bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Evolution of Podocyte Slit-diaphragm Proteins
Authors: Mulukala NSK , Kambhampati V , Qadri SAH , Pasupulati AK 
Published: November 2020

AbstractVertebrates kidneys contribute to the homeostasis by regulating electrolyte, acid-base balance, and prevent protein loss into the urine. Glomerular podocytes constitute blood-urine barrier and podocyte slit-diaphragm, a modified tight junction contributes to the glomerular permselectivity. Nephrin, podocin, CD2AP, and TRPC6 are considered to be crucial members, which largely interact with each other and contribute to the structural and functional integrity of the slit-diaphragm. In this study, we analyzed the distribution of these four-key slit-diaphragm proteins across the organisms for which the genome sequence is available. We found that nephrin has a diverse distribution ranging from nematodes to higher vertebrates whereas podocin, CD2AP, and TRPC6 are predominantly restricted to the vertebrates. In the invertebrates nephrin and its orthologs consist of more immunoglobulin-3 and immunoglobulin-5 domains when compared to the vertebrates wherein, CD80-like C2-set Ig2 domains were predominant. Src Homology-3 (SH3) domain of CD2AP and SPFH domain of podocin are highly conserved among vertebrates. Although the majority of the TRPC6 and its orthologs had conserved ankyrin repeats, TRP, and ion transport domains, the orthologs of TRPC6 present inRhincodon typusandAcanthaster plancido not possess the ankyrin repeats. Intrinsically unstructured regions (IURs), which are considered to contribute to the interactions among these proteins are largely conserved among orthologs of these proteins, suggesting the importance of IURs in the protein complexes that constitute slit-diaphragm. This study for the first time reports the evolutionary insights of vertebrate slit-diaphragm proteins and its invertebrate orthologs.
A region-based method for causal mediation analysis of DNA methylation data
Authors: Yan Qi , Forno Erick , Celedón Juan C. , Chen Wei 
Published: November 2020

ABSTRACTExposure to environmental factors can affect DNA methylation at a CpG site or a genomic region, which can then affect an outcome. In other words, environmental effects on an outcome could be mediated by DNA methylation. To date, single CpG site-based mediation analysis has been employed extensively. More recently, however, there has been considerable interest on studying differentially methylated regions (DMRs), both because DMRs are more likely to have functional effects than single CpG sites and because testing DMRs reduces multiple testing. In this report, we propose a novel causal mediation approach under the counterfactual framework to test the significance of total, direct and indirect effects of predictors on response variable with a methylated region (MR) as the mediator (denoted as MR-Mediation). Functional linear transformation is used to reduce the possible high dimension of the CpG sites in a predefined methylated region and to account for their location information. In our simulation studies, MR-Mediation retained the desired Type I error rates for total, direct and indirect effect tests, for both continuous and binary outcomes. Furthermore, MR-Mediation had better power performance than testing mean methylation level as the mediator in most considered scenarios, especially for indirect effect (i.e., mediated effect) test, which could be more interesting than the other two effect tests. We further illustrate our proposed method by analyzing the methylation mediated effect of exposure to gun violence on total immunoglobulin E (IgE) or atopic asthma among participants in the Epigenetic Variation and Childhood Asthma in Puerto Ricans (EVA-PR) study.
Lymphocyte-Specific Biomarkers Associated with Preterm Birth and Bronchopulmonary Dysplasia
Authors: Bhattacharya Soumyaroop , Mereness Jared A. , Baran Andrea M. , Misra Ravi S. , Peterson Derick R. , Ryan Rita M. , Reynolds Anne Marie , Pryhuber Gloria S. , Mariani Thomas J. 
Published: November 2020

AbstractMany premature babies who are born with neonatal respiratory distress syndrome (RDS) go on to develop Bronchopulmonary Dysplasia (BPD) and later Post-Prematurity Respiratory Disease (PRD) at one year corrected age, characterized by persistent or recurrent lower respiratory tract symptoms frequently related to inflammation and viral infection. Transcriptomic profiles were generated from sorted peripheral blood CD8+ T cells of preterm and full-term infants enrolled with consent in the NHLBI Prematurity and Respiratory Outcomes Program (PROP) at the University of Rochester and the University at Buffalo. We identified outcome-related gene expression patterns following standard methods to identify markers for oxygen utilization and BPD as outcomes in extremely premature infants. We further identified predictor gene sets for BPD based on transcriptomic data adjusted for gestational age at birth (GAB).RNA-Seq analysis was completed for CD8+ T cells from 145 subjects. Among the subjects with highest risk for BPD (born at <29 weeks gestational age (GA); n=72), 501 genes were associated with oxygen utilization. In the same set of subjects, 571 genes were differentially expressed in subjects with a diagnosis of BPD and 105 genes were different in BPD subjects as defined by physiologic challenge. A set of 92 genes could predict BPD with a moderately high degree of accuracy. We consistently observed dysregulation of NRF2, HIPPO and CD40-associated pathways in BPD. Using gene expression data from both premature and full-term subjects (n=116), we identified a 28 gene set that predicted the PRD status with a moderately high level of accuracy.Transcriptomic data from sort-purified peripheral blood CD8+ T cells from 145 preterm and full-term infants identified sets of molecular markers associated with independent development of BPD in extremely premature infants at high risk for the disease and of PRD among the preterm and full-term subjects.
Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals
Authors: Mahajan Swapnil , Kode Vasumathi , Bhojak Keshav , Magdalene Coral M. , Lee Kayla , Manoharan Malini , Ramesh Athulya , Sudheendra HV , Srivastava Ankita , Sathian Rekha , Khan Tahira , Kumar Prasanna , Chakraborty Papia , Chaudhuri Amitabha 
Published: November 2020

ABSTRACTThe COVID-19 pandemic has revealed a range of disease phenotypes in infected patients with asymptomatic, mild or severe clinical outcomes, but the mechanisms that determine such variable outcomes remain unresolved. In this study, we identified immunodominant CD8 T-cell epitopes in the RBD and the non-RBD domain of the spike antigen using a novel TCR-binding algorithm. A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. The T-cell reactivity to the predicted epitopes was higher than the Spike-S1 and S2 peptide pools containing 157 and 158 peptides both in unexposed donors and in convalescent patients suggesting that strong T-cell epitopes are likely to be missed when larger peptide pools are used in assays. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. This finding is in contrast to multiple published studies in which pre-existing T-cell immunity is suggested to arise from shared epitopes between SARS-CoV-2 and other common cold-causing coronaviruses. Whether the presence of pre-existing T-cell immunity provides protection against COVID-19 or contributes to severe disease phenotype remains to be determined in a larger cohort. However, our findings raise the expectation that a significant majority of the global population is likely to have SARS-CoV-2 reactive T-cells because of prior exposure to flu and CMV viruses, in addition to common cold-causing coronaviruses.
Molecular physiology of pumiliotoxin sequestration in a poison frog
Authors: Alvarez-Buylla Aurora , Payne Cheyenne Y. , Vidoudez Charles , Trauger Sunia A. , O’Connell Lauren A. 
Published: November 2020

ABSTRACTPoison frogs bioaccumulate alkaloids for chemical defense from their arthropod diet. Although many alkaloids are accumulated without modification, some poison frog species can metabolize pumiliotoxin (PTX251D) into the more potent allopumiliotoxin (aPTX267A). Despite extensive research characterizing the chemical arsenal of poison frogs, the physiological mechanisms involved in the sequestration and metabolism of individual alkaloids remain unclear. We first performed a feeding experiment with the Dyeing poison frog (Dendrobates tinctorius) to ask if this species can metabolize PTX251Dinto aPTX267Aand what gene expression changes are associated with PTX251Dexposure in the intestines, liver, and skin. We found thatD. tinctoriuscan metabolize PTX251Dinto aPTX267A, and that PTX251Dexposure changed the expression level of genes involved in immune system function and small molecule metabolism and transport. To better understand the functional significance of these changes in gene expression, we then conducted a series of high-throughput screens to determine the molecular targets of PTX251Dand identify potential proteins responsible for metabolism of PTX251Dinto aPTX267A. Although screens of PTX251Dbinding human voltage-gated ion channels and G-protein coupled receptors were inconclusive, we identified human CYP2D6 as a rapid metabolizer of PTX251Din a cytochrome P450 screen. Furthermore, a CYP2D6-like gene had increased expression in the intestines of animals fed PTX, suggesting this protein may be involved in PTX metabolism. These results show that individual alkaloids can modify gene expression across tissues, including genes involved in alkaloid metabolism. More broadly, this work suggests that specific alkaloid classes in wild diets may induce physiological changes for targeted accumulation and metabolism.
Comparing the diversity and relative abundance of free and particle-associated aquatic viruses
Authors: Palermo Christine N. , Shea Dylan W. , Short Steven M. 
Published: November 2020

ABSTRACTMetagenomics has enabled rapid increases in virus discovery, in turn permitting revisions of viral taxonomy and our understanding of the ecology of viruses and their hosts. Inspired by recent discoveries of large viruses prevalent in the environment, we re-assessed the longstanding approach of filtering water through small pore-size filters to separate viruses from cells before sequencing. We studied assembled contigs derived from < 0.45 μm and > 0.45 μm size fractions that were annotated as viral to determine the diversity and relative abundances of virus groups from each fraction. Virus communities were vastly different when comparing the size fractions, indicating that analysis of either fraction alone would provide only a partial perspective of environmental viruses. At the level of virus order/family we observed highly diverse and distinct virus communities in the > 0.45 μm size fractions, whereas the < 0.45 μm size fractions were comprised primarily of highly diverse Caudovirales. The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions with higher relative abundances of cyanophages in the > 0.45 μm size fractions potentially indicating replication within cells during ongoing infections. Many of theMimiviridaeandPhycodnaviridae, and allIridoviridaeandPoxviridaewere detected exclusively in the often disregarded > 0.45 μm size fractions. In addition to observing unique virus communities associated with each size fraction, we detected viruses common to both fractions and argue that these are candidates for further exploration because they may be the product of ongoing or recent lytic events.IMPORTANCEMost studies of aquatic virus communities analyze DNA sequences derived from the smaller, “free virus” size fraction. Our study demonstrates that analysis of virus communities using only the smaller size fraction can lead to erroneously low diversity estimates for many of the larger viruses such asMimiviridae, Phycodnaviridae, Iridoviridae, andPoxviridae, whereas analyzing only the larger, > 0.45 μm size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data shows that examining only the smaller size fraction can lead to underestimation of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.
NUTRITIONAL IMMUNITY, ZINC SUFFICIENCY AND COVID-19 MORTALITY IN SOCIALLY SIMILAR EUROPEAN POPULATIONS
Authors: Singh Samer , Diwaker Amita , Singh Brijesh P. , Singh Rakesh K. 
Published: November 2020

ABSTRACTThe impact of Zinc (Zn) sufficiency/supplementation on COVID-19 associated mortality and incidence (SARS-CoV-2 infections) remains unknown. During an infection, the levels of free Zn are reduced as part of ‘nutritional immunity’ to limit the growth and replication of pathogen and the ensuing inflammatory damage. Considering its key role in immune competency and frequently recorded deficiency in large sections of different populations, Zn has been prescribed for both prophylactic and therapeutic purposes in COVID-19 without any corroborating evidence for its protective role. Multiple trials are underway evaluating the effect of Zn supplementation on COVID-19 outcome in patients getting standard of care treatment. However, the trial designs presumably lack the power to identify negative effects of Zn supplementation, especially in the vulnerable groups of elderly and patients with comorbidities (contributing 9 out of 10 deaths; up to >8000-fold higher mortality). In this study, we have analyzed COVID-19 mortality and incidence (case) data from 23 socially similar European populations with comparable confounders (population: 522.47 million; experiencing up to >150 fold difference in death rates) and at the matching stage of the pandemic (12 March - 26 June 2020; 1st wave of COVID-19 incidence and mortality). Our results suggest a positive correlation between populations’ Zn-sufficiency status and COVID-19 mortality (r(23): 0.7893–0.6849, p-value<0.0003) as well as incidence [r(23):0.8084 to 0.5658; p-value<0.005]. The observed association is contrary to what would be expected if Zn sufficiency was protective in COVID-19. Thus, controlled trials or retrospective analyses of the adverse event patients’ data should be undertaken to correctly guide the practice of Zn supplementation in COVID-19.
Rad51 paralog complex Rad55–Rad57 acts as a molecular chaperone during homologous recombination
Authors: Roy Upasana , Kwon Youngho , Marie Lea , Symington Lorraine , Sung Patrick , Lisby Michael , Greene Eric C. 
Published: November 2020

SummaryHomologous recombination (HR) is essential for the maintenance of genome integrity. Rad51 paralogs fulfill a conserved, but undefined role in HR, and their mutations are associated with increased cancer risk in humans. Here, we use single–molecule imaging to reveal that theSaccharomyces cerevisiaeRad51 paralog complex Rad55–Rad57 promotes the assembly of Rad51 recombinase filaments through transient interactions, providing evidence that it acts as a classical molecular chaperone. Srs2 is an ATP–dependent anti–recombinase that downregulates HR by actively dismantling Rad51 filaments. Contrary to the current model, we find that Rad55– Rad57 does not physically block the movement of Srs2. Instead, Rad55–Rad57 promotes rapid re– assembly of Rad51 filaments after their disruption by Srs2. Our findings support a model in which Rad51 is in flux between free and ssDNA–bound states, the rate of which is dynamically controlled though the opposing actions of Rad55–Rad57 and Srs2.
Epigenomic reprogramming of repetitive noncoding RNAs and IFN-stimulated genes by mutant KRAS
Authors: Reggiardo Roman E. , Maroli Sreelakshmi Velandi , Halasz Haley , Ozen Mehmet , Carrillo David , LaMontagne Erin , Whitehead Lila , Kim Eejung , Malik Shivani , Fernandes Jason , Marinov Georgi , Collisson Eric , Demirci Utkan , Kim Daniel H. 
Published: November 2020

ABSTRACTRAS genes are the most frequently mutated oncogenes in cancer. However, the effects of oncogenic RAS signaling on the noncoding transcriptome are unclear. We analyzed the transcriptomes of human airway epithelial cells transformed with mutant KRAS to define the landscape of KRAS-regulated noncoding RNAs. We found that oncogenic KRAS upregulates noncoding transcripts throughout the genome, many of which arise from transposable elements. These repetitive noncoding RNAs exhibit differential RNA editing in single cells, are released in extracellular vesicles, and are known targets of KRAB zinc-finger proteins, which are broadly down-regulated in mutant KRAS cells and lung adenocarcinomas. Moreover, mutant KRAS induces IFN-stimulated genes through both epigenetic and RNA-based mechanisms. Our results reveal that mutant KRAS remodels the noncoding transcriptome through epigenomic reprogramming, expanding the scope of genomic elements regulated by this fundamental signaling pathway and revealing how mutant KRAS induces an intrinsic IFN-stimulated gene signature often seen in ADAR-dependent cancers.
Olfactory rod cells: a rare cell type in the larval zebrafish olfactory epithelium with an actin-rich apical projection
Authors: Cheung King Yee , Jesuthasan Suresh J. , Baxendale Sarah , van Hateren Nicholas J. , Marzo Mar , Hill Christopher J. , Whitfield Tanya T. 
Published: November 2020

AbstractWe report the presence of a rare cell type, the olfactory rod cell, in the developing zebrafish olfactory epithelium. These cells each bear a single actin-rich rod-like apical projection extending about 10 μm from the epithelial surface. Live imaging with a ubiquitous Lifeact-RFP label indicates that the rods can oscillate. Olfactory rods arise within a few hours of the olfactory pit opening, increase in numbers and size during larval stages, and can develop in the absence of olfactory cilia. Olfactory rod cells differ in morphology from the known classes of olfactory sensory neuron, but express reporters driven by neuronal promoters. The cells also differ from secondary sensory cells such as hair cells of the inner ear or lateral line, or sensory cells in the taste bud, as they are not associated with established synaptic terminals. A sub-population of olfactory rod cells expresses a Lifeact-mRFPruby transgene driven by thesox10promoter. Mosaic expression of this transgene reveals that olfactory rod cells have rounded cell bodies located apically in the olfactory epithelium.
Csf1rbmutation uncouples two waves of microglia development in zebrafish
Authors: Ferrero Giuliano , Miserocchi Magali , Ruggiero Elodie Di , Wittamer Valérie 
Published: November 2020

ABSTRACTIn vertebrates, the ontogeny of microglia, the resident macrophages of the central nervous system, initiates early during development from primitive macrophages. While murine embryonic microglia then persist through life, in zebrafish these cells are transient, as they are fully replaced by an adult population originating from larval hematopoietic stem cell (HSC)-derived progenitors.Colony-stimulating factor receptor 1 (csf1r)is a fundamental regulator of microglia ontogeny in vertebrates, including zebrafish which possess two paralogous genes:csf1raandcsf1rb.While previous work showed invalidation of both genes completely abrogates microglia development, the specific contribution of each paralog remains largely unknown. Here, using a fate-mapping strategy to discriminate between the two microglial waves, we uncover non-overlapping roles forcsf1raandcsf1rbin hematopoiesis, and identifiedcsf1rbas an essential regulator of adult microglia development. Notably, we demonstrate thatcsf1rbpositively regulates HSC-derived myelopoiesis, resulting in macrophage deficiency, including microglia, in adult mutant animals. Overall, this study contributes to new insights into evolutionary aspects of Csf1r signaling and provides an unprecedented framework for the functional dissection of embryonic versus adult microgliain vivo.
The epithelial-mesenchymal transcription factorSNAI1represses transcription of the tumor suppressor miRNAlet-7in cancer
Authors: Wang H , Chirshev E , Hojo N , Suzuki T , Bertucci A , Pierce M , Perry C , Wang R , Zink J , Glackin CA , Ioffe YJ , Unternaehrer JJ 
Published: November 2020

AbstractWe aimed to determine the mechanism of epithelial-mesenchymal transition (EMT)-induced stemness in cancer cells. Cancer relapse and metastasis are caused by rare stem-like cells within tumors. Studies of stem cell reprogramming have linkedlet-7repression and acquisition of stemness with the EMT factor,SNAI1. The mechanisms for the loss oflet-7in cancer cells are incompletely understood. In four carcinoma cell lines from breast cancer, pancreatic cancer and ovarian cancer and in ovarian cancer patient-derived cells, we analyzed stem cell phenotype and tumor growth via mRNA, miRNA, and protein expression, spheroid formation, and growth in patient-derived xenografts. We show that treatment with EMT-promoting growth factors orSNAI1overexpression increased stemness and reducedlet-7expression, whileSNAI1knockdown reduced stemness and restoredlet-7expression. Rescue experiments demonstrate that the pro-stemness effects ofSNAI1are mediated vialet-7. In vivo, nanoparticle-delivered siRNA successfully knocked downSNAI1in orthotopic patient-derived xenografts, accompanied by reduced stemness and increasedlet-7expression, and reduced tumor burden. Chromatin immunoprecipitation demonstrated thatSNAI1binds the promoters of variouslet-7family members, and luciferase assays revealed thatSNAI1represseslet-7transcription. In conclusion, theSNAI1/let-7axis is an important component of stemness pathways in cancer cells, and this study provides a rationale for future work examining this axis as a potential target for cancer stem cell-specific therapies.Novelty and ImpactThis study provides new insight into molecular mechanisms by which EMT transcription factorSNAI1exerts its pro-stemness effects in cancer cells, demonstrating its potential as a stem cell-directed target for therapy.In vitroandin vivo, mesoporous silica nanoparticle-mediatedSNAI1knockdown resulted in restoration of let-7 miRNA, inhibiting stemness and reducing tumor burden. Our studies validatein vivonanoparticle-delivered RNAi targeting theSNAI1/let-7axis as a clinically relevant approach.