large proportions of vacuoles after only 24 h under alkaline stress, making DBL positivity an earlier and more robust marker for differentiating parasites than BAG1 transcription which accumulates more slowly (see  FIG. 1C ). WT vacuoles became robustly DBL +  after 48 h under alkaline stress. By contrast, no ΔBFD1 vacuoles developed DBL positivity under identical conditions. 
     Complementation with the WT but not the ΔMYB allele of BFD1 restored differentiation and revealed nuclear localization of the transgenes ( FIGS. 17C and 17D ). ΔBFD1 parasites also failed to differentiate spontaneously or when induced with the small molecule Compound 1 ( FIG. 17D ), and in both cases complementation with full-length BFD1 restored differentiation to WT levels (Radke et al., 2006). 
     Example 9: ΔBFD1 Parasites Fail to Form Brain Cysts in Mice 
     To determine whether BFD1 is necessary for the formation of tissue cysts in animals, acute virulence and chronic infection of mice were assessed. CD-1 female mice were infected by intraperitoneal injection with 500 tachyzoites of WT, ΔBFD1, or ΔBFD1::BFD1 WT  parasites ( FIG. 18A ). Morbidity and mortality were comparable among the three strains ( FIGS. 18B and 18C ), indicating that BFD1 is dispensable for the acute symptoms of  Toxoplasma  infection. The marginal increase in ΔBFD1::BFD1 WT  virulence may be attributed to the faster growth rate observed by plaque formation ( FIG. 18D ). Brain cysts from WT and ΔBFDP:BFD1 WT  infections were morphologically identical, with a DBL positive cyst wall surrounding hundreds of bradyzoites ( FIG. 18D ). Starting at 2 weeks post-infection, cyst burden was measured by examining the brains of infected animals. Cyst numbers ranged from several hundred to several thousand per animal infected with WT or ΔBFD1::BFD1 WT  parasites; however, cysts were never isolated from ΔBFD1-infected animals ( FIG. 18E ). Similar results were observed in experiments conducted with CBA/J mice ( FIG. 19 ). Taken together, these results reveal that loss of BFD1 results in a specific and complete defect in tissue cyst formation during animal infections. 
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