bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous, Topologically Guided Protein Crystallization Controls Bacterial Surface Layer Self-Assembly
Authors: Comerci Colin J. , Herrmann Jonathan , Yoon Joshua , Jabbarpour Fatemeh , Zhou Xiaofeng , Nomellini John F. , Smit John , Shapiro Lucy , Wakatsuki Soichi , Moerner W.E. 
Published: February 2019

AbstractBacteria assemble the cell envelope using localized enzymes to account for growth and division of a topologically complicated surface1–3. However, a regulatory pathway has not been identified for assembly and maintenance of the surface layer (S-layer), a 2D crystalline protein coat surrounding the curved 3D surface of a variety of bacteria4,5. By specifically labeling, imaging, and tracking native and purified RsaA, the S-layer protein (SLP) fromC. crescentus, we show that protein self-assembly alone is sufficient to assemble and maintain the S-layerin vivo. By monitoring the location of newly produced S-layer on the surface of living bacteria, we find that S-layer assembly occurs independently of the site of RsaA secretion and that localized production of new cell wall surface area alone is insufficient to explain S-layer assembly patterns. When the cell surface is devoid of a pre-existing S-layer, the location of S-layer assembly depends on the nucleation characteristics of SLP crystals, which grow by capturing RsaA molecules freely diffusing on the outer bacterial surface. Based on these observations, we propose a model of S-layer assembly whereby RsaA monomers are secreted randomly and diffuse on the lipopolysaccharide (LPS) outer membrane until incorporated into growing 2D S-layer crystals. The complicated topology of the cell surface enables formation of defects, gaps, and grain boundaries within the S-layer lattice, thereby guiding the location of S-layer assembly without enzymatic assistance. This unsupervised mechanism poses unique challenges and advantages for designing treatments targeting cell surface structures or utilizing S-layers as self-assembling macromolecular nanomaterials. As an evolutionary driver, 2D protein self-assembly rationalizes the exceptional S-layer subunit sequence and species diversity6.
Lead optimisation of dehydroemetine for repositioned use in malaria
Authors: Panwar Priyanka , Burusco Kepa K. , Abubaker Muna , Matthews Holly , Gutnov Andrey , Fernández-Álvaro Elena , Bryce Richard A. , Wilkinson James , Nirmalan Niroshini 
Published: February 2019

AbstractDrug repositioning offers an effective alternative tode novodrug design to tackle the urgent need for novel anti-malarial treatments. The anti-amoebic compound, emetine dihydrochloride, has been identified as a potentin-vitroinhibitor of the multi-drug resistant strain K1 ofPlasmodium falciparum(IC50: 47 nM + 2.1 nM). 2,3-dehydroemetine, a synthetic analogue of emetine dihydrochloride has been claimed to have less cardiotoxic effects than emetine. The structures of two diastereoisomers of 2,3-dehydroemetine were modelled on the reported emetine binding site on cryo-EM structure 3J7A and it was found that(-)-R,S-dehydroemetine mimicked the bound pose of emetine more closely than(-)-S,S-dehydroisoemetine.(-)-R,S-dehydroemetine was also found to be highly potent against the multi-drug resistant K1 strain ofP. falciparumin comparison with(-)-S,S-dehydroisoemetine, which loses its potency due to the change of configuration at C-1’. In addition to its effect on the asexual erythrocytic stages ofP. falciparum, the compounds exhibited gametocidal properties with no cross-resistance against any of the multi-drug resistant strains tested. Drug interaction studies showed(-)-R,S-dehydroemetine to have synergistic antimalarial activity with atovaquone and proguanil. Emetine dihydrochloride, and(-)-R,S-dehydroemetine failed to show any inhibition of the hERG potassium channel and displayed atovoquone-like activity on the mitochondrial membrane potential.
MAGMA: inference of sparse microbial association networks
Authors: Cougoul Arnaud , Bailly Xavier , Wit Ernst C. 
Published: February 2019

AbstractMicroorganisms often live in symbiotic relationship with their environment and they play a central role in many biological processes. They form a complex system of interacting species. Within the gut micro-biota these interaction patterns have been shown to be involved in obesity, diabetes and mental disease. Understanding the mechanisms that govern this ecosystem is therefore an important scientific challenge. Recently, the acquisition of large samples of microbiota data through metabarcoding or metagenomics has become easier.Until now correlation-based network analysis and graphical modelling have been used to identify the putative interaction networks formed by the species of microorganisms, but these methods do not take into account all features of microbiota data. Indeed, correlation-based network cannot distinguish between direct and indirect correlations and simple graphical models cannot include covariates as environmental factors that shape the microbiota abundance. Furthermore, the compositional nature of the microbiota data is often ignored or existing normalizations are often based on log-transformations, which is somewhat arbitrary and therefore affects the results in unknown ways.We have developed a novel method, called MAGMA, for detecting interactions between microbiota that takes into account the noisy structure of the microbiota data, involving an excess of zero counts, overdispersion, compositionality and possible covariate inclusion. The method is based on Copula Gaus-sian graphical models whereby we model the marginals with zero-inflated negative binomial generalized linear models. The inference is based on an efficient median imputation procedure combined with the graphical lasso.We show that our method beats all existing methods in recovering microbial association networks in an extensive simulation study. Moreover, the analysis of two 16S microbial data studies with our method reveals interesting new biology.MAGMA is implemented as an R-package and is freely available at https://gitlab.com/arcgl/rmagma, which also includes the scripts used to prepare the material in this paper.
MAUI-seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction
Authors: Fields Bryden , Moeskjær Sara , Friman Ville-Petri , Andersen Stig U. , Young J. Peter W. 
Published: February 2019

AbstractBackgroundSequencing and PCR errors are a major challenge when characterising genetic diversity using high-throughput amplicon sequencing (HTAS).ResultsWe have developed a multiplexed HTAS method, MAUI-seq, which uses unique molecular identifiers (UMIs) to improve error correction by exploiting variation among sequences associated with a single UMI. We show that two main advantages of this approach are efficient elimination of chimeric and other erroneous reads, outperforming DADA2 and UNOISE3, and the ability to confidently recognise genuine alleles that are present at low abundance or resemble chimeras.ConclusionsThe method provides sensitive and flexible profiling of diversity and is readily adaptable to most HTAS applications, including microbial 16S rRNA profiling and metabarcoding of environmental DNA.
Identification of genes with enriched expression in early developing mouse cone photoreceptors
Authors: Buenaventura Diego F. , Corseri Adrianne , Emerson Mark M. 
Published: February 2019

ABSTRACTCone photoreceptors are the critical first cells that mediate high acuity vision. Despite their importance and their potential use in cell-based therapies for retinal diseases, there is a lack of knowledge about the early developmental stages of these cells. Here we characterize the expression of the homeobox transcription factor Lhx4 as an early and enriched cone photoreceptor expressed gene in both chicken and mouse. A Lhx4 GFP reporter mouse was found to recapitulate this early cone photoreceptor expression and was used to purify and profile embryonic mouse cone photoreceptors by single cell RNA sequencing. This enrichment in cone photoreceptors allowed for the robust identification of genes associated with the early cone transcriptome and also identified subpopulations of these cells. A comparison to previously reported datasets allowed the classification of genes according to developmental timing, cell type specificity, and whether they were regulated by the rod transcription factor Nrl. This analysis has extended the set of known early cone enriched genes and identified those that are regulated independently of Nrl. This report furthers our knowledge of the transcriptional events that occur in early cone photoreceptors.
DNA Nanostructures Coordinate Gene Silencing in Mature Plants
Authors: Zhang Huan , Demirer Gozde S. , Zhang Honglu , Ye Tianzheng , Goh Natalie S. , Aditham Abhishek J. , Cunningham Francis J. , Fan Chunhai , Landry Markita P. 
Published: February 2019

AbstractPlant bioengineering may generate high yielding and stress-resistant crops amidst a changing climate and a growing global population (1–3). However, delivery of biomolecules to plants relies onAgrobacteriuminfection (4) or biolistic particle delivery (5), the former of which is only amenable to DNA delivery. The difficulty in delivering functional biomolecules such as RNA to plant cells is due to the plant cell wall which is absent in mammalian cells and poses the dominant physical barrier to exogenous biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells, however, nanoparticle-mediated delivery remains unexplored for passive biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver small interfering RNAs (siRNAs), and effectively silence a constitutively-expressed gene inNicotiana benthamianaleaves. We show that nanostructure internalization into plant cells and the corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies, but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures, and details both the design parameters of importance for plant cell internalization, and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.
Single cell profiling of CRISPR/Cas9-induced OTX2 deficient retinas reveals fate switch from restricted progenitors
Authors: Ghinia Tegla Miruna G. , Buenaventura Diego F. , Kim Diana Y. , Thakurdin Cassandra , Gonzalez Kevin C. , Emerson Mark M. 
Published: February 2019

AbstractDevelopment of the vertebrate eye, like many developmental systems, depends on genes that are used iteratively in multiple distinct processes. The OTX2 transcription factor is one such gene, with a requirement for eye formation, photoreceptor formation, and retinal pigment epithelium specification, among others. Recent evidence has suggested that OTX2 is also expressed in subsets of retinal progenitor cells with restricted fate choices. However, given the multiple roles for OTX2 and limitations of conventional conditional knockout strategies, the functional significance of this expression is unknown. Here we use CRISPR/Cas9 gene editing to produce mutations of OTX2, identifying similar phenotypes to those observed in human patients. In addition, we use single cell RNA sequencing to determine the functional consequences of OTX2 gene editing by CRISPR/Cas9 on the population of cells derived from OTX2-expressing retinal progenitor cells. We not only confirm that OTX2 is required for the generation of photoreceptors, but also for maintaining the proliferative potential of cells and suppressing the formation of specific retinal fates. These include subtypes of retinal ganglion and horizontal cells normally associated with these progenitor types, suggesting that in this context OTX2 functions to repress sister cell fate choices. Upregulation of key transcription factors involved in the formation of these cells was observed suggesting that OTX2 is upstream of critical nodes of gene regulatory networks of these alternative fates.
SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets
Authors: Portik Daniel M. , Wiens John J. 
Published: February 2019

AbstractPhylogenies with extensive taxon sampling have become indispensable for many types of ecological and evolutionary studies. Many large-scale trees are based on a “supermatrix” approach, which involves amalgamating thousands of published sequences for a group. Constructing up-to-date supermatrices can be challenging, especially as new sequences may become available almost constantly. Additionally, genomic datasets (composed of thousands of loci) are becoming common in phylogenetics and phylogeography, and present novel challenges for constructing such datasets.Here we present SuperCRUNCH, a Python toolkit for assembling large phylogenetic datasets. It can be applied to GenBank sequences, unpublished sequences, or combinations of GenBank and unpublished data. SuperCRUNCH constructs local databases and uses them to conduct rapid searches for user-specified sets of taxa and loci. Sequences are parsed into putative loci and passed through rigorous filtering steps. A post-filtering step allows for selection of one sequence per taxon (i.e. species-level supermatrix) or retention of all sequences per taxon (i.e. population-level dataset). Importantly, SuperCRUNCH can generate “vouchered” population-level datasets, in which voucher information is used to generate multi-locus phylogeographic datasets. SuperCRUNCH offers many options for taxonomy resolution, similarity filtering, sequence selection, alignment, and file manipulation.We demonstrate the range of features available in SuperCRUNCH by generating a variety of phylogenetic datasets. Output datasets include traditional species-level supermatrices, large-scale phylogenomic matrices, and phylogeographic datasets. Finally, we briefly compare the ability of SuperCRUNCH to construct species-level supermatrices to alternative approaches. SuperCRUNCH generated a large-scale supermatrix (1,400 taxa and 66 loci) from 16GB of GenBank data in ∼1.5 hours, and generated population-level datasets (<350 samples, <10 loci) in <1 minute. It outperformed alternative methods for supermatrix construction in terms of taxa, loci, and sequences recovered.SuperCRUNCH is a modular bioinformatics toolkit that can be used to assemble datasets for any taxonomic group and scale (kingdoms to individuals). It allows rapid construction of supermatrices, greatly simplifying the process of updating large phylogenies with new data. It is also designed to produce population-level datasets. SuperCRUNCH streamlines the major tasks required to process phylogenetic data, including filtering, alignment, trimming, and formatting. SuperCRUNCH is open-source, documented, and available at https://github.com/dportik/SuperCRUNCH.
Quantitative analysis of the ThrbCRM1-centered gene regulatory network
Authors: Souferi Benjamin , Emerson Mark M. 
Published: February 2019

AbstractEnhancer activity is determined by both the activity and occupancy of transcription factors as well as the specific sequences they bind. Experimental investigation of this dynamic requires the ability to manipulate components of the system, ideally in as close to an in vivo context as possible. Here we use electroporation of plasmid reporters to define critical parameters of a specific cis-regulatory element, ThrbCRM1, during retinal development. ThrbCRM1 is associated with cone photoreceptor genesis and activated in a subset of developing retinal cells that co-express the Otx2 and Onecut1 (OC1) transcription factors. Variation of reporter plasmid concentration was used to generate dose response curves and revealed an effect of binding site availability on the number and strength of cells with reporter activity. Critical sequence elements of the ThrbCRM1 element were defined using both mutagenesis and misexpression of the Otx2 and OC1 transcription factors in the developing retina. Additionally, these experiments suggest that the ThrbCRM1 element is co-regulated by Otx2 and OC1 even under conditions of sub-optimal binding of OC1.Summary StatementSystematic variation of the levels of a transcriptional reporter plasmid, its trans-acting factors, and transcription factor binding sites reveals properties of a retinal enhancer during development.
OsCYP71D8L as a key regulator involved in growth and stress response by mediating gibberellins and cytokinins homeostasis in rice
Authors: Zhou Jiahao , Li Zeyu , Xiao Guiqing , Huang Rongfeng , Zhang Haiwen 
Published: February 2019

AbstractPhytohormones are pivotal in the regulation of plant growth and development, and acclimation to adverse environments. Multiple cytochrome P450 monooxygenases (CYP450s) are involved in the biosynthesis and catabolism of phytohormones. Here, we reported that a CYP450 member of CYP71 clan, OsCYP71D8L, participated in the control of multiple agronomic traits and abiotic stress responses by affecting gibberellin (GA) and cytokinin (CK) homeostasis in rice. We found that its gain-of-function mutant (cyp71d8l) and transgenic plants overexpressing OsCYP71D8L (OsCYP71D8L-OE) displayed similar phenotypes such as dwarfed plant, reduced panicle length and grain number per panicle. In OsCYP71D8L-OE seedlings, endogenous GAs and CKs was notably decreased and increased as compared with wild type (WT), respectively. Correspondingly, the dwarfed plant and less developed root of cyp71d8l and OsCYP71D8L-OE seedlings could be rescued by exogenous GA3, but more exacerbated by exogenous 6-BA. Importantly, cyp71d8l and OsCYP71D8L-OE seedlings maintained high chlorophyll contents and low reactive oxygen species level, and showed significantly enhanced tolerances to drought and high salt compared with WT. Thus, our results suggest that OsCYP71D8L plays roles in regulating rice growth and stress responses by coordinating GAs and CKs homeostasis, and it is useful to engineer stress-tolerant rice.
C. eleganssynMuv B proteins regulate spatial and temporal chromatin compaction during development
Authors: Costello Meghan E. , Petrella Lisa N. 
Published: February 2019

AbstractTissue-specific establishment of repressive chromatin through creation of compact chromatin domains during development is necessary to ensure proper gene expression and cell fate.C. eleganssynMuv B proteins are important for the soma/germline fate decision and mutants demonstrate ectopic germline gene expression in somatic tissue, especially at high temperature. We show thatC. eleganssynMuv B proteins regulate developmental chromatin compaction and that timing of chromatin compaction is temperature sensitive in both wild-type and synMuv B mutants. Chromatin compaction in mutants is delayed into developmental time-periods when zygotic gene expression is upregulated and demonstrates an anterior-to-posterior pattern. Loss of this patterned compaction coincides with the developmental time-period of ectopic germline gene expression that leads to a developmental arrest in synMuv B mutants. Thus, chromatin organization throughout development is regulated both spatially and temporally by synMuv B proteins to establish repressive chromatin in a tissue-specific manner to ensure proper gene expression.
Unveiling the transcriptome complexity of the High- and Low- Zinc & Iron accumulating Indian wheat (Triticum aestivum L.) cultivars
Authors: Mishra Vinod Kumar , Gupta Saurabh , Chand Ramesh , Yadav Punam Singh , Singh Satish Kumar , Joshi Arun Kumar , Varadwaj Pritish Kumar 
Published: February 2019

AbstractDevelopment of Zinc (Zn), Iron (Fe) and other minerals rich grains along with various stress tolerance and susceptible (STR) wheat genotype, will help to reduce globally spread malnutrition problem. Current study deals with transcriptome profiling of 4 high- and 3 low- Zn & Fe accumulating wheat genotypes (HZFWGs) and (LZFWGs). Functional characterization of expressed and high and low specific genes, accompanied by metabolic pathways analysis reveals, phenylpropanoid biosynthesis, and other associated pathways are mainly participating in plant stress defense mechanism in both genotypes. Chlorophyll synthesis, Zn & Fe binding, metal ion transport, and ATP-Synthase coupled transport mechanism are highly active in HZFWGs while in LZFWGs ribosomal formation, biomolecules binding activities and secondary metabolite biosynthesis. Transcripts accountable for minerals uptake and purine metabolism in HZFWGs are highly enriched. Identified transcripts may be used for marker-assisted selection and breeding to develop minerals rich crops.
SHIV.CH505-infected infant and adult rhesus macaques exhibit similar HIV Env-specific antibody kinetics, despite distinct T-follicular helper (Tfh) and germinal center B cell landscapes
Authors: Nelson Ashley N. , Goswami Ria , Dennis Maria , Tu Joshua , Mangan Riley J. , Saha Pooja T. , Cain Derek W. , Shen Xiaoying , Shaw George M. , Bar Katharine , Hudgens Michael , Pollara Justin , Paris Kristina De , Van Rompay Koen K.A. , Permar Sallie R. 
Published: February 2019

AbstractPediatric HIV infection remains a large global health concern despite the widespread use of antiretroviral therapy (ART). Thus, global elimination of pediatric HIV infections will require the development of novel immune-based approaches, and understanding infant immunity to HIV is critical to guide the rational design of these intervention strategies. Despite their immunological immaturity, HIV-infected children develop broadly neutralizing antibodies (bnAbs) more frequently and earlier than adults do. Furthermore, T-follicular helper (Tfh) cells have been associated with bnAb development in HIV-infected children and adults. To further our understanding of age-related differences in the development of HIV-specific immunity, we evaluated the generation of virus-specific humoral immune responses in infant (n=6) and adult (n=12) rhesus macaques (RMs) infected with a transmitted/founder (T/F) simian-human immunodeficiency virus (SHIV.C.CH505). The plasma HIV envelope-specific IgG antibody kinetics were similar in SHIV-infected infant and adult RMs, with no significant differences in the magnitude or breadth of these responses. Interestingly, autologous tier 2 virus neutralization responses also developed with similar frequency and kinetics in infant and adult RMs, despite infants exhibiting significantly higher Tfh and germinal center B cell frequencies compared to adults. Our results indicate that the humoral immune response to SHIV infection develops with similar kinetics among infant and adult RMs, suggesting that the early life immune system is equipped to respond to HIV-1 and promote the production of neutralizing HIV antibodies.ImportanceThere is a lack of understanding on how the maturation of the infant immune system influences immunity to HIV infection, or how these responses differ from those of adults. Improving our knowledge of infant HIV immunity will help guide antiviral intervention strategies that take advantage of the unique infant immune environment to successfully elicit protective immune responses. We utilized a rhesus macaque model of SHIV infection as a tool to distinguish the differences in HIV humoral immunity in infants versus adults. Here, we demonstrate that the kinetics and quality of the infant humoral immune response to HIV are highly comparable to that of adults during the early phase of infection, despite distinct differences in their Tfh responses, indicating that slightly different mechanisms may drive infant and adult humoral immunity.