bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning (decision tree analysis) identifies ecological selectivity patterns across the end-Permian mass extinction
Authors: Foster William J. , Ayzel Georgy , Isson Terry T. , Mutti Maria , Aberhan Martin 
Published: October 2020

AbstractDecision tree algorithms are rarely utilized in paleontological research, and here we show that machine learning algorithms can be used to identify determinants of extinction as well as predict extinction risk. This application of decision tree algorithms is important because the ecological selectivity of mass extinctions can reveal critical information on organismic traits as key determinants of extinction and hence the causes of extinction. To understand which factors led to the mass extinction of life during an extreme global warming event, we quantified the ecological selectivity of marine extinctions in the well-studied South China region during the end-Permian mass extinction using the categorized gradient boosting algorithm. We find that extinction selectivity varies between different groups of organisms and that a synergy of multiple environmental stressors best explains the overall end-Permian extinction selectivity pattern. Extinction risk was greater for genera that were limited to deep-water habitats, had a stationary mode of life, possessed a siliceous skeleton or, less critically, had calcitic skeletons. These selective losses directly link the extinction to the environmental effects of rapid injections of carbon dioxide into the ocean-atmosphere system, specifically the combined effects of expanded oxygen minimum zones, rapid warming, and ocean acidification.
Evolutionary diversification of tiny ocean predators
Authors: Latorre Francisco , Deutschmann Ina M. , Labarre Aurelie , Obiol Aleix , Krabberød Anders , Pelletier Eric , Sieracki Michael E. , Cruaud Corinne , Jaillon Olivier , Massana Ramon , Logares Ramiro 
Published: October 2020

ABSTRACTUnicellular eukaryotic predators have a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionary-diverse organisms have been combined into a single functional group (Heterotrophic flagellates), overlooking their organismal differences. Here we investigate four evolutionary related species belonging to one cosmopolitan family of uncultured marine picoeukaryotic predators: MAST-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A & C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using Single-Cell Genomics. Analyses of 69 single-cells recovered 66-83% of the MAST-4A/B/C/E genomes, which displayed substantial inter-species divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition co-excluded each other (A & C) in the surface global ocean, while species with a different set of GHs appeared to be able to co-exist (species B & C) suggesting further niche diversification associated to prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. Altogether, we show that minute ocean predators from the same family may have different biogeography and genomic content, which need to be accounted to better comprehend marine food webs.
Mirage: A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model
Authors: Fukunaga Tsukasa , Iwasaki Wataru 
Published: October 2020

AbstractReconstruction of gene-content evolutionary history is an essential approach for understanding how complex biological systems have been organized. However, the existing gene-content evolutionary models cannot formulate complex and heterogeneous gene gain/loss processes, which reflect diverse evolutionary events and greatly depend on gene families. In this study, we developed Mirage (MIxture model with aRealistic evolutionary rate model forAncestralGenomeEstimation), which allows different gene families to have flexible gene gain/loss rates, but reasonably limits the number of parameters to be estimated by the expectation-maximization algorithm. Simulation analysis showed that Mirage can accurately estimate complex and heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that our evolutionary model better fits genome data from various taxonomic groups than other models. Using Mirage, we revealed that gene families of metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated. The source code of Mirage is freely available athttps://github.com/fukunagatsu/Mirage.
Chia (Salvia hispanica) gene expression atlas elucidates dynamic spatio-temporal changes associated with plant growth and development
Authors: Gupta Parul , Geniza Matthew , Naithani Sushma , Phillips Jeremy , Haq Ebaad , Jaiswal Pankaj 
Published: October 2020

AbstractChia (Salvia hispanicaL.), now a popular superfood, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids. At present, the genomic and genetic information available in the public domain for this crop is scanty, which hinders understanding its growth and developmental processes and impedes genetic improvement through genomics-assisted methods. We report RNA-seq based comprehensive transcriptome atlas of Chia across 13 different tissue types covering vegetative and reproductive growth stages. We generated ∼394 million raw reads from transcriptome sequencing, of which ∼355 million high-quality reads were used to generatede novoreference transcriptome assembly and the tissue-specific transcript assemblies. After quality assessment of merged assemblies and using redundancy reduction methods, 82,663 reference transcripts were identified. Of these, 53,200 transcripts show differential expression in at least one sample and provide information on spatio-temporal modulation of gene expression in Chia. We identified genes involved in the biosynthesis of omega-3 and omega-6 polyunsaturated fatty acids, and various terpenoid compounds. The study also led to the identification of 633 differentially expressed transcription factors from 53 gene families. The coexpression analysis suggested that members of the B3, bZIP, ERF, WOX, AP2, MYB, C3H, EIL, LBD, DBB, Nin-like, and HSF transcription factor gene families play key roles in the regulation of target gene expression across various developmental stages. This study also identified 2,411 simple sequence repeat (SSRs) as potential genetic markers residing in the transcribed regions. The transcriptome atlas provides essential genomic resources for basic research, applications in plant breeding, and annotation of the Chia genome.
Long-term soil fungal community recovery after fire is impacted by climate change
Authors: McGee Spencer , Tidwell Alyssa , Riggs Erin , Veltkamp Hannah , Zahn Geoffrey 
Published: October 2020

AbstractThough much is known about fungal importance to forest health, there is very little information about factors that impact soil fungal community recovery time after a fire. Soil samples were taken from burn sites within one ecotype of temperate coniferous forest in Utah over a 20-year chronosequence. Sites were selected from available historic burns and were similar in plant community structure, elevation, slope, and aspect. Fungal DNA from these samples was compared to soil from paired unburned sites nearby to measure community similarity and estimate soil fungal recovery rates. Differences between paired burned and unburned sites remained fairly stable over a decadal time scale overall, but fungal community structure was found to recover more quickly in areas with a higher average annual temperatures. A significant positive correlation in community recovery was seen in areas with a difference of as little as two degrees celsius per year. The only other environmental variable that significantly interacted with time since burn was annual mean precipitation. As global temperatures increase, alpine fires are increasing as well, but these results suggest that fungal community recovery time will be shortened under new climate scenarios.
CELL ATLAS OF THE CHICK RETINA: SINGLE CELL PROFILING IDENTIFIES 136 CELL TYPES
Authors: Yamagata Masahito , Yan Wenjun , Sanes Joshua R. 
Published: October 2020

SUMMARYRetinal structure and function have been studied in many vertebrate orders, but molecular characterization has been largely confined to mammals. We used single-cell RNA sequencing (scRNA-seq) to generate a cell atlas of the chick retina. From ∼40,000 single cell transcriptomes, we identified 136 cell types distributed among the six classes conserved across vertebrates – photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and glial cells. To match molecular profiles to morphology, we adapted a method for CRISPR-based integration of reporters into selectively expressed genes. For Müller glia, we found that transcriptionally distinct cells were regionally localized along the anterior-posterior, dorsal-ventral and central-peripheral retinal axes. We also identified immature photoreceptor, horizontal cell and oligodendrocyte types that persist into late embryonic stages. Finally, we analyzed relationships among chick, mouse and primate retinal cell classes and types. Taken together, our results provide a foundation for anatomical, physiological, evolutionary, and developmental studies of the avian visual system.
Misoprostol Treatment Prevents Hypoxia-Induced Cardiac Dysfunction Through a 14-3-3 and PKA regulatory motif on Bnip3
Authors: Martens Matthew D. , Seshadri Nivedita , Nguyen Lucas , Chapman Donald , Henson Elizabeth S. , Xiang Bo , Falk Landon , Mendoza Arielys , Rattan Sunil , Gibson Spencer B. , Keijzer Richard , Saleem Ayesha , Hatch Grant M. , Doucette Christine A. , Karch Jason M. , Dolinsky Vernon W. , Dixon Ian M. , West Adrian R. , Rampitsch Christof , Gordon Joseph W. 
Published: October 2020

AbstractSystemic hypoxia is a common element in most perinatal emergencies and is a known driver of Bnip3 expression in the neonatal heart. Bnip3 plays a prominent role in the evolution of necrotic cell death, disrupting ER calcium homeostasis and initiating mitochondrial permeability transition (MPT). Emerging evidence suggests a cardioprotective role for the prostaglandin E1 analogue misoprostol during periods of hypoxia, but the mechanisms for this protection are not completely understood. Using a combination of mouse and cell models, we tested if misoprostol is cardioprotective during neonatal hypoxic injury by altering Bnip3 function. Here we report that hypoxia elicits mitochondrial-fragmentation, MPT, reduced ejection fraction, and evidence of necroinflammation, which were abrogated with misoprostol treatment or Bnip3 knockout. Through molecular studies we show that misoprostol leads to PKA-dependent Bnip3 phosphorylation at threonine-181, and subsequent redistribution of Bnip3 from mitochondrial Opa1 and the ER through an interaction with 14-3-3 proteins. Taken together, our results demonstrate a role for Bnip3 phosphorylation in the regulation of cardiomyocyte contractile/metabolic dysfunction, and necroinflammation. Furthermore, we identify a potential pharmacological mechanism to prevent neonatal hypoxic injury.
Identification of key immune regulatory genes in HIV–1 Progression
Authors: Hossain Sk Md Mosaddek , Khatun Lutfunnesa , Ray Sumanta , Mukhopadhyay Anirban 
Published: October 2020

AbstractIn the last few decades, application of DNA microarray technology has sprung up as a powerful technique for discovering stage specific changes in expression pattern of a disease progression. Human Immunodeficiency Virus (HIV) infection causes Acquired Immunodeficiency Syndrome (AIDS) which is one of the most devastating diseases affecting humankind. Here, we have proposed a framework to examine the difference among microarray gene expression data of uninfected and three different HIV–1 infection stages using module preservation statistics. Initially, we detected differentially expressed genes among all the stages and identified coexpression modules by using topological overlap as a dissimilarity measure. To examine relationship among co-expression modules, we have compiled a module eigenegene network for each sample category which models similarity among all coexpression modules. To further examine the network, we have found clusters in it which are termed as ‘meta-modules’. Different module preservation statistics with two composite statistics: “Zsummary” and “MedianRank” are utilized to examine changes in structure of coexpression modules. We have applied our proposed methodology to discover modular changes between uninfected and acute samples, acute and chronic samples, chronic and AIDS samples. We have found several interesting results on preservation characteristics of gene modules across different stages. Some genes are identified to be preserved in a pair of stages while alter their characteristics across other stages. We further validated the obtained results using permutation test and classification techniques. Biological significance of the obtained modules have been examined using gene ontology and pathway based analysis. Additionally, we have detected key immune regulatory hub genes in the associated protein-protein interaction networks (PPINs) of the differentially expressed genes (DEGs) using twelve topological and centrality analysis methods. Moreover, we have analyzed the key immune regulatory genes which interacts with HIV-1 proteins inside the preserved and perturbed meta-modules across different HIV-1 stages and thus likely to act as potential biomarkers in HIV–1 progression.
Clock proteins regulate spatiotemporal organization of clock genes to control circadian rhythms
Authors: Xiao Yangbo , Yuan Ye , Jimenez Mariana , Soni Neeraj , Yadlapalli Swathi 
Published: October 2020

ABSTRACTCircadian clocks regulate ∼24 hour oscillations in gene expression, behavior, and physiology. While the molecular and neural mechanisms of circadian rhythms are well characterized, how cellular organization of clock components controls circadian clock regulation remains poorly understood. Here, we elucidate how clock proteins regulate circadian rhythms by controlling the spatiotemporal organization of clock genes. Using high-resolution live imaging techniques we demonstrate thatDrosophilaclock proteins are concentrated in a few discrete foci and are organized at the nuclear envelope; these results are in contrast to longstanding expectations that clock proteins are diffusely distributed in the nucleus. We also show that clock protein foci are highly dynamic and change in number, size, and localization over the circadian cycle. Further, we demonstrate that clock genes are positioned at the nuclear periphery by the clock proteins precisely during the circadian repression phase, suggesting that subnuclear localization of clock genes plays an important role in the control of rhythmic gene expression. Finally, we show that Lamin B receptor, a nuclear envelope protein, is required for peripheral localization of clock protein foci and clock genes and for normal circadian rhythms. These results reveal that clock proteins form dynamic nuclear foci and play a hitherto unexpected role in the subnuclear reorganization of clock genes to control circadian rhythms, identifying a novel mechanism of circadian regulation. Our results further suggest a new role for clock protein foci in the clustering of clock-regulated genes during the repression phase to control gene co-regulation and circadian rhythms.SIGNIFICANCEAlmost all living organisms have evolved circadian clocks to tell time. Circadian clocks regulate ∼24-hour oscillations in gene expression, behavior and physiology. Here, we reveal the surprisingly sophisticated spatiotemporal organization of clock proteins and clock genes and its critical role in circadian clock function. We show, in contrast to current expectations, that clock proteins are concentrated in a few discrete, dynamic nuclear foci at the nuclear envelope during the repression phase. Further, we uncovered several unexpected features of clock protein foci, including their role in positioning the clock genes at the nuclear envelope precisely during the repression phase to enable circadian rhythms. These studies provide fundamental new insights into the cellular mechanisms of circadian rhythms and establish direct links between nuclear organization and circadian clocks.
Increased light availability enhances tolerance against ocean acidification stress inHalimeda opuntia
Authors: Wei Zhangliang , Long Chao , Zhang Yating , Huo Yuanzi , Yang Fangfang , Long Lijuan 
Published: October 2020

AbstractAlthough the adverse impacts of ocean acidification (OA) on marine calcifiers have been investigated substantially, the anti-stress abilities regulated by increased light availability are unclear. Herein, the interactive effects of three light levels combined with twopCO2concentrations on the physiological acclimation of the calcifying macroalgaHalimeda opuntiawere investigated using apCO2–light coupling experiment. The results indicate that OA exhibits an adverse role in influencing algal growth, calcification, photosynthesis and other physiological performances inH. opuntia.The relative growth rate in elevatedpCO2significantly declined by 13.14%–41.29%, while net calcification rates decreased by nearly three-fold under OA. Notably, increased light availability could enhance stress resistance by the accumulation of soluble organic molecules, especially soluble carbohydrate, soluble protein and free amino acids, and in combination with metabolic enzyme-driven activities alleviated OA stress. Carotenoid content in low light conditions accumulated remarkably and rapid light curves for relative electron transport rate was significantly enhanced by increasing light intensities, indicating that this new organization of the photosynthetic machinery inH. opuntiaaccommodated light variations and elevatedpCO2conditions. Taken together, the results describe stress resistance by the enhancement of metabolic performance in marine calcifiers to mitigate OA stress.One sentence summaryIncreased light availability enhances stress resistance inHalimeda opuntiaby the accumulation of soluble organic molecules and enzyme-driven activities to alleviate ocean acidification stress.Credit authorship contribution statementFangfang Yang and Lijuan Long conceived and designed the experiments. Zhangliang Wei performed the experiments and wrote the paper. Yuanzi Huo analyzed the data, while Chao Long and Yating Zhang contributed materials and analysis tools. Lijuan Long agrees to serve as the author responsible for contact and communication.HighlightsElevatedpCO2adversely affects the physiological performance ofHalimeda.Moderately high light increases soluble organic molecules and enzymatic-driven activities.Increased light availability enablesH. opuntiato alleviate the negative effects of ocean acidification.
A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells
Authors: Shamie Isaac , Duttke Sascha H. , la Cour Karottki Karen J. , Han Claudia Z. , Hansen Anders H. , Hefzi Hooman , Xiong Kai , Li Shangzhong , Roth Sam , Tao Jenhan , Lee Gyun Min , Glass Christopher K. , Kildegaard Helene Faustrup , Benner Christopher , Lewis Nathan E. 
Published: October 2020

ABSTRACTChinese hamster ovary (CHO) cells, with their human-compatible glycosylation and high protein titers, are the most widely used cells for producing biopharmaceuticals. Engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the Chinese hamster genome were computationally predicted and are frequently inaccurate. Here, we revised TSS annotations for 15,308 Chinese hamster genes and 4,478 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. The experimental realignment and discovery of TSSs now expose previously hidden motifs, such as the TATA box. We further demonstrate, by targeting the glycosyltransferase geneMgat3, how accurate annotations readily facilitate activating silent genes by CRISPRa to obtain more human-like glycosylation. Together, we envision our annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies.
HectoSTAR microLED optoelectrodes for large-scale, high-precisionin invoopto-electrophysiology
Authors: Kim Kanghwan , Vöröslakos Mihály , Fernández-Ruiz Antonio , Parizi Saman S. , Ko Eunah , Hendrix Blake , Seymour John P. , Wise Kensall D. , Buzsáki György , Yoon Euisik 
Published: October 2020

AbstractWe present a device that can be utilized for a large-scale in vivo extracellular recording, from more than 250 electrodes, with the capability to optically modulate activities of neurons located at more than a hundred individual stimulation targets at the anatomical resolution.
LyticBacteroides uniformisbacteriophages exhibiting host tropism congruent with diversity generating retroelement
Authors: Hedzet Stina , Accetto Tomaž , Rupnik Maja 
Published: October 2020

AbstractIntestinal phages are abundant and important component of gut microbiota, but our knowledge remains limited to only a few isolated and characterized representatives targeting numerically dominant gut bacteria. Here we describe isolation of human intestinal phages infectingBacteroides uniformis. Bacteroidesis one of the most common bacterial groups in the global human gut microbiota, however, to date not manyBacteroidesspecific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, withinSiphoviridaefamily and represent the first lytic phages, genomes of which encode diversity generating retroelements (DGR). This region is assumed to promote phage adaptation to the rapidly changing environmental conditions and to broaden its host range. Three isolated phages showed 99,83% genome identity but infected distinctB. uniformisstrains. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% aa similarity to Bacuni phages in the genomes ofB. acidifaciensandPrevotellasp.. Despite the abundance ofBacteroideswithin human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.ImportanceThe lack of common marker gene in viruses require a precise characterization of diverse isolated phages to enhance metagenomic analyses and to understand their role in gut microbiota. Here we report the isolation of phages representing a new genus with characteristics so far not known or rarely described in intestinal phages. They are the first lytic phages specific forBacteroides uniformis, a bacterial representative of the prevalent genus in the gut of humans and animals. Additionally, they are the first lytic phages containing specific regions (diversity generating retroelement) that putatively influence host tropism. The ability to switch constantly the targeted populations of the host species could provide an evolutionary advantage to these bacteriophages and may affect intra species diversity.