bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allele pairing at Sun1-enriched domains at the nuclear periphery viaT1A3tandem DNA repeats
Authors: Balasooriya Gayan I. , Spector David L. 
Published: April 2023

AbstractSpatiotemporal gene regulation is fundamental to the biology of diploid cells. Therefore, effective communication between two alleles and their geometry in the nucleus is important. However, the mechanism that fine-tunes the expression from each of the two alleles of an autosome is enigmatic. Establishing an allele-specific gene expression visualization system in living cells, we show that alleles of biallelically expressedCthandTtc4genes are paired prior to acquiring monoallelic expression. We found that active alleles of monoallelic genes are preferentially localized at Sun1-enriched domains at the nuclear periphery. These peripherally localized active DNA loci are enriched with adenine-thymidine-rich tandem repeats that interact with Hnrnpd and reside in a Hi-C-defined A compartment within the B compartment. Our results demonstrate the biological significance ofT1A3tandem repeat sequences in genome organization and how the regulation of gene expression, at the level of individual alleles, relates to their spatial arrangement.
Late gene therapy limits the restoration of retinal function in a mouse model of retinitis pigmentosa
Authors: Scalabrino Miranda L. , Thapa Mishek , Wang Tian , Sampath Alapakkam P. , Chen Jeannie , Field Greg D. 
Published: April 2023

AbstractRetinitis pigmentosa is an inherited photoreceptor degeneration that begins with rod loss followed by cone loss and eventual blindness. Gene therapies are being developed, but it is unknown how retinal function depends on the time of intervention. To uncover this dependence, we utilized a mouse model of retinitis pigmentosa capable of artificial genetic rescue. This model enables a benchmark of best-case gene therapy by removing the variables that complicate the ability to answer this vital question. Complete genetic rescue was performed at 25%, 50%, and 70% rod loss (early, mid and late, respectively). Early and mid treatment restored retinal function to near wild-type levels, specifically the sensitivity and signal fidelity of retinal ganglion cells (RGCs), the ‘output’ neurons of the retina. However, some anatomical defects persisted. Late treatment retinas exhibited continued, albeit slowed, loss of sensitivity and signal fidelity among RGCs, as well as persistent gliosis. We conclude that gene replacement therapies delivered after 50% rod loss are unlikely to restore visual function to normal. This is critical information for administering gene therapies to rescue vision.
Determinants of cytoplasmic microtubule depolymerization during ciliogenesis inChlamydomonas reinhardtii
Authors: Dougherty Larissa L , Avasthi Prachee 
Published: April 2023

ABSTRACTAt the core of cilia are microtubules which are important for establishing length and assisting ciliary assembly and disassembly; however, another role for microtubule regulation on ciliogenesis lies outside of the cilium. The microtubule cytoskeleton is a highly dynamic structure which polymerizes and depolymerizes rapidly to assist in cellular processes. These processes have been studied across various organisms with chemical as well as genetic perturbations. However, these have generated conflicting data in terms of the role of cytoplasmic microtubules (CytoMTs) and free tubulin dynamics during ciliogenesis. Here we look at the relationship between ciliogenesis and cytoplasmic microtubule dynamics inChlamydomonas reinhardtiiusing chemical and mechanical perturbations. We find that not only can stabilized CytoMTs allow for normal ciliary assembly, but high calcium concentrations and low pH-induced deciliation cause CytoMTs to depolymerize separately from ciliary shedding. In addition, we find that ciliary shedding through mechanical shearing, cilia regenerate earlier despite intact CytoMTs. Our data suggests that cytoplasmic microtubules are not a sink for a limiting pool of cytoplasmic tubulin inChlamydomonas, depolymerization that occurs following deciliation is a consequence rather than a requirement for ciliogenesis, and intact CytoMTs in the cytoplasm and the proximal cilium support more efficient ciliary assembly.
Evolution of neuronal cell classes and types in the vertebrate retina
Authors: Hahn Joshua , Monavarfeshani Aboozar , Qiao Mu , Kao Allison , Kölsch Yvonne , Kumar Ayush , Kunze Vincent P , Rasys Ashley M. , Richardson Rose , Baier Herwig , Lucas Robert J. , Li Wei , Meister Markus , Trachtenberg Joshua T. , Yan Wenjun , Peng Yi-Rong , Sanes Joshua R. , Shekhar Karthik 
Published: April 2023

AbstractThe basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.
Genomic language model predicts protein co-regulation and function
Authors: Hwang Yunha , Cornman Andre L. , Kellogg Elizabeth H. , Ovchinnikov Sergey , Girguis Peter R. 
Published: April 2023

AbstractDeciphering the relationship between a gene and its genomic context is fundamental to understanding and engineering biological systems. Machine learning has shown promise in learning latent relationships underlying the sequence-structure-function paradigm from massive protein sequence datasets. However, to date, limited attempts have been made in extending this continuum to include higher order genomic context information. Evolutionary processes dictate the specificity of genomic contexts in which a gene is found across phylogenetic distances, and these emergent genomic patterns can be leveraged to uncover functional relationships between gene products. Here, we trained a genomic language model (gLM) on millions of metagenomic scaffolds to learn the latent functional and regulatory relationships between genes. gLM learns contextualized protein embeddings that capture the genomic context as well as the protein sequence itself, and encode biologically meaningful and functionally relevant information (e.g. enzymatic function, taxonomy). Our analysis of the attention patterns demonstrates that gLM is learning co-regulated functional modules (i.e. operons). Our findings illustrate that gLM’s unsupervised deep learning of the metagenomic corpus is an effective and promising approach to encode functional semantics and regulatory syntax of genes in their genomic contexts and uncover complex relationships between genes in a genomic region.
Pancreatic loss of Mig6 alters murine endocrine cell fate and protects functional beta cell mass in an STZ-induced model of diabetes
Authors: Bauer Brandon M. , Irimia Jose M. , Bloom-Saldana Elizabeth , Jeong Jae-Wook , Fueger Patrick T. 
Published: April 2023

ABSTRACTBackgroundMaintaining functional beta cell mass (BCM) to meet glycemic demands is essential to preventing or reversing the progression of diabetes. Yet the mechanisms that establish and regulate endocrine cell fate are incompletely understood. We sought to determine the impact of deletion of mitogen-inducible gene 6 (Mig6), a negative feedback inhibitor of epidermal growth factor receptor (EGFR) signaling, on mouse endocrine cell fate. The extent to which loss of Mig6 might protect against loss of functional BCM in a multiple very low dose (MVLD) STZ-induced model of diabetes was also determined.MethodsTen-week-old male mice with whole pancreas (Pdx1:Cre, PKO) and beta cell-specific (Ins1:Cre, BKO) knockout of Mig6 were used alongside control (CON) littermates. Mice were given MVLD STZ (35 mg/kg for five days) to damage beta cells and induce hyperglycemia. In vivo fasting blood glucose and glucose tolerance were used to assess beta cell function. Histological analyses of isolated pancreata were utilized to assess islet morphology and beta cell mass. We also identified histological markers of beta cell replication, dedifferentiation, and death. Isolated islets were used to reveal mRNA and protein markers of beta cell fate and function.ResultsPKO mice had significantly increased alpha cell mass with no detectable changes to beta or delta cells. The increase in alpha cells alone did not impact glucose tolerance, BCM, or beta cell function. Following STZ treatment, PKO mice had 18±8% higher BCM than CON littermates and improved glucose tolerance. Interestingly, beta cell-specific loss of Mig6 was insufficient for protection, and BKO mice had no discernable differences compared to CON mice. The increase in BCM in PKO mice was the result of decreased beta cell loss and increased beta cell replication. Finally, STZ-treated PKO mice had more Ins+/Gcg+ bi-hormonal cells compared to controls suggesting alpha to beta cell trans differentiation.ConclusionsMig6 exerted differential effects on alpha and beta cell fate. Pancreatic loss of Mig6 reduced beta cell loss and promoted beta cell growth following STZ. Thus, suppression of Mig6 may provide relief of diabetes.
A correlative study of the genomic underpinning of virulence traits and drug tolerance ofCandida auris
Authors: Yang Bo , Vaisvil Benjamin , Schmitt Daniel , Collins Joseph , Young Eric , Kapatral Vinayak , Rao Reeta 
Published: April 2023

AbstractCandida aurisis an opportunistic fungal pathogen with high mortality rates that presents a clear and present threat to public health. The risk ofC. aurisinfection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well-known. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns ofC. auriscarbon metabolism, drug resistance, and macrophage interaction. We chose to study twoC. aurisisolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we found that B11220 was missing a 12.8 kb gene cluster encoding proteins related to alternative sugar utilization, possibly L-rhamnose. We show that B11221, which has the cluster, more readily assimilates and utilizes D-galactose and L-rhamnose. B11221 also exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both strains grown on glucose or galactose showed that genes associated with translation were upregulated in B11221, and the putative L-rhamnose gene cluster was upregulated when grown on D-galactose. These findings reinforce the growing evidence of a link between metabolism and tolerance. Since immune system evasion depends heavily on the cell surface, we characterized cell wall composition and macrophage evasion for the two strains. We found that B11221 has far less β-1,3-glucan exposure, a key determinant of immune system evasion, and resists phagocytosis by macrophages compared to B11220. In a transcriptomic analysis of both strains co-cultured with macrophages we found that B11221 upregulates genes associated with early stages of growth and transcription factors that regulate transport. These key differences in growth and membrane composition could explain the resistance to phagocytosis and increased stress tolerance in general of B11221, and indicates another connection between metabolism and immune system evasion. Taken together, these data show that membrane composition, metabolism, and transport all correlate with colonization, drug resistance, and immune system evasion inC. auris.
Ticks (Acari: Ixodida) on synanthropic small and medium-sized mammals in areas of the northeastern United States infested with the Asian longhorned tick,Haemaphysalis longicornis
Authors: Ferreira Francisco C. , González Julia , Milholland Matthew T. , Tung Grayson A. , Fonseca Dina M. 
Published: April 2023

AbstractThe northeastern United States is a hot spot for tick-borne diseases. Adding to an already complex vector landscape, in 2017 large populations of the invasiveHaemaphysalis longicornis, the Asian longhorned tick, were detected in New Jersey (NJ) and later found to be widespread from Connecticut to Georgia. In its native range in northeastern Asia,H. longicornisis considered an important vector of deadly pathogens to humans, companion animals, and livestock. To identify the primary hosts ofH. longicorniswe surveyed synanthropic small and medium-sized mammals in three different sites in suburban New Brunswick, NJ. Specifically, we collected approximately 9,000 tick specimens belonging to nine species from 11 different species of mammals sampled between May and September 2021. We found thatH. longicornisfeeds more frequently on rodents than previously thought, and that this invasive tick is likely exposed to important enzootic and zoonotic pathogens. Overall, we obtained detailed information about the seasonal dynamics and feeding patterns of six tick species common in the northeastern US,Haemaphysalis longicornis,Amblyomma americanum, Dermacentor variabilis, Ixodes scapularis, I. texanusandI. cookei. We found that unlikeI. scapularisthat feeds on mammals of all sizes,H. longicornisfeeds on hosts following the general pattern ofA. americanum, favoring larger species such as skunks, groundhogs, and raccoons. However, our survey revealed that unlikeA. americanum,H. longicornisreaches high densities on Virginia opossum. Overall, the newly invasiveH. longicorniswas the most abundant tick species both on multiple host species and in the environment, raising significant questions regarding its role in the epidemiology of tick-borne pathogens, especially those affecting livestock, companion animals and wildlife. In conclusion, our findings provide valuable insights into the tick species composition on mammal hosts in New Jersey and the ongoing national expansion ofH. longicornis.
Δ246p53 is a new p53 isoform that responds to DNA damage and regulates tumour growth
Authors: Parkar Shrutee N. , López-Iniesta Maria José , Ramalho Ana Catarina , Kimura Koto , Zhao Jingyuan , da Silva Rita Filipa , Romão Luísa , Candeias Marco M 
Published: April 2023

ABSTRACTp53is with little doubt one of the most powerful genes in our genome, as it makes growthvsarrest, repairvsreplacement, metabolismvsanabolism, lifevsdeath decisions in the cell. One wrong action and a healthy cell is lost or transforms into cancer. So it is not surprising thatp53is also one of the most tightly regulated and complex genes.p53alone encodes for more than 10 RNA variants and 15 different protein forms. Here we identify yet another p53 protein isoform of around 18 KDa that we named Δ246p53. Δ246p53 is translated from an alternative translation initiation site (TIS) in codon 246. TIS-246 is preceded by a strong Kozak sequence and seems to be conserved in vertebrates, from sea lamprey to humans. Δ246p53’s origin and expression in cells were confirmed by frameshift and start codon mutations as well as siRNA and an antisense oligo targeting TIS-246, which knocked-down Δ246p53 with little or no effect on full-length (FL) p53 protein levels. Δ246p53 was induced by DNA damage in several cell lines tested and triggered senescence and impaired tumour formation/growth in colony formation assays. Lastly, we show that Δ246p53 binds to FLp53 and affects the transactivation ofp21, a known senescence activator. Our results add a new piece to the centre of the p53 puzzle, a previously unreported inside regulator of p53, which in the future may help us better understand p53’s still mystifying role in senescence and ageing.
DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins
Authors: Kong Shuyao , Zhu Mingyuan , Scarpin M. Regina , Pan David , Jia Longfei , Martinez Ryan E. , Alamos Simon , Vadde Batthula Vijaya Lakshmi , Garcia Hernan G. , Qian Shu-Bing , Brunkard Jacob O. , Roeder Adrienne H. K. 
Published: April 2023

SUMMARYRobustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutantdevelopment related myb-like1(drmy1), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show thatdrmy1has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.
Multiple rotavirus species encode fusion-associated small transmembrane (FAST) proteins with cell type-specific activity
Authors: Veletanlic Vanesa , Sartalamacchia Kylie , Diller Julia R. , Ogden Kristen M. 
Published: April 2023

ABSTRACTFusion-associated small transmembrane (FAST) proteins are viral nonstructural proteins that mediate cell-cell fusion to form multinucleated syncytia. We previously reported that human species B rotavirus NSP1-1 is a FAST protein that induces syncytia in primate epithelial cells but not rodent fibroblasts. We hypothesized that the NSP1-1 proteins of other rotavirus species could also mediate cell-cell fusion and that fusion activity might be limited to cell types derived from homologous hosts. To test this hypothesis, we predicted the structure and domain organization of NSP1-1 proteins of species B rotavirus from a human, goat, and pig, species G rotavirus from a pigeon and turkey, and species I rotavirus from a dog and cat. We cloned these sequences into plasmids and transiently expressed the NSP1-1 proteins in avian, canine, hamster, human, porcine, and simian cells. Regardless of host origin of the virus, each NSP1-1 protein induced syncytia in primate cells, while few induced syncytia in other cell types. To identify the domains that determined cell-specific fusion activity for human species B rotavirus NSP1-1, we engineered chimeric proteins containing domain exchanges with the p10 FAST protein from Nelson Bay orthoreovirus. Using the chimeric proteins, we found that the N-terminal and transmembrane domains determined the cell type specificity of fusion activity. Although the species and cell type criteria for fusion activity remain unclear, these findings suggest that rotavirus species B, G, and I NSP1-1 are functional FAST proteins whose N termini play a role in specifying the cells in which they mediate syncytia formation.IMPORTANCEMechanisms of membrane fusion and determinants of host range for pathogens remain poorly understood. Improved understanding of these concepts could open new areas for therapeutic development and shed light on virus epidemiology. Our analyses of NSP1-1 proteins from species B, G, and I rotaviruses provide insights into the diversity of domain features tolerated by functional FAST proteins. Further, the observation that all putative FAST proteins tested can induce syncytia formation in at least some cell types provides evidence that rotaviruses that encode NSP1-1 proteins are fusogenic viruses. Finally, although the criteria for their specificity remain unclear, our observations regarding fusion capacities of different NSP1-1 proteins and of chimeric FAST proteins suggest a potential role for rotavirus FAST proteins in determining the efficiency of viral replication within a given host or cell type.
Classifier for the Rapid Simultaneous Determination of Sleep-Wake States and Seizures in Mice
Authors: Harvey Brandon J. , Olah Viktor J. , Aiani Lauren M. , Rosenberg Lucie I. , Pedersen Nigel P. 
Published: April 2023

AbstractIndependent automated scoring of sleep-wake and seizures have recently been achieved; however, the combined scoring of both states has yet to be reported. Mouse models of epilepsy typically demonstrate an abnormal electroencephalographic (EEG) background with significant variability between mice, making combined scoring a more difficult classification problem for manual and automated scoring. Given the extensive EEG variability between epileptic mice, large group sizes are needed for most studies. As large datasets are unwieldy and impractical to score manually, automatic seizure and sleep-wake classification are warranted. To this end, we developed an accurate automated classifier of sleep-wake states, seizures, and the post-ictal state. Our benchmark was a classification accuracy at or above the 93% level of human inter-rater agreement. Given the failure of parametric scoring in the setting of altered baseline EEGs, we adopted a machine-learning approach. We created several multi-layer neural network architectures that were trained on human-scored training data from an extensive repository of continuous recordings of electrocorticogram (ECoG), left and right hippocampal local field potential (HPC-L and HPC-R), and electromyogram (EMG) in the murine intra-amygdala kainic acid model of medial temporal lobe epilepsy. We then compared different network models, finding a bidirectional long short-term memory (BiLSTM) design to show the best performance with validation and test portions of the dataset. The SWISC (sleep-wake and the ictal state classifier) achieved >93% scoring accuracy in all categories for epileptic and non-epileptic mice. Classification performance was principally dependent on hippocampal signals and performed well without EMG. Additionally, performance is within desirable limits for recording montages featuring only ECoG channels, expanding its potential scope. This accurate classifier will allow for rapid combined sleep-wake and seizure scoring in mouse models of epilepsy and other neurologic diseases with varying EEG abnormalities, thereby facilitating rigorous experiments with larger numbers of mice.