bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Fkh1 Forkhead Associated Domain Promotes ORC Binding to a Subset of DNA Replication Origins in Budding Yeast
Authors: Hoggard Timothy , Hollatz Allison J. , Cherney Rachel , Fox Catherine A. 
Published: March 2021

AbstractThe pioneer event in eukaryotic DNA replication is binding of chromosomal DNA by the origin recognition complex (ORC), which directs the formation of origins, the specific chromosomal regions where DNA will be unwound for the initiation of DNA synthesis. In all eukaryotes, incompletely understood features of chromatin promote ORC-DNA binding. Here, we uncover a role for the Fkh1 (forkhead homolog) protein, and, in particular, its forkhead associated (FHA) domain in promoting ORC-origin binding and origin activity at a subset of origins inSaccharomyces cerevisiae.The majority of the FHA-dependent origins within the experimental subset examined contain a distinct Fkh1 binding site located 5’ of and proximal to their ORC sites (5’-FKH-T site). Epistasis experiments using selected FHA-dependent origins provided evidence that the FHA domain promoted origin activity through Fkh1 binding directly to this 5’ FKH-T site. Nucleotide substitutions within two of these origins that enhanced the affinity of their ORC sites for ORC bypassed these origins’ requirement for their 5’ FKH-T sites and for the FHA domain. Significantly, direct assessment of ORC-origin binding by ChIPSeq provided evidence that this mechanism affected ~25% of yeast origins. Thus, this study reveals a new mechanism to enhance ORC-origin binding in budding yeast that requires the FHA domain of the conserved cell-cycle transcription factor Fkh1.
Taxon-specific phytoplankton growth, nutrient utilization, and light limitation in the oligotrophic Gulf of Mexico
Authors: Yingling Natalia , Kelly Thomas B. , Shropshire Taylor A. , Landry Michael R. , Selph Karen E. , Knapp Angela N. , Kranz Sven A. , Stukel Michael R. 
Published: March 2021

ABSTRACTThe highly stratified, oligotrophic regions of the oceans are predominantly nitrogen limited in the surface ocean and light limited at the deep chlorophyll maximum (DCM). Hence, determining light and nitrogen co-limitation patterns for diverse phytoplankton taxa is crucial to understanding marine primary production throughout the euphotic zone. During two cruises in the deep-water Gulf of Mexico, we measured primary productivity (H13CO3−), nitrate uptake (15NO3−), and ammonium uptake (15NH4+) throughout the water column. Primary productivity declined with depth from the mixed-layer to the DCM, averaging 27.1 mmol C m−2d−1. The fraction of growth supported by NO3−was consistently low, with upper euphotic zone values ranging from 0.01 to 0.14 and lower euphotic zone values ranging from 0.03 to 0.44. Nitrate uptake showed strong diel patterns (maximum during the day), while ammonium uptake exhibited no diel variability. To parameterize taxon-specific phytoplankton nutrient and light utilization, we used a data assimilation approach (Bayesian Markov Chain Monte Carlo) including primary productivity, nutrient uptake, and taxon-specific growth rate measurements. Parameters derived from this analysis define distinct niches for five phytoplankton taxa (Prochlorococcus, Synechococcus, diatoms, dinoflagellates, and prymnesiophytes) and may be useful for constraining biogeochemical models of oligotrophic open-ocean systems.
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell
Authors: Puray-Chavez Maritza , LaPak Kyle M. , Schrank Travis P. , Elliott Jennifer L. , Bhatt Dhaval P. , Agajanian Megan J. , Jasuja Ria , Lawson Dana Q. , Davis Keanu , Rothlauf Paul W. , Jo Heejoon , Lee Nakyung , Tenneti Kasyap , Eschbach Jenna E. , Mugisha Christian Shema , Vuong Hung R. , Bailey Adam L. , Hayes D. Neil , Whelan Sean P.J. , Horani Amjad , Brody Steven L. , Goldfarb Dennis , Major M. Ben , Kutluay Sebla B. 
Published: March 2021

ABSTRACTEstablishedin vitromodels for SARS-CoV-2 infection are limited and include cell lines of non-human origin and those engineered to overexpress ACE2, the cognate host cell receptor. We identified human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of ACE2. Infection of H522 cells required the SARS-CoV-2 spike protein, though in contrast to ACE2-dependent models, spike alone was not sufficient for H522 infection. Temporally resolved transcriptomic and proteomic profiling revealed alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type-I interferon signaling. Focused chemical screens point to important roles for clathrin-mediated endocytosis and endosomal cathepsins in SARS-CoV-2 infection of H522 cells. These findings imply the utilization of an alternative SARS-CoV-2 host cell receptor which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.
Expression levels of long noncoding natural antisense transcripts overlapping theUGT73C6gene affect rosette size ofArabidopsis thaliana
Authors: Meena Shiv Kumar , Heidecker Michel , Engelmann Susanne , Jaber Ammar , de Vries Tebbe , Baumann-Kaschig Katja , Abel Steffen , Behrens Sven-Erik , Gago-Zachert Selma 
Published: March 2021

SummaryNatural antisense long noncoding RNAs (lncNATs) are involved in the regulation of gene expression in plants, modulating different relevant developmental processes and responses to various stimuli. We identified and characterized two lncNATs (NAT1UGT73C6andNAT2UGT73C6, collectivelyNATsUGT73C6) inArabidopsis thalianathat are transcribed from a gene overlappingUGT73C6, a member of theUGT73Csubfamily of genes encoding UDP-glycosyltransferases (UGTs). Expression of bothNATsUGT73C6is developmentally controlled and occurs independently of the transcription ofUGT73C6incis. Downregulation ofNATsUGT73C6levels through artificial microRNAs results in a reduction of the rosette area, while constitutive overexpression ofNAT1UGT73C6orNAT2UGT73C6leads to the opposite phenotype, an increase in rosette size. This activity ofNATsUGT73C6relies on its RNA sequence, and, although modulation ofUGT73C6inciscannot be excluded, the observed phenotypes are not a consequence of the regulation ofUGT73C6intrans. TheNATsUGT73C6levels were shown to affect cell proliferation and thus individual leaf size. Consistent with this concept, our data suggest that theNATsUGT73C6modulate the expression levels of key transcription factors involved in regulating leaf growth by modulating cell proliferation. These findings thus reveal an additional regulatory layer on the process of leaf growth.
Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases
Authors: de Klein Niek , Tsai Ellen A. , Vochteloo Martijn , Baird Denis , Huang Yunfeng , Chen Chia-Yen , van Dam Sipko , Deelen Patrick , Bakker Olivier B. , Garwany Omar El , Ouyang Zhengyu , Marshall Eric E. , Zavodszky Maria I. , van Rheenen Wouter , Bakker Mark K. , Veldink Jan , Gaunt Tom R. , Runz Heiko , Franke Lude , Westra Harm-Jan 
Published: March 2021

AbstractGaining insight into the downstream consequences of non-coding variants is an essential step towards the identification of therapeutic targets from genome-wide association study (GWAS) findings. Here we have harmonized and integrated 8,727 RNA-seq samples with accompanying genotype data from multiple brain-regions from 14 datasets. This sample size enabled us to perform bothcis- andtrans-expression quantitative locus (eQTL) mapping. Upon comparing the brain cortexcis-eQTLs (for 12,307 unique genes at FDR<0.05) with a large bloodcis-eQTL analysis (n=31,684 samples), we observed that brain eQTLs are more tissue specific than previously assumed.We inferred the brain cell type for 1,515cis-eQTLs by using cell type proportion information. We conducted Mendelian Randomization on 31 brain-related traits usingcis-eQTLs as instruments and found 159 significant findings that also passed colocalization. Furthermore, two multiple sclerosis (MS) findings had cell type specific signals, a neuron-specificcis-eQTL forCYP24A1and a macrophage specificcis-eQTL forCLECL1.To further interpret GWAS hits, we performedtrans-eQTL analysis. We identified 2,589trans-eQTLs (at FDR<0.05) for 373 unique SNPs, affecting 1,263 unique genes, and 21 replicated significantly using single-nucleus RNA-seq data from excitatory neurons.We also generated a brain-specific gene-coregulation network that we used to predict which genes have brain-specific functions, and to perform a novel network analysis of Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS) and Parkinson’s disease (PD) GWAS data. This resulted in the identification of distinct sets of genes that show significantly enriched co-regulation with genes inside the associated GWAS loci, and which might reflect drivers of these diseases.
Top-down control of hippocampal signal-to-noise by prefrontal long-range inhibition
Authors: Malik Ruchi , Li Yi , Schamiloglu Selin , Sohal Vikaas S. 
Published: March 2021

SummaryThe prefrontal cortex (PFC) is postulated to exert ‘top-down control’ by modulating information processing throughout the brain to promote specific actions based on current goals. However, the pathways mediating top-down control remain poorly understood. In particular, knowledge about direct prefrontal connections that might facilitate top-down prefrontal control of information processing in the hippocampus remains sparse. Here we describe novel monosynaptic long-range GABAergic projections from PFC to hippocampus. These preferentially inhibit vasoactive intestinal polypeptide expressing interneurons, which are known to disinhibit hippocampal microcircuits. Indeed, stimulating prefrontal–hippocampal GABAergic projections increases hippocampal feedforward inhibition and reduces hippocampal activityin vivo. The net effect of these actions is to specifically enhance the signal-to-noise ratio for hippocampal representations of objects. Correspondingly, stimulation of PFC-to-hippocampus GABAergic projections promotes object exploration. Together, these results elucidate a novel top-down pathway in which long-range GABAergic projections target disinhibitory microcircuits, thereby enhancing signals and network dynamics underlying exploratory behavior.
The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasionin vivo
Authors: Smith Jayson J. , Xiao Yutong , Parsan Nithin , Medwig-Kinney Taylor N. , Martinez Michael A. Q. , Moore Frances E. Q. , Palmisano Nicholas J. , Kohrman Abraham Q. , Reyes Mana Chandhok Delos , Adikes Rebecca C. , Liu Simeiyun , Bracht Sydney A. , Zhang Wan , Wen Kailong , Kratsios Paschalis , Matus David Q. 
Published: March 2021

SUMMARYChromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as histone subunits, and chromatin regulating factors (CRFs) are associated with a variety of disease mechanisms including cancer metastasis, in which cancer co-opts cellular invasion programs functioning in healthy cells during development. Here we utilizeCaenorhabditis elegansanchor cell (AC) invasion as anin vivomodel to identify the suite of chromatin agents and CRFs that promote cellular invasiveness. We demonstrate that the SWI/SNF ATP-dependent chromatin remodeling complex is a critical regulator of AC invasion, with pleiotropic effects on both G0cell cycle arrest and activation of invasive machinery. Using targeted protein degradation and enhanced RNA interference (RNAi) vectors, we show that SWI/SNF contributes to AC invasion in a dose-dependent fashion, with lower levels of activity in the AC corresponding to aberrant cell cycle entry and increased loss of invasion. Our data specifically implicate the SWI/SNF BAF assembly in the regulation of the G0cell cycle arrest in the AC, whereas the SWI/SNF PBAF assembly promotes AC invasion via cell cycle-independent mechanisms, including attachment to the basement membrane (BM) and activation of the pro-invasivefos-1/FOS gene. Together these findings demonstrate that the SWI/SNF complex is necessary for two essential components of AC invasion: arresting cell cycle progression and remodeling the BM. The work here provides valuable single-cell mechanistic insight into how the SWI/SNF assemblies differentially contribute to cellular invasion and how SWI/SNF subunit-specific disruptions may contribute to tumorigeneses and cancer metastasis.SUMMARY STATEMENTCellular invasion through the basement membrane by theC. elegansanchor cell requires both BAF and PBAF SWI/SNF assemblies to arrest the cell cycle and promote the expression of pro-invasive genes.
Scaling of subcellular structures with cell length through decelerated growth
Authors: McInally Shane G. , Kondev Jane , Goode Bruce L. 
Published: March 2021

AbstractHow cells tune the size of their subcellular parts to scale with cell size is a fundamental question in cell biology. Until now, most studies on the size control of organelles and other subcellular structures have focused on scaling relationships with cell volume, which can be explained by limiting pool mechanisms. Here, we uncover a distinct scaling relationship with cell length rather than volume, revealed by mathematical modeling and quantitative imaging of yeast actin cables. The extension rate of cables decelerates as they approach the rear of the cell, until cable length matches cell length. Further, the deceleration rate scales with cell length. These observations reveal a new mode of scaling that senses the linear dimensions of a cell.One Sentence SummaryAs actin cables in yeast cells grow longer, their extension rate decelerates, enabling the cable length to match cell length.
EHF is essential for epidermal and colonic epithelial homeostasis and suppressesApc-initiated colonic tumorigenesis
Authors: Reehorst Camilla M. , Nightingale Rebecca , Luk Ian Y. , Jenkins Laura , Koentgen Frank , Williams David S. , Darido Charbel , Tan Fiona , Anderton Holly , Chopin Michael , Schoffer Kael , Eissmann Moritz F. , Buchert Michael , Mouradov Dmitri , Sieber Oliver M , Ernst Matthias , Dhillon Amardeep S. , Mariadason John M. 
Published: March 2021

AbstractBackgroundEts homologous factor (EHF) is a member of the epithelial-specific Ets (ESE) transcription factors. EHF is specifically expressed in epithelial tissues, however its role in development and epithelial homeostasis is largely uncharacterized.MethodsWe generated a novel mouse strain in which the Ets DNA binding domain (exon 8) of Ehf was flanked by loxP sites (EhfLox/Lox). To inactivate Ehf in the whole body,EhfLox/Loxmice were crossed toCMVCremice, which were then bred out to generate germlineEhfnull (Ehf−/−) mice. To inactivate Ehf specifically in the intestinal epithelium,EhfLox/Loxmice were bred to tamoxifen-inducibleVillinCre-ERT2mice.EhfLox/Loxmice were also crossed to tamoxifen-inducibleCdx2CreERT2;ApcLox/+mice to determine the impact of Ehf deletion on Apc-initiated colon cancer development.ResultsTranscripts encoding the Ets binding domain of EHF were effectively deleted in all tissues inEhf−/−mice.Ehf−/−mice were born at the expected Mendelian ratio, but showed reduced body weight gain and developed a series of pathologies during their lifespan that led the majority ofEhf−/−mice to reach an ethical endpoint within one year of age. Most prominent of these were the development of papillomas in the chin, and abscesses in the preputial glands (males) or vulvae (females) which showed evidence of Staphylococcus and Proteus infection. Consistent with the development of papillomas, the epidermis ofEhf−/−mice showed evidence of mild hyperplasia. A subset ofEhf−/−mice also developed cataracts and corneal ulcers. EHF is highly expressed in the colonic epithelium andEhf−/−mice displayed increased susceptibility to dextran sodium sulphate-induced colitis. This phenotype was confirmed in intestinal-specific Ehf knockout mice, and histopathological analyses revealed reduced numbers of goblet cells and extensive transcriptional reprogramming in the colonic epithelium. Finally, colon-specific deletion ofEhfenhancedApc-initiated adenoma development, unveiling a novel, tumour suppressive role for EHF in colorectal cancer.ConclusionThe Ets DNA-binding domain of EHF is essential for post-natal homeostasis of the epidermis and colonic epithelium, and functions as a tumour suppressor in the colon.
A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis
Authors: Song Fangchao , Kuehl Jennifer V. , Chandran Arjun , Arkin Adam P. 
Published: March 2021

ABSTRACTBacterial communities in water, soil, and humans play an essential role in environmental ecology and human health. PCR-based amplicon analysis, such as 16S ribosomal RNA sequencing, is a fundamental tool for quantifying and studying microbial composition, dynamics, and interactions. However, given the complexity of microbial communities, a substantial number of samples becomes necessary to analyses that parse the factors that determine microbial composition. A common bottleneck in performing these kinds of experiments is genomic DNA (gDNA) extraction, which is time-consuming, expensive, and often biased on the types of species. Direct PCR methods are a potentially simpler and more accurate alternative to gDNA extraction methods that do not require the intervening purification step. In this study, we evaluated three variations of direct PCR methods using diverse heterogeneous bacterial cultures, ZymoBIOMICS Microbial Community Standards, and groundwater. By comparing direct PCR methods with DNeasy blood and tissue kits and DNeasy Powersoil kits, we found a specific variant of the direct PCR method exhibits a comparable overall efficiency to the conventional DNeasy Powersoil protocol. We also found the method showed higher efficiency for extracting gDNA from the gram negative strains compared to DNeasy blood and tissue protocol. This direct PCR method is 1600 times cheaper ($0.34 for 96 samples), 10 times simpler (15 min hands-on time for 96 samples) than DNeasy Powersoil protocol. The direct PCR method can also be fully automated, and is compatible with small volume samples, thereby permitting scaling of samples and replicates needed to support high-throughput large-scale bacterial community analysis.IMPORTANCEUnderstanding bacterial interaction and assembling in complex microbial communities using 16S ribosomal RNA sequencing normally requires a large experimental load. However, the current DNA extraction methods including cell disruption and genomic DNA purification are normally biased, costly, time and labor consuming, and not amenable to miniaturization by droplets or 1536 well plates due to the significant DNA loss during purification step for tiny volume and low cell density samples. Direct PCR method could potentially solve these problems. In this study, we demonstrate a direct PCR method which exhibits similar efficiency as the widely used method – DNeasy Powersoil protocol, while 1600 times cheaper and 10 times faster to execute. This simple, cost-effective, and automation friendly direct PCR based 16S ribosomal RNA sequencing method allows us to study the dynamics, microbial interaction and assembly of varying microbial communities in a high throughput fashion.
Feline leukemia virus (FeLV) endogenous and exogenous recombination events result in multiple FeLV-B subtypes during natural infection
Authors: Erbeck Katelyn , Gagne Roderick B. , Kraberger Simona , Chiu Elliott S. , Roelke Parker Melody , VandeWoude Sue 
Published: March 2021

AbstractFeline leukemia virus (FeLV) is associated with a range of clinical signs in felid species. The primary hosts of FeLV are domestic cats of the Felis genus that also harbor endogenous FeLV (enFeLV) elements stably integrated in their genomes. EnFeLV elements display 86% nucleotide identity to exogenous, horizontally transmitted FeLV (FeLV-A). Variation between enFeLV and FeLV-A is primarily in the long terminal repeat (LTR) and env regions, which potentiates generation of FeLV-B recombinant subtypes during natural infection with enhanced virulence. The aim of this study was to examine exogenous FeLV (exFeLV) and enFeLV recombination events in a natural FeLV epizootic. We previously described that of 32 individuals in a closed colony with productive FeLV-A infection, 22 had detectable circulating FeLV-B. We cloned and sequenced the env gene of FeLV-B, FeLV-A, and enFeLV spanning known recombination breakpoints, examining between 1-13 clones per individual to assess sequence diversity and recombination sites. We documented multiple recombination breakpoints resulting in the production of unique FeLV-B genotypes. At least half of the cats harbored more than one FeLV-B variant, and almost all animals had variants similar to those recovered from at least one other individual in the colony. This analysis reveals that FeLV-B is predominantly generated de novo within each host, though horizontal transmission may be inferred based upon FeLV-B sequence identities between individuals. This work represents a comprehensive analysis of endogenous-exogenous retroviral interactions with important insights into host-viral interactions that underlie disease pathogenesis in a natural setting.ImportanceFeline leukemia virus (FeLV) is a felid retrovirus associated with a variety of disease outcomes. Exogenous FeLV-A is the most common horizontally transmitted virus subgroup. Domestic cats (Felis catus) harbor endogenous copies of FeLV (enFeLV) in their genomes. Recombination between FeLV-A and enFeLV may result in emergence of largely replication-defective, but highly virulent recombinant strains. FeLV-B, the most common recombinant form, results when enFeLV env recombines with FeLV-A during FeLV replication. This study evaluated endogenous-exogenous recombination outcomes in a naturally-infected closed colony of domestic cats to determine recombination sites and FeLV-B genotypic heterogeneity associated with enhanced disease virulence. While FeLV-A and enFeLV genotypes were highly conserved, a large number of unique FeLV-B variants were identified in association with predicted recombination hotspots. The findings provide insight into recombination events between viral and host genomes that result in new, and potentially more pathogenic, viral strains.
ZFP207controls pluripotency by multiple post-transcriptional mechanisms
Authors: Malla Sandhya , Bhattarai Devi Prasad , Melguizo-Sanchis Dario , Atanasoai Ionut , Groza Paula , Román Ángel-Carlos , Zhu Dandan , Lee Dung-Fang , Kutter Claudia , Aguilo Francesca 
Published: March 2021

AbstractThe pluripotent state is not solely governed by the action of the core transcription factors Oct4, Sox2, and Nanog, but also by a series of co-transcriptional and post-transcriptional events, including alternative splicing (AS) and the interaction of RNA-binding proteins (RBPs) with defined subpopulations of RNAs. Zinc Finger Protein 207 (ZFP207) is an essential transcription factor for mammalian embryonic development. Here, we employ multiple functional analyses to characterize the role of ZFP207 in mouse embryonic stem cells (ESCs). We find that ZFP207 plays a pivotal role in ESC maintenance, and silencing ofZfp207leads to severe neuroectodermal differentiation defects. In striking contrast to human ESCs, ZFP207 does not transcriptionally regulate stem cell and neuronal-related genes but exerts its effects by control AS networks and acting as an RBP. Our study expands the role of ZFP207 to maintain ESC identity, and underscores ZFP207 functional versatility with key roles in neural fate commitment.