bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical learning of distractor co-occurrences facilitates visual search
Authors: Thorat Sushrut , Quek Genevieve , Peelen Marius V. 
Published: May 2022

AbstractVisual search is facilitated by knowledge of the relationship between the target and the distractors, including both where the target is likely to be amongst the distractors and how it differs from the distractors. Whether the statistical structure amongst distractors themselves, unrelated to target properties, facilitates search is less well understood. Here, we assessed the benefit of distractor structure using novel shapes whose relationship to each other was learned implicitly during visual search. Participants searched for target items in arrays of shapes that comprised either four pairs of co-occurring distractor shapes (structured scenes) or eight distractor shapes randomly partitioned into four pairs on each trial (unstructured scenes). Across five online experiments (N=1140), we found that after a period of search training, participants were more efficient when searching for targets in structured than unstructured scenes. This structure-benefit emerged independently of whether the position of the shapes within each pair was fixed or variable, and despite participants having no explicit knowledge of the structured pairs they had seen. These results show that implicitly learned co-occurrence statistics between distractor shapes increases search efficiency. Increased efficiency in the rejection of regularly co-occurring distractors may contribute to the efficiency of visual search in natural scenes, where such regularities are abundant.
Spatiotemporal Profiling of Seed-Associated Microbes of an Aquatic, Intermediate Recalcitrant Species,Zizania palustrisL. and the Impact of Anti-Microbial Seed Treatments
Authors: Gietzel Clare , McGilp Lillian , Kimball Jennifer A. 
Published: May 2022

AbstractNorthern wild rice (NWR;Zizania palustrisvar.interior) (NWR) is an ecologically important, annual, aquatic species native to North America, that is also cultivated in irrigated paddies in Minnesota and California. NWR seeds are desiccation-sensitive and must be kept in hydrated conditions, in which viability can decline rapidly within the first two years of storage. During this period, microbial growth is rampant and the relationship between these communities and the viability of NWR seed is unclear. In this study, we cultured and identified bacteria and fungi found in 27 NWR seed stocks, collected over a five-year period from three locations and four NWR genotypes. Results revealed that microbial communities were heavily dependent on seed viability and communities began shifting after one year of seed storage. Fungi became more prominent as years in storage increased suggesting that fungi begin to outcompete bacteria. Spatial analysis of locations and genotypes revealed a core set of microbes found across locations and genotypes.PenicilliumandPseudomonaswere ubiquitous in NWR hydrated seed storage. We also evaluated the efficacy of four antimicrobial treatments at reducing microbial growth in hydrated NWR seed storage. These treatments did not reduce or drastically change microbial growth or seed viability. However, previously undetected microbes were identified after treatments, which suggested a disruption to the major constituents of the microbiome. Overall, this study identified common microbial constituents found in an aquatic, recalcitrant species, adapted for a cold climate, during seed storage and provides a foundation for future studies to evaluate the effect of microbial communities on NWR seed viability during hydrated storage.
Importance of Mobile Genetic Element Immunity in Numerically AbundantTrichodesmiumClades
Authors: Webb Eric A. , Held Noelle A. , Zhao Yiming , Graham Elaina , Conover Asa E. , Semones Jake , Lee Michael D. , Feng Yuanyuan , Fu Feixue , Saito Mak A. , Hutchins David A. 
Published: May 2022

AbstractThe colony-forming cyanobacteriaTrichodesmiumspp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient, open ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe the genetic potential of the genus via significantly improved genomic assemblies of strainsTrichodesmium thiebautiiH94,Trichodesmium erythraeum2175, and 17 newTrichodesmiummetagenome-assembled genomes (MAGs, >50% complete) from hand-picked,Trichodesmiumcolonies spanning the Atlantic Ocean. Phylogenomics identified ∼four N2fixing clades ofTrichodesmiumacross the transect, withT. thiebautiidominating the colony-specific reads. Pangenomic analyses showed that allT. thiebautiiMAGs are enriched in defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas hereafter). Surprisingly, this CRISPR-Cas system was absent in allT. erythraeumgenomes and MAGs, vertically inherited byT. thiebautii, and correlated with increased signatures of horizontal gene transfer. Multiple lines of evidence indicate that the CRISPR-Cas system is functional in situ: 1.TrichodesmiumCRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified, 2. HighTrichodesmiumspacer sequence variability indicating rapid adaptation, and 3. metaproteomic and transcriptomic expression analyses detecting the CRISPR-Cas system components inTrichodesmiumcolonies from the Atlantic and Pacific Oceans. These data suggest that phage or mobile genetic element immunity inT. thiebautiicould contribute to their success, gene diversity, and numerical dominance overT. erythraeumin the oceans, thus warranting furtherTrichodesmiumvirome investigations.Significance statementOur work identifies CRISPR-Cas immunity as a phylogenetically distinct, environmentally expressed factor in the speciation of closely related N2-fixingTrichodesmiumclades. These findings suggest that differential phage predation and resistance could be a previously overlooked selective pressure in the genus, potentially leading to the current numerical dominance ofT. thiebautiioverT. erythraeumin the oceans. Furthermore, while the currently CO2-limitedT. erythraeumis expected to be a ‘winner’ of anthropogenic climate change, their predicted higher phage sensitivity thanT. thiebautiicould challenge this outcome.
Histone H2A serine-1 phosphorylation is a chaperone dependent signal for dimerization with H2B and for enhanced deposition
Authors: Onikubo Takashi , Wang Wei-Lin , Shechter David 
Published: May 2022

ABSTRACTMultiple histone chaperones and histone modifications are involved in the folding, transport, and re-lease of histones onto newly replicated DNA. Little is known about histone H2A-H2B pre-deposition his-tone modifications and their regulation of histone deposition. We previously showed that H2A serine 1 phosphorylation (H2AS1ph) is enriched on the soluble egg histones and on zygotic chromatin in Xenopus embryos. Here, we demonstrate that H2AS1 phosphorylation is required for a timely incorporation of H2A-H2B into the pronuclear chromatin. Our analysis revealed that exogenous H2AS1A-H2B dimers were poorly incorporated into pronuclei in egg extract compared with wildtype and H2AS1E-H2B dimers. Chaperone-mediated deposition using histones purified from pronuclei showed that neither Nap1 nor Nucleoplasmin (Npm2) histone deposition was directly affected by endogenous histone posttranslational modification. We further demonstrate that H2AS1 phosphorylation was dependent on Npm2 and required H2B. Surprisingly, Nap1 was incapable of promoting H2AS1 phosphorylation. These results suggest that serine 1 phosphorylation signals a specific state of H2A-H2B dimer bound by Nucleoplasmin. Neither Npm2 nor Nap1 exhibited preference for binding H2AS1A or H2AS1E mutant histones or dimers with H2B in vitro. We propose that H2AS1 phosphorylation is a pre-deposition modification that signals for the proper dimerization of H2A-H2B, which in turn activates downstream effectors leading to H2A-H2B deposition.
Vegetation formation in Staphylococcus aureus endocarditis inversely correlates with RNAIII and sarA expression in invasive clonal complex 5 (CC5) isolates
Authors: Kinney Kyle J. , Stach Jessica M. , Kulhankova Katarina , Brown Matthew , Salgado-Pabón Wilmara 
Published: May 2022

AbstractInfective endocarditis (IE) is one of the most feared and lethal diseases caused by Staphylococcus aureus. Once established, the infection is fast-progressing and tissue destructive. S. aureus of the clonal complex 5 (CC5) commonly cause IE yet are severely understudied. IE results from bacterial colonization and formation of tissue biofilms (known as vegetations) on injured or inflamed cardiac endothelium. S. aureus IE is promoted by adhesins, coagulases, and superantigens, with the exotoxins and exoenzymes likely contributing to tissue destruction and dissemination. Expression of the large repertoire of virulence factors required for IE and sequelae is controlled by complex regulatory networks. We investigated the temporal expression of the global regulators agr (RNAIII), rot, sarS, sarA, sigB, and mgrA in 8 invasive CC5 isolates and established intrinsic expression patterns associated with IE outcomes. We show that vegetation formation, as tested in the rabbit model of IE, inversely correlates with RNAIII and sarA expression during growth in Todd-Hewitt broth (TH). Large vegetations with severe sequelae arise from strains with high-level expression of colonization factors but slower transition towards expression of the exotoxins. Overall, strains proficient in vegetation formation, a hallmark of IE, exhibit lower expression of RNAIII and sarA. Simultaneous high expression of RNAIII, sarA, sigB, and mgrA is the one phenotype assessed in this study that fails to promote IE. Thus, RNAIII and sarA expression that provides for rheostat control of colonization and virulence genes, rather than an on and off switch, promote both vegetation formation and lethal sepsis.
A Coxiella burnetii effector interacts with the host PAF1 complex and suppresses the innate immune response
Authors: Fischer Natasha Lopes , Boyer Mark A. , Bradley William P. , Spruce Lynn A. , Fazelinia Hossein , Shin Sunny 
Published: May 2022

AbstractIntracellular bacteria such as the pathogen Coxiella burnetii inject effector proteins into the host cell that promote productive infection. One common strategy of pathogen effectors is to suppress host immune responses to enable pathogen replication. The C. burnetii type IV secretion system translocates a large number of effectors into host cells that collectively promote intracellular bacterial replication, but the individual functions of most of these effectors are poorly understood. In this study, we describe a C. burnetii effector, CBU1314, that localizes to the nucleus and inhibits NF-κB-, MAPK-, and type I IFN-dependent gene expression. Mechanistically, we find that CBU1314 interacts with the PAF1 complex (PAF1C), a central host transcriptional complex that regulates expression of inflammatory genes in innate immune cells. Notably, we find that PAF1 promotes immune gene expression in response to various immune agonists and C. burnetii infection. Moreover, we find that PAF1 is critical for restricting intracellular C. burnetii replication. Overall, our findings uncover PAF1C as a host target of a C. burnetii effector and reveal new insight into how intracellular bacterial pathogens subvert cell- intrinsic innate defenses.SignificanceIntracellular bacteria often employ secreted effector proteins to modulate cellular processes and survive intracellularly. The study of these effectors can provide valuable insight into microbial pathogenesis and host biology. Here, we describe a Coxiella burnetii effector that inhibits multiple host signaling pathways and modulates the innate immune response. This effector interacts with the host PAF1 complex (PAF1C), a central regulator of transcription. Furthermore, we show that PAF1 is necessary for maximal gene expression downstream of various innate immune receptors and restricts bacterial replication during infection. Overall, our study elucidates the function of a C. burnetii effector in evading the immune response and provides insight into the role of PAF1C in cell-intrinsic defense against bacterial pathogens.
Is single nucleus ATAC-seq accessibility a qualitative or quantitative measurement?
Authors: Miao Zhen , Kim Junhyong 
Published: May 2022

AbstractSingle nucleus ATAC-seq is a key assay for gene regulation analysis. Existing approaches to scoring feature matrices from sequencing reads are inconsistent with each other, creating differences in downstream analysis, and displaying artifacts. We show that even with sparse single cell data, quantitative counts are informative for estimating a cell’s regulatory state, which calls for consistent treatment. We propose Paired-Insertion-Counting (PIC) as a uniform method for snATAC-seq feature characterization.
Intrinsic furin-mediated cleavability of the spike S1/S2 site from SARS-CoV-2 variant B.1.1.529 (Omicron)
Authors: Lubinski Bailey , Jaimes Javier A. , Whittaker Gary R. 
Published: May 2022

AbstractThe ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. SARS-CoV-2 The variant B.1.1.529 (Omicron) emerged in late 2020 and has continued to evolve and is now present in several distinct sub-variants. Here, we analyzed the “furin cleavage site” of the spike protein of SARS-CoV-2 B.1.1.529 (Omicron variant) in vitro, to assess the role of two key mutations (spike, N679K and P681H) that are common across all subvariants compared to the ancestral B.1 virus and other notable lineages. We observed significantly increased intrinsic cleavability with furin compared to an original B lineage virus (Wuhan-Hu1), as well as to two variants, B.1.1.7 (Alpha) and B.1.617 (Delta) that subsequently had wide circulation. Increased furin-mediated cleavage was attributed to the N679K mutation, which lies outside the conventional furin binding pocket. Our findings suggest that B.1.1.529 (Omicron variant) has gained genetic features linked to intrinsic furin cleavability, in line with its evolution within the population as the COVID-19 pandemic has proceeded.
A remarkable expansion of oligopeptide transporter genes in rust fungi (Pucciniales) suggests a specialization in nutrients acquisition for obligate biotrophy
Authors: Guerillot Pamela , Salamov Asaf , Louet Clémentine , Morin Emmanuelle , Frey Pascal , Grigoriev Igor V. , Duplessis Sébastien 
Published: May 2022

AbstractNutrients acquisition by rust fungi during their biotrophic growth has been assigned to a few transporters expressed in haustorial infection structures. We performed a comparative genomic analysis of all transporter genes (hereafter termed transportome) classified according to the Transporter Classification Database (TCDB) focusing specifically on rust fungi (order Pucciniales) versus other species in the Dikarya. We also surveyed expression of transporter genes in the poplar rust fungus for which transcriptomics data are available across the whole life cycle. Despite a significant increase in gene number, rust fungi presented a reduced transportome compared to a vast majority of fungi in the Dikarya. However, a few transporter families in the subclass Porters showed significant expansions. Noteworthy, three metal transport-related families involved in the import, export and sequestration of metals were expanded in Pucciniales and expressed at various stages of the rust life cycle suggesting a tight regulation of metal homeostasis. The most remarkable gene expansion in the Pucciniales was observed for the oligopeptide transporter (OPT) family with 25 genes in average compared to seven to 14 genes in the other surveyed taxonomical ranks. A phylogenetic analysis showed several specific expansion events at the root of the order Pucciniales with subsequent expansions in rust taxonomical families. The OPT genes showed dynamic expression patterns along the rust life cycle and more particularly during infection of the poplar host tree, suggesting a specialization for the acquisition of nitrogen and sulfur through the transport of oligopeptides from the host during biotrophic growth.
CandidatusNealsonbacteria (OD1) are biomass recycling ectosymbionts of methanogenic archaea in a stable benzene-degrading enrichment culture
Authors: Chen Xu , Molenda Olivia , Brown Christopher T. , Toth Courtney R. A. , Guo Shen , Luo Fei , Howe Jane , Nesbø Camilla L. , He Christine , Montabana Elizabeth A. , Cate Jamie H. D. , Banfield Jillian F. , Edwards Elizabeth A. 
Published: May 2022

SummaryThe Candidate Phyla Radiation (CPR) is a very large group of bacteria with no pure culture representatives, first discovered by metagenomic analyses. Within the CPR, candidate phylum Parcubacteria (previously referred to as OD1) within the candidate superphylum Patescibacteria is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within theCandidateclade Nealsonbacteria. Because of its persistence over many years, we hypothesized thatCa. Nealsonbacteria DGGOD1a must serve an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10 fold) increase in the absolute abundance ofCa. Nealsonbacteria DGGOD1a only when the consortium was amended with crude cell lysate. These results implicateCa. Nealsonbacteria in biomass recycling. Fluorescent in situ hybridization and cryogenic transmission electron microscope images revealed thatCa. Nealsonbacteria DGGOD1a cells were attached to larger archaealMethanothrixcells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of otherCa. Nealsonbacteria found in anoxic environments.
In silico identification of novel peptides as potential modulators of Aβ42 Amyloidogenesis
Authors: Kundal Kavita , Paramasivam Santhosh , Mitra Amit , Sarkar Nandini 
Published: May 2022

AbstractAlzheimer’s Disease is a neurodegenerative disease for which no cure is available at present. The presence of amyloid plaques in the extracellular space of neural cells is the key feature of this fatal disease. Amyloid-Beta (Aβ) is a 40-42 amino acid peptide and the main component of amyloid plaques. This peptide is produced by the proteolysis of Amyloid Precursor Protein by presenilin. Deposition of 42 residual Aβ peptides forms fibrils structure, leading to disruption of neuron synaptic transmission, inducing neural cell toxicity, ultimately leading to neuron death. To modulate the amyloidosis of Aβ peptides, various novel peptides have been investigated via molecular docking and molecular dynamic simulation studies. The sequence-based peptides were designed and investigated for their interaction with Aβ42 monomer and fibril using the molecular docking method, and their influence on the structural stability of target proteins was studied using molecular simulations. According to the docking results, amongst all the synthetic peptides, the peptide YRIGY (P6) has the highest binding affinity with Aβ42 fibril, and the peptide DKAPFF (P12) shows better binding with Aβ42 monomer. Moreover, simulation results also suggest that the higher the binding affinity, the better the inhibitory action. From these findings, it is suggested that both the peptides can modulate the amyloidogenesis, but peptide (P6) has better potential for the disaggregation of the fibrils, whereas peptide P12 stabilizes the native structure of the Aβ42 monomer more effectively and hence can serve as a potential amyloid inhibitor. Thus, these peptides can be explored as therapeutic agents against Alzheimer’s Disease.
Subcortical brain volumes in young infants exposed to antenatal maternal depression: Findings from a South African birth cohort
Authors: Groenewold Nynke A. , Wedderburn Catherine J. , Pellowski Jennifer A. , Fouché Jean-Paul , Michalak Liza , Roos Annerine , Woods Roger P. , Narr Katherine L. , Zar Heather J. , Donald Kirsten A. , Stein Dan J. 
Published: May 2022

ABSTRACTBackgroundSeveral studies have reported enlarged amygdala and smaller hippocampus volumes in children and adolescents exposed to maternal depression. It is unclear whether similar volumetric differences are detectable in the infants’ first weeks of life, following exposurein utero. We investigated subcortical volumes in 2-to-6 week old infants exposed to antenatal maternal depression (AMD) from a South African birth cohort.MethodsAMD was measured with the Beck Depression Inventory 2ndedition (BDI-II) at 28-32 weeks gestation. T2-weighted structural images were acquired during natural sleep on a 3T Siemens Allegra scanner. Subcortical regions were segmented based on the University of North Carolina neonatal brain atlas. Volumetric estimates were compared between AMD-exposed (BDI-II⍰20) and unexposed (BDI-II<14) infants, adjusted for age, sex and total intracranial volume using analysis of covariance.ResultsLarger volumes were observed in AMD-exposed (N=49) compared to unexposed infants (N=75) for the right amygdala (1.98% difference,p=0.039) and bilateral caudate nucleus (left: 5.78% difference, p=0.001; right: 6.06% difference,p<0.001). A significant AMD-by-sex interaction was found for the hippocampus (left:F(1,118)=4.80,p=0.030; right:F(1,118)=5.16,p=0.025), reflecting greater volume in AMD-exposed females (left: 5.09% difference,p=0.001, right: 3.53% difference,p=0.010), but not males.ConclusionsVolumetric differences in subcortical regions can be detected in AMD-exposed infants soon after birth, suggesting structural changes may occurin utero. Female infants might exhibit volumetric changes that are not observed in male infants. The potential mechanisms underlying these early volumetric differences, and their significance for long-term child mental health, require further investigation.
Usage and awareness of antiviral medications for COVID-19
Authors: Kojima N , Klausner JD 
Published: May 2022

AbstractWe surveyed people that recently tested positive for SARS-CoV-2 to assess the frequency and correlates of early treatment seeking behavior. Among high risk respondents, 66.0% were aware of treatment for COVID-19 and 36.3% had sought treatment, however only 1.7% reported use of an antiviral for SARS-CoV-2 infection. More public outreach is needed to raise awareness of the benefits of treatment for COVID-19.