bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing and annotation of the endangered wild buffalo (Bubalus arnee) mitogenome for taxonomic and hybridization assessment
Authors: Pacha Ankit Shankar , Nigam Parag , Pandav Bivash , Mondol Samrat 
Published: May 2020

AbstractThe wild water buffalo (Bubalus arnee) is one of the most endangered and least studied large bovid in the Indian subcontinent. India retains 90% of the global population as two fragmented populations in Assam and Chhattisgarh, both threatened by habitat loss and degradation, hunting, disease from livestock, and hybridization with the domestic buffalos. For the first time, we sequenced the 16,357 bp long mitogenome of pure wild water buffalo from both populations. The annotated genes included 13 protein-coding genes, 22 tRNA, two ribosomal genes, and a non-coding control region. Comparative mitogenome analyses showed both populations are genetically similar but significantly different from domestic buffalo. We also identified structural differences in seven tRNA secondary structures between both species. Both wild and domestic water buffalo formed sister clades which were paraphyletic to genus Bos. This study provides baseline information on wild buffalo mitogenome for further research on phylogeny, phylogeography and hybrid assessment and help conserving this endangered species.
Medial Prefrontal Cortex Interacts with the Anteromedial Thalamus in Motivation and Dopaminergic Activity
Authors: Yang Chen , Hu Yuzheng , Talishinsky Aleksandr D. , Potter Christian T. , Ramsey Leslie A. , Kesner Andrew J. , Don Reuben F. , Junn Sue , Tan Aaron , Pierce Anne F. , Nicolas Celine , Calva Coleman B. , Su Conghui , Mejia-Aponte Carlos A. , Wang Dong V. , Lu Hanbing , Yang Yihong , Ikemoto Satoshi 
Published: May 2020

AbstractHow does the prefrontal cortex (PFC) regulate motivated behavior? Our experiments characterize the circuits of the PFC regulating motivation, reinforcement and dopamine activity, revealing a novel cortico-thalamic loop. The stimulation of medial PFC (mPFC) neurons activated many downstream regions, as shown by functional MRI. Axonal terminal stimulation of mPFC neurons in downstream regions, including the anteromedial thalamic nucleus (AM), reinforced behavior and activated midbrain dopaminergic neurons. The stimulation of AM neurons projecting to the mPFC also reinforced behavior and activated dopamine neurons, and mPFC and AM showed a positive-feedback loop organization. Reciprocal excitatory functional connectivity, as well as co-activation of the two regions, was found in human participants who watched reinforcing videos. Our results suggest that this cortico-thalamic loop regulates motivation, reinforcement and dopaminergic neuron activity.
The role of microglia membrane potential in chemotaxis
Authors: Laprell Laura , Schulze Christian , Brehme Marie-Luise , Oertner Thomas G. 
Published: May 2020

AbstractMicroglia react to danger signals by rapid and targeted extension of cellular processes towards the source of the signal. This positive chemotactic response is accompanied by a hyperpolarization of the microglia membrane. Here we show that optogenetic depolarization of microglia has little effect on baseline motility, but significantly slows down the chemotactic response. Reducing the extracellular Ca2+concentration mimics the effect of optogenetic depolarization. As the membrane potential sets the driving force for Ca2+entry, hyperpolarization is an integral part of rapid stimulus-response coupling in microglia. Compared to typical excitable cells such as neurons, the sign of the activating response is inverted in microglia, leading to inhibition by depolarizing channelrhodopsins.
THE IMPACT OF MISTRANSLATION ON PHENOTYPIC VARIABILITY AND FITNESS
Authors: Samhita Laasya , Raval Parth K , Stephenson Godwin , Thutupalli Shashi , Agashe Deepa 
Published: May 2020

ABSTRACTPhenotypic variation is widespread in natural populations, and can significantly alter their ecology and evolution. Phenotypic variation often reflects underlying genetic variation, but also manifests via non-heritable mechanisms. For instance, translation errors result in about 10% of cellular proteins carrying altered sequences. Thus, proteome diversification arising from translation errors can potentially generate phenotypic variability, in turn increasing variability in the fate of cells or of populations. However, this link remains unverified. We manipulated mistranslation levels inEscherichia coli, and measured phenotypic variability between single cells (individual level variation), as well as replicate populations (population level variation). Monitoring growth and survival, we find that mistranslation indeed increases variation acrossE. colicells, but does not consistently increase variability in growth parameters across replicate populations. Interestingly, although any deviation from the wild type (WT) level of mistranslation reduces fitness in an optimal environment, the increased variation is associated with a survival benefit under stress. Hence, we suggest that mistranslation-induced phenotypic variation can impact growth and survival and has the potential to alter evolutionary trajectories.
Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at theFADSlocus
Authors: Mathieson Iain , Day Felix R. , Barban Nicola , Tropf Felix C. , Brazel David M. ,   eQTLGen Consortium,   BIOS Consortium, Vaez Ahmad , van Zuydam Natalie , Bitarello Bárbara D. , Snieder Harold , den Hoed Marcel , Ong Ken K. , Mills Melinda C. , Perry John R.B. ,   on behalf of the Human Reproductive Behaviour Consortium
Published: May 2020

AbstractIdentifying genetic determinants of reproductive success may highlight mechanisms underlying fertility and also identify alleles under present-day selection. Using data in 785,604 individuals of European ancestry, we identify 43 genomic loci associated with either number of children ever born (NEB) or childlessness. These loci span diverse aspects of reproductive biology across the life course, including puberty timing, age at first birth, sex hormone regulation and age at menopause. Missense alleles inARHGAP27were associated with increased NEB but reduced reproductive lifespan, suggesting a trade-off between reproductive ageing and intensity. As NEB is one component of evolutionary fitness, our identified associations indicate loci under present-day natural selection. Accordingly, we find that NEB-increasing alleles have increased in frequency over the past two generations. Furthermore, integration with data from ancient selection scans identifies a unique example of an allele—FADS1/2gene locus—that has been under selection for thousands of years and remains under selection today. Collectively, our findings demonstrate that diverse biological mechanisms contribute to reproductive success, implicating both neuro-endocrine and behavioural influences.
Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s disease
Authors: Ping Lingyan , Kundinger Sean R. , Duong Duc M. , Yin Luming , Gearing Marla , Lah James J. , Levey Allan I. , Seyfried Nicholas T. 
Published: May 2020

AbstractAlzheimer’s disease (AD) is characterized by an early, asymptomatic phase (AsymAD) in which individuals exhibit amyloid-beta (Aβ) plaque accumulation in the absence of clinically detectable cognitive decline. Here we report an unbiased multiplex quantitative proteomic and phosphoproteomic analysis using tandem mass tag (TMT) isobaric labeling of human post-mortem cortex (n=27) across pathology-free controls, AsymAD and symptomatic AD individuals. With off-line high-pH fractionation and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on an Orbitrap Lumos mass spectrometer, we identified 11,378 protein groups across three TMT 11-plex batches. Immobilized metal affinity chromatography (IMAC) was used to enrich for phosphopeptides from the same TMT-labeled cases and 51,736 phosphopeptides were identified. Of these, 48,992 were quantified by TMT reporter ions representing 33,652 unique phosphosites. Two reference standards in each TMT 11-plex were included to assess intra- and inter-batch variance at the protein and peptide level. This comprehensive human brain proteome and phosphoproteome dataset will serve as a valuable resource for the identification of biochemical, cellular and signaling pathways altered during AD progression.
Dramatic reduction of psychiatric emergency consultations during lockdown linked to COVID-19 in Paris and suburbs
Authors: Pignon Baptiste , Gourevitch Raphaël , Tebeka Sarah , Dubertret Caroline , Cardot Hélène , Masson Valérie Dauriac-Le , Trebalag Anne-Kristelle , Barruel David , Yon Liova , Hemery François , Loric Marie , Rabu Corentin , Pelissolo Antoine , Leboyer Marion , Schürhoff Franck , Pham-Scottez Alexandra 
Published: May 2020

ABSTRACTAimsThe COVID-19 pandemic and associated lockdown may have psychiatric consequences and increase the number of psychiatric emergency consultations. This study aimed to compare the number and characteristics of emergency psychiatric consultations during the four first weeks of the lockdown in three psychiatric emergency services from Paris and its suburbs, and to compare them to the same period in 2019.MethodsThree psychiatric centers in Paris and its suburbs took part in the study. We compared the number of total psychiatric emergency consultations during the 4 first weeks of the lockdown in France to the corresponding 4 weeks in 2019. We also compared the number of consultations during these 4-week time periods in 2020 and 2019 across different diagnostic categories.ResultsIn the 4 first weeks of the lockdown in France, 553 emergency psychiatry consultations were carried out, compared to 1224 consultations during the corresponding period of 2019, representing a 54.8 % decrease. This decrease was evident across all psychiatric disorders, including anxiety (number of consultations in 2020 representing 36.1 % of 2019), mood (41.1 %), and psychotic disorders (57.3 %). The number of suicide attempts also decreased (number of suicide attempts in 2020 representing 42.6 % of 2019). In comparison to 2019, the proportion of total consultations for anxiety disorders also decreased (16.6 % vs. 20.8 %), whilst the proportion of total consultations increased for psychotic disorders (31.1 % vs. 24.1 %).ConclusionsThe total number of psychiatric emergency consultations during lockdown dramatically decreased. The psychological consequences of lockdown may be delayed, indicating that psychiatric services should be prepared for a secondary increase in emergency presentations.
Normal Childhood Brain Growth and a Universal Sex and Anthropomorphic Relationship to Cerebrospinal Fluid
Authors: Peterson Mallory R. , Cherukuri Venkateswararao , Paulson Joseph N. , Ssentongo Paddy , Kulkarni Abhaya V. , Warf Benjamin C. , Monga Vishal , Schiff Steven J. 
Published: May 2020

AbstractObjectThe study of brain size and growth has a long and contentious history, yet normal brain volume development has yet to be fully described. In particular, the normal brain growth and cerebrospinal fluid (CSF) accumulation relationship is critical to characterize because it is impacted in numerous conditions of early childhood where brain growth and fluid accumulation are affected such as infection, hemorrhage, hydrocephalus, and a broad range of congenital disorders. This study aims to describe normal brain volume growth, particularly in the setting of cerebrospinal fluid accumulation.MethodsWe analyzed 1067 magnetic resonance imaging (MRI) scans from 505 healthy pediatric subjects from birth to age 18 to quantify component and regional brain volumes. The volume trajectories were compared between the sexes and hemispheres using Smoothing Spline ANOVA. Population growth curves were developed using Generalized Additive Models for Location, Scale, and Shape.ResultsBrain volume peaked at 10-12 years of age. Males exhibited larger age-adjusted total brain volumes than females, and body size normalization procedures did not eliminate this difference. The ratio of brain to CSF volume, however, revealed a universal age-dependent relationship independent of sex or body size.ConclusionsThese findings enable the application of normative growth curves in managing a broad range of childhood disease where cognitive development, brain growth, and fluid accumulation are interrelated.
Contiguous Erosion of the Inactive X in Human Pluripotency Concludes With Global DNA Hypomethylation
Authors: Bansal Prakhar , Pinter Stefan F. 
Published: May 2020

SUMMARYFemale human pluripotent stem cells (hPSCs) are prone to undergoing X chromosome erosion (XCE), a progressive loss of key epigenetic features on the inactive X that initiates with repression ofXIST, the long non-coding RNA required for X inactivation. As a result, previously silenced genes on the eroding X (Xe) reactivate, some of which are thought to provide selective advantages. To-date, the sporadic and progressive nature of XCE has largely obscured its scale, dynamics, and key transition events.To address this knowledge gap, we performed an integrated analysis of DNA methylation (DNAme), chromatin accessibility, and gene expression across hundreds of hPSC samples. Differential methylation across the Xe enables ordering female hPSCs across a trajectory of XCE from initiation to terminal stages. Our results identify a crucialcis-regulatory element forXISTexpression, trace contiguously growing domains of reactivation to a few euchromatic origins on the Xi, and indicate that the late-stage Xe impairs DNAme genome-wide. Surprisingly, from this altered epigenetic landscape emerge select features of naïve pluripotency, suggesting its link to X chromosome dosage may be partially conserved in human embryonic development.
Mitochondria Controlled mTORC1 Activation Compartmentalizes Translation Initiation Factor eIF4E to Augment Intracellular Trafficking and Extracellular Export of miRNA in Mammalian Cells
Authors: Chatterjee Susanta , Chakrabarty Yogaditya , Banerjee Saikat , Ghosh Souvik , Bhattacharyya Suvendra N. 
Published: May 2020

AbstractDefective intracellular trafficking and export of miRNAs has been observed in senescent mammalian cells having impaired mitochondrial potential. Similar to what happens in senescent cells, Uncoupling Protein 2 mediated depolarization of mitochondrial membrane potential results in progressive sequestration of miRNAs with polysomes and lowered release of miRNAs through extracellular vesicles. Supporting importance of mitochondrial membrane potential on miRNAs’ fate determination, impaired miRNA-trafficking process in growth retarded human cells has been found to be reversed in presence of Genipin an inhibitor of Uncoupling Protein 2. Mitochondrial detethering of endoplasmic reticulum in mitochondria depolarized cells, found to be responsible for defective compartmentalization of translation initiation factor eIF4E to ER attached polysomes. It causes retarded translation process of target mRNAs with rER attached polysomes to ensure reduced intracellular trafficking and extracellular export of miRNAs. We have identified a reduced activity of mTORC1 complex in mitochondria defective cells to cause reduced phosphorylation of eIF4E-BP1 to cause retarded eIF-4E targeting to ER attached polysome. Cumulatively, these data suggest intricate involvement of mitochondrial membrane potential and dynamics to determine stability of miRNAs in mammalian cells by affecting sub-cellular locations and export of miRNPs by affecting mTORC1 complex, the regulator of the protein translational machinery.Significance statementHow the reduced mitochondrial activity in growth retarded cells causes defective miRNA export is an open question. Mitochondrial defects induces a retarded subcellular miRNP trafficking in human cells to cause an upregulation in cellular miRNA content by reducing extracellular vesicle-mediated export of miRNA. We have identified a defective compartmentalization of translation initiation factor eIF4E in mitochondria-ER detethered mammalian cells to cause the retarded intracellular miRNA movement and export Activity of mTORC1 complex, a key regulator of protein translation in mammalian cells, is found to be responsible for ER-compartmentalization of eIF4E. mTORC1 activity reduction in growth retarded and mitochondria detethered cells influences the cell fate by acting on miRNA-mRNA axis. This is a unique way how mitochondrial activity is linked with protein translation and gene repression control in mammalian cells.
The RAC1 activator Tiam1 regulates centriole duplication through controlling PLK4 levels
Authors: Porter Andrew P. , White Gavin R. M. , Ogg Erinn-Lee , Whalley Helen J. , Malliri Angeliki 
Published: May 2020

SummaryCentriole duplication is tightly controlled to maintain correct centriole number through the cell cycle. A key component of this control is the regulated degradation of PLK4, the master regulator of centriole duplication. Here we show that the Rac1 guanine nucleotide exchange factor (GEF) Tiam1 localises to centrosomes during S-phase, where it is required for maintenance of normal centriole number. Depletion of Tiam1 leads to an increase in centrosomal PLK4, centriole overduplication and ultimately to lagging chromosomes at anaphase and aneuploidy. The effects of Tiam1 depletion can be rescued by re-expression of wild-type Tiam1 and catalytically inactive (GEF*) Tiam1, but not by Tiam1 mutants unable to bind to the F-box protein βTRCP, implying that Tiam1 regulates PLK4 levels through promoting βTRCP-mediated degradation.
Combining auxin-induced degradation and RNAi screening identifies novel genes involved in lipid bilayer stress sensing inCaenorhabditis elegans
Authors: Venz Richard , Korosteleva Anastasiia , Ewald Collin Y. 
Published: May 2020

AbstractAlteration of the lipid composition of biological membranes interferes with their function and can cause tissue damage by triggering apoptosis. Upon lipid bilayer stress, the endoplasmic reticulum mounts a stress response that is similar to the unfolded protein response. However, only a few genes are known to regulate lipid bilayer stress. Here, we performed a suppressor screen that combined the auxin-inducible degradation (AID) system with conventional RNAi inC. elegansto identify members of the lipid bilayer stress response. AID-mediated knockdown of the mediator MDT-15, a protein required for the upregulation of fatty acid desaturases, caused activation of a lipid bilayer stress sensitive reporters. We screened through almost allC. eleganskinases and transcription factors using RNAi by feeding. We report the identification of 8 genes that have not been implicated previously with lipid bilayer stress before inC. elegans. These suppressor genes includeskn-1/NRF1,2,3 andlet-607/CREB3. Our candidate suppressor genes suggest a network of transcription factors and the integration of multiple tissues for a centralized lipotoxicity response in the intestine. Additionally, we propose and demonstrate the proof-of-concept for combining AID and RNAi as a new screening strategy.
Effects of cellular stress on pigment production inRhodotorula mucilaginosa/alborubescensAJB01 strain from the Caribbean region of Colombia
Authors: Cortes Alejandra Garcia , Vásquez Julián Andres Garcia , Díaz Yani Cristina Aranguren , Castrillón Mauricio Ramirez 
Published: May 2020

ABSTRACTConsidering that a large proportion of industrially used pigments are toxic and potentially mutagenic, with some having carcinogenic effects, it is essential to replace them as well as eliminate them from industrial effluents. The discovery of biopigments has received considerable attention from the industry sector. The main objective of this study was to increase the production of carotenoid pigments in naturally pigmented yeast by subjecting the yeast to various cellular stresses. The fungal strainRhodotorula mucilaginosa/alborubescensAJB01 was isolated from a food sample collected in Barranquilla, Colombia, and one of the pigments produced was β-carotene. This strain was subjected to various stress conditions, including osmotic stress using different salts, physical stress by ultraviolet (UV) light, and light stress using different photoperiods. The optimal growth conditions for carotenoid production were determined to be 1 min of UV light, 0.5 mg/L of magnesium sulfate, and 18:6 h light/dark period, which resulted in a carotenoid yield of 118.3 μg of carotenoid per gram of yeast.
METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies - Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses
Authors: Saunders Jaclyn K. , Gaylord David , Held Noelle , Symmonds Nick , Dupont Chris , Shepherd Adam , Kinkade Danie , Saito Mak A. 
Published: May 2020

AbstractWe present METATRYP version-2 software that identifies shared peptides across organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include: ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the Least Common Ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). Major expansion of the marine database confirms low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed for ocean metaproteomics and has been integrated into the Ocean Protein Portal (https://oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https://metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A Coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa, sharing 0.1% peptides or less (1 peptide) with the Influenza A & B pan-proteomes, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches.Statement of significanceWhen assigning taxonomic attribution in bottom-up metaproteomics, the potential for shared tryptic peptides among organisms in mixed communities should be considered. The software program METATRYP v 2 and associated interactive web portals enables users to identify the frequency of shared tryptic peptides among taxonomic groups and evaluate the occurrence of specific tryptic peptides within complex communities. METATRYP facilitates phyloproteomic studies of taxonomic groups and supports the identification and evaluation of potential metaproteomic biomarkers.