bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks
Authors: Cadena Santiago A. , Willeke Konstantin F. , Restivo Kelli , Denfield George , Sinz Fabian H. , Bethge Matthias , Tolias Andreas S. , Ecker Alexander S. 
Published: May 2022

AbstractResponses to natural stimuli in area V4 – a mid-level area of the visual ventral stream – are well predicted by features from convolutional neural networks (CNNs) trained on image classification. This result has been taken as evidence for the functional role of V4 in object classification. However, we currently do not know if and to what extent V4 plays a role in solvingothercomputational objectives. Here, we investigated normative accounts of V4 (and V1 for comparison) by predicting macaque single-neuron responses to natural images from the representations extracted by 23 CNNs trained on different computer vision tasks including semantic, geometric, 2D, and 3D types of tasks. We found that V4 was best predicted by semantic classification features and exhibited high task selectivity, while the choice of task was less consequential to V1 performance. Consistent with traditional characterizations of V4 function that show its high-dimensional tuning to various 2D and 3D stimulus directions, we found that diverse non-semantic tasks explained aspects of V4 function beyond those captured by individual semantic tasks. Nevertheless, jointly considering the features of a pair of semantic classification tasks was sufficient to yield one of our top V4 models, solidifying V4’s main functional role in semantic processing and suggesting that V4’s affinity to 2D or 3D stimulus properties found by electrophysiologists can result from semantic functional goals.
Disentangling the historical routes to community assembly in the global epicentre of biodiversity
Authors: Reijenga Bouwe Rutger , Freeman Benjamin G , Murrell David J , Pigot Alex L 
Published: May 2022

AbstractAimThe coexistence and turnover of species along elevation gradients makes tropical mountains hotspots of biodiversity. However, understanding the historical processes through which species arising in geographic isolation (i.e. allopatry) assemble along the same mountain slope (i.e. sympatry) remains a major challenge. Multiple models have been proposed including, (1) the sorting of already elevationally divergent species, (2) the displacement of elevation upon secondary contact, potentially followed by convergence, or (3) elevational conservatism, in which ancestral elevational ranges are retained. However, the relative contribution of these processes to generating patterns of elevational overlap and turnover is unknown.LocationTropical mountains of Central- and South-America.Time periodThe last 12 myr.Major taxa studiedBirds.MethodsWe collate a dataset of 165 avian sister pairs containing estimates of phylogenetic age, geographical and regional elevational range overlap. We develop a framework based on continuous-time Markov models to infer the relative frequency of different historical pathways in explaining present day overlap and turnover of sympatric species along elevational gradients.ResultsWe show that the turnover of closely related bird species across elevation can predominantly be explained by displacement of elevation ranges upon contact (81%) rather than elevational divergence in allopatry (19%). In contrast, overlap along elevation gradients is primarily (88%) explained by conservatism of elevational ranges rather than displacement followed by elevational expansion (12%).Main conclusionsBird communities across tropical elevation gradients are assembled through a mix of processes, including the sorting, displacement and conservatism of species elevation ranges. The dominant role of conservatism in explaining co-occurrence of species on mountain slopes rejects more complex scenarios requiring displacement followed by subsequent expansion. The ability of closely related species to coexist without elevational divergence provides a direct and thus faster pathway to sympatry and may help explain the exceptional species richness of tropical mountains.
A multi-domain connector links the outer membrane and cell wall in deep-branching bacteria
Authors: von Kügelgen Andriko , van Dorst Sofie , Alva Vikram , Bharat Tanmay A. M. 
Published: May 2022

AbstractDeinococcus radiodurans is a deep-branching extremophilic bacterium that is remarkably tolerant to numerous environmental stresses, including large doses of ultraviolet radiation and extreme temperatures. It can even survive in outer space for several years. This endurance of D. radiodurans has been partly ascribed to its atypical cell envelope comprising an inner membrane, a large periplasmic space with a thick peptidoglycan (PG) layer, and an outer membrane (OM) covered by a surface layer (S-layer). Despite intense research, molecular principles governing envelope organization and OM stabilization are unclear in D. radiodurans and related bacteria. Here, we report an electron cryomicroscopy (cryo-EM) structure of the abundant D. radiodurans OM protein SlpA, showing how its C-terminal segment forms homotrimers of 30-stranded β-barrels in the OM, whereas its N-terminal segment forms long, homotrimeric coiled coils linking the OM to the PG layer via S-layer homology (SLH) domains. Using the power of structure prediction and sequence-based bioinformatics, we further show that SlpA-like proteins are widespread in deep-branching Gram-negative bacteria, plausibly constituting an ancestral superfamily of OM-PG connectors, important for organizing the cell envelopes of many bacteria. Finally, combining our atomic structures with tomography of cell envelopes, we report a model for the cell surface of D. radiodurans, with implications on understanding the cell surface organization and hyperstability of D. radiodurans and related bacteria. Furthermore, the widespread occurrence of SlpA-like OM-PG connectors in deep-branching bacteria will help in understanding the evolutionary transition between Gram-negative and Gram-positive bacteria.
ERK pathway activation inhibits ciliogenesis and causes defects in motor behavior, ciliary gating, and cytoskeletal rearrangement
Authors: Dougherty Larissa L , Dutta Soumita , Avasthi Prachee 
Published: May 2022

ABSTRACTMitogen-activated protein kinase (MAPK) pathways are well known regulators of the cell cycle but they have also been found to control ciliary length in a wide variety of organisms and cell types from Caenorhabditis elegans neurons to mammalian photoreceptors through unknown mechanisms. ERK1/2 is a MAP kinase in human cells that is predominantly phosphorylated by MEK1/2 and dephosphorylated by the phosphatase DUSP6. We have found that the ERK1/2 activator/DUSP6 inhibitor, (E)-2-benzylidine-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI), inhibits ciliary maintenance in Chlamydomonas and hTERT-RPE1 cells and assembly in Chlamydomonas. These effects involve inhibition of total protein synthesis, microtubule organization, membrane trafficking, and partial kinesin-2 motor dynamics. Our data provide evidence for various avenues for BCI-induced ciliary shortening and impaired ciliogenesis that gives mechanistic insight into how MAP kinases can regulate ciliary length.
NON-TARGETED METABOLOMICS REVEAL DIFFERENCES IN THE METABOLIC PROFILE OF THE FALL ARMYWORM STRAINS WHEN FEEDING DIFFERENT FOOD SOURCES
Authors: Oliveira Nathalia C. , Phelan Larry , Labate Carlos A. , Cônsoli Fernando L. 
Published: May 2022

ABSTRACTSpodoptera frugiperda, the fall armyworm (FAW), is an important polyphagous agricultural pest feeding on nearly 350 host plants. FAW is undergoing incipient speciation with two well-characterized host-adapted strains, the “corn” (CS) and “rice” (RS) strains, which are morphologically identical but carry several genes under positive selection for host adaptation. We used non-targeted metabolomics based on gas chromatography/mass spectrometry to identify differences in metabolite profiles of the larval gut ofCSandRSfeeding on different host plants. Larvae were fed on artificial diet, maize, rice, or cotton leaves from eclosion to the sixth instar, when they had their midgut dissected for the analysis. This study revealed that the midgut metabolome of FAW varied due to larval diet and differed between the FAW host-adapted strains. Additionally, we identified several candidate metabolites that may be involved in the adaptation ofCSandRSto their host plants. Our findings provide clues toward the gut metabolic activities of the FAW strains.
Nucleotide resolution genetic mapping in pigs by publicly accessible whole genome imputation
Authors: Ding Rongrong , Savegnago Rodrigo , Liu Jinding , Long Nanye , Tan Cheng , Cai Gengyuan , Zhuang Zhanwei , Wu Jie , Yang Ming , Qiu Yibin , Ruan Donglin , Quan Jianping , Zheng Enqin , Hong Linjun , Li Zicong , Tan Suxu , Bedhane Mohammd , Schnabel Robert , Steibel Juan , Gondro Cedric , Yang Jie , Huang Wen , Wu Zhenfang 
Published: May 2022

AbstractGenetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in the genetic improvement animals. Despite recent advances in high throughput genotyping technologies, resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2,259 whole genome sequenced animals representing 44 pig breeds. We optimized the imputation procedure to achieve an average concordance rate in excess of 97%, non-reference concordance rate 91%, and r2 0.89. We demonstrated that genotype imputation using this resource can dramatically improve resolution of genetic mapping. Finally, we developed a public web server (swimgeno.org) to allow the pig genetics community to fully utilize this resource. We expect the resource and server to significantly facilitate genetic mapping and accelerate genetic improvement in pigs.
ParA and its functions that go beyond chromosome segregation in Caulobacter crescentus
Authors: Menikpurage Inoka P. , Puentes-Rodriguez Stephanie G. , Elaksher Rawan A. , Mera Paola E. 
Published: May 2022

AbstractMaintaining the integrity of the chromosome after the completion of each cell cycle is paramount for bacterial survival. Mechanistic details remain incomplete for how bacteria manage to retain intact chromosomes in each daughter cell after each cell division. In this study, we examined the partitioning protein ParA and its functions on chromosomal maintenance that go beyond triggering the onset of chromosome segregation. Our data demonstrate that ParA can promote the onset of chromosome replication initiation in Caulobacter crescentus cells with sub-physiological levels of the replication initiator protein DnaA. Increasing the cellular levels of ParA results in over-initiation of chromosome replication in this bacterium. We show that the ability of ParA to impact replication initiation is independent from ParA’s ability to trigger the onset of chromosome segregation. Surprisingly, our work revealed that perturbing the balance of the components of ParA’s nucleotide-dependent cycle can have severe defects in cell cycle coordination and can potentially be lethal to the cell. Increasing the levels of different forms of ParA also impacted cell length independent of their replication initiation frequencies. Our results, together with past observations, suggest a model where ParA can serve as a checkpoint coordinating various cell cycle events involved in maintenance of the chromosome.
The Microbiome and Volatile Organic Compounds Reflect the State of Decomposition in an Indoor Environment
Authors: Cappas Veronica M. , Davenport Emily R. , Sykes Dan G. 
Published: May 2022

AbstractBecause of the variety of factors that can affect the decomposition process, it can be difficult to determine the post-mortem interval (PMI). The process is highly dependent on microbial activity, and volatile organic compounds (VOCs) are a by-product of this activity. Given both have been proposed to assist in PMI determination, a deeper understanding of this relationship is needed. The current study investigates the temporal evolution of the microbiome and VOC profile of a decomposing human analog (swine) in a controlled, indoor environment. Microbial communities and VOCs were sampled at six-time points, up to the active decay phase. Sampling locations included the abdominal area, anus, right ear canal, and right nostril. Bacterial communities were found to significantly change during decomposition (p-value < 0.001), and communities evolved differently based on sampling location. The families Moraxellaceae, Planococcaceae, Lactobacillaceae, and Staphylococcaceae drove these community shifts. From random forest analysis, the nostril sampling location was determined to be the best location to predict stage of decomposition. Individual VOCs exhibited large temporal shifts through decomposition stage in contrast to smaller shifts when evaluated based on functional groups. Finally, pairwise linear regression models between abdominal area bacteria and selected VOCs were assessed; Planococcaceae and Tissierellaceae were significantly correlated to indole. Overall, this study provides an exploratory analysis to support the connection between the microbiome, VOCs, and their relationship throughout decomposition.ImportanceThis research provides valuable insight into the complex process of decomposition, which is pertinent to forensic death investigations. The temporal evolution of both the microbiome and volatile organic compounds (VOCs) were characterized as a function of stage of decomposition and evaluated their interdependency upon one another. In turn, this information may assist in determining time since death, and fill a knowledge gap about VOC-bacteria associations during the decay process.
Functional gene analysis and cultivation experiments predict the degradation of diverse extracellular polysaccharides by ubiquitous taxa in pustular microbial mats from Shark Bay, Western Australia
Authors: Cutts Elise , Schauberger Clemens , Skoog Emilie , Bosak Tanja 
Published: May 2022

AbstractMicrobial exopolymeric substances (EPSs) form the organic, polysaccharide-rich matrix of marine microbial mats and can mediate the binding and precipitation of carbonate minerals therein. Here, we investigate the molecular ecology of carbohydrate degradation and production in pustular mats from Shark Bay, Western Australia, by analyzing 84 metagenome-assembled genomes (MAGs) and the composition of microbial communities enriched from a pustular mat on various polysaccharide substrates. The annotation of 4000 genes from hundreds of carbohydrate-active enzyme (CAZyme) families in the MAGs and mapping of polysaccharide-degrading CAZymes to their predicted substrates identify trends in the distribution and localization of degradation-associated CAZymes across different bacterial phyla. The compositions of microbial communities enriched on a range of polysaccharides inoculated with pustular mat material support the predicted trends. The combined metagenomic and experimental analyses reveal a widespread potential for EPS degradation among MAGs from Shark Bay pustular mats and suggest distinct roles for some phyla that are reported at high abundances in mats. Specifically, Bacteroidetes are likely to be primary degraders of polysaccharide EPSs, alongside Planctomycetes and a small subset of Alphaproteobacteria and Gammaproteobacteria. Planctomycetes, some Bacteroidetes, Verrucomicrobia, Myxococcota and Anaerolineae are also predicted to favor degradation of sulfated substrates, which are present in the EPS matrix of pustular mats. Large sets of functionally varied CAZymes without signal peptides tagging them for export implicate Anaerolineae and Verrucomicrobia in degrading the downstream products of primary EPS degradation.ImportanceModern marine microbial mats are rich in exopolymeric substances (EPSs) — complex, high molecular weight polymers secreted by bacteria — that mediate the formation of carbonate minerals and the preservation of microbial textures in mats. However, the organisms involved in EPS cycling in these mats have not been identified and the links between EPS degradation, carbonate precipitation, and microbial ecology in mats remain poorly understood. We define distinct roles in EPS cycling for many major microbial taxa that are both ubiquitous and abundant in pustular microbial mats from Shark Bay, Australia. The large genomic potential of these microbes for the modification and degradation of diverse extracellular organic polymers provides a blueprint for future studies aimed at quantifying and verifying the specific contributions of these microbes to EPS degradation, carbon cycling and carbonate precipitation.
A framework to trace microbial engraftment at the strain level during fecal microbiota transplantation
Authors: Jiang Yiqi , Wang Shuai , Wang Yanfei , Zhang Xianglilan , Li Shuaicheng 
Published: May 2022

AbstractBackgroundFecal microbiota transplantation (FMT) may treat microbiome-associated diseases effectively. However, the mechanism and pattern of the FMT process require expositions. Previous studies indicated the necessity to track the FMT process at the microbial strain level. At this moment, shotgun metagenomic sequencing enables us to study strain variations during the FMT.ResultWe implemented a software package PStrain-tracer to study microbial strain variations during FMT from the shotgun metagenomic sequencing data. The package visualizes the strain alteration and traces the microbial engraftment during the FMT process. We applied the package to two typical FMT datasets: one ulcerative colitis (UC) dataset and one Clostridium difficile infection (CDI) dataset. We observed that when the engrafted species has more than one strain in the source sample, 99.3% of the engrafted species will engraft only a subset of strains. We further confirmed that the all-or-nothing manner unsuited the engraftment of species with multiple strains by heterozygous single-nucleotide polymorphisms (SNPs) count, revealing that strains prefer to engraft independently. Furthermore, we discovered a primary determinant of strain engrafted success is their proportion in species, as the engrafted strains from the donor and the pre-FMT recipient with proportions 33.10 % (p-value = 6e − 06) and 37.08 % (p-value = 9e − 05) significantly higher than ungrafted strains on average, respectively. All the datasets indicated that the diversity of strains bursts after FMT and decreases to one after eight weeks for twelve species. Previous studies neglected strains with their corresponding species showing insignificant differences between different samples. With the package, from the UC dataset, we successfully determined the strain variations of the species Roseburia intestinalis, a beneficial species reducing intestinal inflammation, colonized in the cured UC patient being engrafted from the donor, even if the patient hosted the same species yet before treatment. We found seven strains in donors from the CDI dataset and one strain in pre-FMT recipients from eight species that associated CDI FMT failure.ConclusionPStrain-tracer is the first framework that tracks strain alterations in metagenomic sequencing data of FMT. PStrain-tracer implemented several methods specialized for FMT experiment samples, such as visualization of strains abundance alteration in the FMT experiment and determinant strains detection in FMT failure. We applied PStrain-tracer on two published datasets, uncovered novel strains related to FMT failure, and demonstrated the necessity of analyzing the whole-genome shotgun metagenomic data of FMT at the strain level. We also developed an online visualizer of PStrain-tracer for the users to adjust their visualized results online. The package is available at https://github.com/deepomicslab/PStrain-tracer.
The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules
Authors: Zhang Chuwen , Fang Yun-Xin , Yin Xiuran , Lai Hongfei , Kuang Zenggui , Zhang Tianxueyu , Xu Xiang-Po , Wegener Gunter , Wang Jiang-Hai , Dong Xiyang 
Published: May 2022

AbstractBackgroundGas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Sedimentary organic matter and upward methane fluids represent two important sources of carbon and energy for deep biosphere. However, which metabolism dominates the deep subseafloor of gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas-hydrate rich sediments up to 49 meters below seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions, and performed metagenomic and metatranscriptomic analyses to characterize microbial diversity and their role in carbon mineralization.ResultsComparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones clearly distinguish from those below the SMI. Chloroflexota, are most abundant above the SMI, whereas Caldatribacteriota dominate below the SMI. Verrucomicrobiota, Bathyarchaeia and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest roles in fermentation of macromolecule. By contrast, sulfate reducers and methanogens, organisms that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs of the ANME-1 group thrived in or slightly below the current sulfate methane interface. Rare members from Heimdallarchaeia were identified to encode the potential for anaerobic oxidation of short-chain hydrocarbons.ConclusionsThese findings indicate that fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes.
Multi-modal analysis and integration of single-cell morphological data
Authors: Govek Kiya W. , Crawford Jake , Saturnino Artur B. , Zoga Kristi , Hart Michael P. , Camara Pablo G. 
Published: May 2022

AbstractHigh-resolution imaging-based single-cell profiling has transformed the study of cells in their spatial context. However, the lack of quantitative methods that can summarize the great diversity of complex cell shapes found in tissues and infer associations with other single-cell data modalities limits current analyses. Here, we report a general computational framework for the multi-modal analysis and integration of single-cell morphological data. We build upon metric geometry to construct cell morphology latent spaces, where distances in these spaces indicate the amount of physical deformation needed to change the morphology of one cell into that of another. Using these spaces, we integrate morphological data across technologies and leverage associated single-cell RNA-seq data to infer relations between morphological and transcriptomic cellular processes. We apply this framework to imaging and multi-modal data of neurons and glia to uncover genes related to neuronal plasticity. Our approach represents a strategy for incorporating cell morphological data into single-cell omics analyses.