bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting
Authors: Torino Stefania , Dhurandhar Mugdha , Stroobants Annelore , Claessens Raf , Efremov Rouslan G. 
Published: October 2022

AbstractUsing single particle cryogenic electron microscopy (cryo-EM) high-resolution structures of proteins in different conformations can be reconstructed. Protein function often involves transient functional conformations, which can be resolved using time-resolved cryo-EM (trEM). In trEM, reactions are arrested after a defined delay time by rapid vitrification of protein solution on the EM grid. Despite the increasing interest in trEM among the cryo-EM community, making trEM samples with a time resolution below 100 ms remains challenging. Here we report the design and the realization of a time-resolved cryo-plunger that combines a droplet-based microfluidic mixer with a laser-induced generator of microjets that allows rapid initiation of reaction and rapid plunge-freezing of cryo-EM grids. Using this approach, a time resolution of 5 ms was achieved and the protein density map was reconstructed to a spatial resolution of 2.1 Å. We performed trEM experiments on GroEL:GroES chaperonin complex, these resolved the kinetics of the complex formation and visualized putative short-lived conformations of GroEL-ATP complex.
A spatial-attentional mechanism underlies action-related distortions of time judgement
Authors: Cao Liyu 
Published: October 2022

AbstractTemporal binding has been understood as an illusion in timing judgement. When an action triggers an outcome (e.g. a sound) after a brief delay, the action is reported to occur later than if the outcome does not occur, and the outcome is reported to occur earlier than a similar outcome not caused by an action. We show here that an attention mechanism underlies the seeming illusion of timing judgement. In one method, participants watch a rotating clock hand and report event times by noting the clock hand position when the event occurs. We find that visual spatial attention is critically involved in shaping event time reports made in this way. This occurs because action and outcome events result in shifts of attention around the clock rim, thereby biasing the perceived location of the clock hand. Using a probe detection task to measure attention, we show a difference in the distribution of visual spatial attention between a single-event condition (sound only or action only) and a two-event agency condition (action plus sound). Participants accordingly report the timing of the same event (the sound or the action) differently in the two conditions: spatial attentional shifts masquerading as temporal binding. Furthermore, computational modelling based on the attention measure can reproduce the temporal binding effect. Studies that use time judgement as an implicit marker of voluntary agency should first discount the artefactual changes in event timing reports that actually reflect differences in spatial attention. The study also has important implications for related results in mental chronometry obtained with the clock-like method since Wundt, as attention may well be a critical confounding factor in the interpretation of these studies.
The annotation and function of the Parkinson’s and Gaucher disease-linked geneGBA1has been concealed by its protein-coding pseudogeneGBAP1
Authors: Gustavsson Emil K. , Sethi Siddharth , Gao Yujing , Brenton Jonathan W. , García-Ruiz Sonia , Zhang David , Garza Raquel , Reynolds Regina H. , Evans James R. , Chen Zhongbo , Grant-Peters Melissa , Macpherson Hannah , Montgomery Kylie , Dore Rhys , Wernick Anna I. , Arber Charles , Wray Selina , Gandhi Sonia , Esselborn Julian , Blauwendraat Cornelis , Douse Christopher H. , Adami Anita , Atacho Diahann A.M. , Kouli Antonina , Quaegebeur Annelies , Barker Roger A. , Englund Elisabet , Platt Frances , Jakobsson Johan , Wood Nicholas W. , Houlden Henry , Saini Harpreet , Bento Carla F. , Hardy John , Ryten Mina 
Published: October 2022

ABSTRACTThe human genome contains numerous duplicated regions, such as parent-pseudogene pairs, causing sequencing reads to align equally well to either gene. The extent to which this ambiguity complicates transcriptomic analyses is currently unknown. This is concerning as many parent genes have been linked to disease, includingGBA1,causally linked to both Parkinson’s and Gaucher disease. We find that most of the short sequencing reads that map toGBA1, also map to its pseudogene,GBAP1. Using long-read RNA-sequencing in human brain, where all reads mapped uniquely, we demonstrate significant differences in expression compared to short-read data. We identify novel transcripts from bothGBA1andGBAP1, including protein-coding transcripts that are translatedin vitroand detected in proteomic data, but that lack GCase activity. By combining long-read with single-nuclear RNA-sequencing to analyse brain-relevant cell types we demonstrate that transcript expression varies by brain region with cell-type-selectivity. Taken together, these results suggest a non-lysosomal function for both GBA1 and GBAP1 in brain. Finally, we demonstrate that inaccuracies in annotation are widespread among parent genes, with implications for many human diseases.
Npr3 regulates neural crest and cranial placode progenitors formation through its dual function as clearance and signaling receptor
Authors: Devotta Arun , Juraver-Geslin Hugo , Griffin Casey , Saint-Jeannet Jean-Pierre 
Published: October 2022

ABSTRACTNatriuretic peptide signaling has been implicated in a broad range of physiological processes, regulating blood volume and pressure, ventricular hypertrophy, fat metabolism, and long bone growth. Here we describe a completely novel role for natriuretic peptide signaling in the control of neural crest (NC) and cranial placode (CP) progenitors formation. Among the components of this signaling pathway, we show that natriuretic peptide receptor 3 (Npr3) plays a pivotal role by differentially regulating two developmental programs through its dual function as clearance and signaling receptor. Using a combination of MO-based knockdowns, pharmacological inhibitors and rescue assays we demonstrate that Npr3 cooperate with guanylate cyclase natriuretic peptide receptor 1 (Npr1) and natriuretic peptides (Nppa/Nppc) to regulate NC and CP formation, pointing at a broad requirement of this signaling pathway in early embryogenesis. We propose that Npr3 acts as a clearance receptor to regulate local concentrations of natriuretic peptides for optimal cGMP production through Npr1 activation, and as a signaling receptor to control cAMP levels through inhibition of adenylyl cyclase. The intracellular modulation of these second messengers therefore participates in the segregation of NC and CP cell populations.
VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction From Assembly Graphs
Authors: Luo Runpeng , Lin Yu 
Published: October 2022

AbstractWith the high mutation rate in viruses, a mixture of closely related viral strains (called viral quasispecies) often co-infect an individual host. Reconstructing individual strains from viral quasispecies is a key step to characterizing the viral population, revealing strain-level genetic variability, and providing insights into biomedical and clinical studies. Reference-based approaches of reconstructing viral strains suffer from the lack of high-quality references due to high mutation rates and biased variant calling introduced by a selected reference. De novo methods require no references but face challenges due to errors in reads, the high similarity of quasispecies, and uneven abundance of strains.In this paper, we propose VStrains, a de novo approach for reconstructing strains from viral quasispecies. VStrains incorporates contigs, paired-end reads, and coverage information to iteratively extract the strain-specific paths from assembly graphs. We benchmark VStrains against multiple state-of-the-art de novo and reference-based approaches on both simulated and real datasets. Experimental results demonstrate that VStrains achieves the best overall performance on both simulated and real datasets under a comprehensive set of metrics such as genome fraction, duplication ratio, NGA50, error rate,etc.AvailabilityVStrains is freely available athttps://github.com/MetaGenTools/VStrains.
Identification of two novel heterodimeric ABC transporters in melanoma: ABCB5β/B6 and ABCB5β/B9
Authors: Gerard Louise , Duvivier Laurent , Fourrez Marie , Salazar Paula , Sprimont Lindsay , Xia Di , Ambudkar Suresh V. , Gottesman Michael M. , Gillet Jean-Pierre 
Published: October 2022

AbstractABCB5 is a member of the ABC transporter superfamily composed of 48 transporters, which have been extensively studied for their role in cancer multidrug resistance and, more recently, in tumorigenesis. ABCB5 has been identified as a marker of skin progenitor cells, melanoma, and limbal stem cells. It has also been associated with multidrug resistance in several cancers. The unique feature of ABCB5 is that it exists as both a full transporter (ABCB5FL) and a half transporter (ABCB5β). Several studies have shown that the ABCB5β homodimer does not confer multidrug resistance, in contrast to ABCB5FL. In this study, using three complementary techniques; (1) nanoluciferase-based bioluminescence resonance energy transfer, (2) co-immunoprecipitation, and (3) proximity ligation assay, we identified two novel heterodimers in melanoma: ABCB5β/B6 and ABCB5β/B9. Both heterodimers could be expressed in high-five insect cells and ATPase assays revealed that they have a basal ATPase activity. These results are an important step toward untangling the functional role of ABCB5β in melanocytes and melanoma.
Structural foundation for the role of enterococcal PrgB in conjugation, biofilm formation and virulence
Authors: Sun Wei-Sheng , Lassinantti Lena , Järvå Michael , Schmitt Andreas , Beek Josy ter , Berntsson Ronnie P-A 
Published: October 2022

AbstractType 4 Secretion Systems are a main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. In Gram-positives, these secretion systems often rely on surface adhesins to enhance cellular aggregation and mating pair formation. One of the best studied adhesins is PrgB from the conjugative plasmid pCF10 ofEnterococcus faecalis,which has been shown to play major roles in conjugation, biofilm formation and importantly also in bacterial virulence. SinceprgBorthologs exist on a large number of conjugative plasmids in various different species, this makes PrgB a model protein for this widespread virulence factor. After characterizing the polymer adhesin domain of PrgB previously, we here report the structure for almost the entire remainder of PrgB, which reveals that PrgB contains four immunoglobulin-like domains. Based on this new insight, we re-evaluate previously studied variants and present newin vivodata where specific domains or conserved residues have been removed. For the first time, we can show a decoupling of cellular aggregation from biofilm formation and conjugation inprgBmutant phenotypes. Based on the presented data, we propose a new functional model to explain how PrgB mediates its different functions. We hypothesize that the Ig-like domains act as a rigid stalk that presents the polymer adhesin domain at the right distance from the cell wall.
From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals,PocilloporaandPorites
Authors: Deshuraud Romane , Ottaviani Alexandre , Poulain Julie , Leprêtre Marine , Beluche Odette , Mahieu Eric , Lebled Sandrine , Belser Caroline , Rouan Alice , Moulin Clementine , Boissin Emilie , Bourdin Guillaume , Iwankow Guillaume , Romac Sarah , Agostini Sylvain , Banaigs Bernard , Boss Emmanuel , Bowler Chris , Vargas Colomban de , Douville Eric , Flores Michel , Furla Paola , Galand Pierre , Lombard Fabien , Pesant Stéphane , Reynaud Stéphanie , Sullivan Matthew B , Sunagawa Shinichi , Thomas Olivier , Troublé Romain , Thurber Rebecca Vega , Voolstra Christian R. , Wincker Patrick , Zoccola Didier , Planes Serge , Allemand Denis , Gilson Eric , Forcioli Didier 
Published: October 2022

AbstractCoral reefs are of paramount importance in marine ecosystems, where they provide support for a large part of the biodiversity. Being quite sensitive to global changes, they are therefore the prime targets for biodiversity conservation policies. However, such conservation goals require accurate species identification, which are notoriously difficult to get in these highly morphologically variable organisms, rich in cryptic species. There is an acute need for easy-to-use and resolutive species diagnostic molecular markers. The present study builds on the huge sequencing effort developed during the TARA Pacific expedition to develop a genotyping strategy to assign coral samples to the correct species within two coral genera (PoritesandPocillopora). For this purpose, we developed a technique that we called “Divergent Fragment” based on the sequencing of a less than 2kb long diagnostic genomic fragment determined from the metagenomic data of a subset of the corals collected. This method has proven to be rapid, resolvable and cost-effective. Sequencing of PCR fragments nested along the species diagnostic fragment allowed us to assign 232 individuals of the genusPocilloporaand 247 individuals of the genusPoritesto previously identified independent genetic lineages (i.e. species). This genotyping method will allow to fully analyze the coral samples collected across the Pacific during the Tara Pacific expedition and opens technological perspectives in the field of population genomics-guided conservation.
The cellular Notch1 Protein Promotes KSHV reactivation in an Rta-dependent manner
Authors: DeCotiis-Mauro Jennifer , Han Sun M. , Mello Helena , Goyeneche Corey , Marchesini-Tovar Giuseppina , Jin Lianhua , Bellofatto Vivian , Lukac David M. 
Published: October 2022

AbstractThe cellular Notch signal transduction pathway is intimately associated with infections by Kaposi’s sarcoma-associated herpesvirus (KSHV) and other gamma-herpesviruses. RBP-Jk, the cellular DNA binding component of the canonical Notch pathway, is the key Notch downstream effector protein in virus-infected and uninfected animal cells. Reactivation of KSHV from latency requires the viral lytic switch protein, Rta, to form complexes with RBP-Jk on numerous sites within the viral DNA. Constitutive Notch activity is essential for KSHV pathophysiology in models of Kaposi’s sarcoma (KS) and Primary Effusion Lymphoma (PEL), and we demonstrate that Notch1 is also constitutively active in infected Vero cells. Although the KSHV genome contains >100 RBP-Jk DNA motifs, we show that none of the four isoforms of activated Notch can productively reactivate the virus from latency in a highly quantitative trans-complementing reporter virus system. Nevertheless, Notch contributed positively to reactivation because broad inhibition of Notch1-4 with gamma secretase inhibitor (GSI) or expression of dominant negative mastermind-like1 (dnMAML1) coactivators severely reduced production of infectious KSHV from Vero cells. Reduction of KSHV production is associated with gene specific reduction of viral transcription in both Vero and PEL cells. Specific inhibition of Notch1 by siRNA partially reduces production of infectious KSHV, and NICD1 forms promoter-specific complexes with viral DNA during reactivation. We conclude that constitutive Notch activity is required for robust production of infectious KSHV, and our results implicate activated Notch1 as a pro-viral member of a MAML1/RBP-Jk/DNA complex during viral reactivation.ImportanceKaposi’s sarcoma-associated herpesvirus (KSHV) manipulates the host cell oncogenic Notch signaling pathway for viral reactivation from latency and cell pathogenesis. KSHV reactivation requires that the viral protein Rta functionally interacts with RBP-Jk, the DNA binding component of the Notch pathway, and with promoter DNA to drive transcription of productive cycle genes. We show that the Notch pathway is constitutively active during KSHV reactivation and is essential for robust production of infectious virus progeny. Inhibiting Notch during reactivation reduces expression of specific viral genes yet does not affect growth of the host cells. Although Notch cannot reactivate KSHV alone, the requisite expression of Rta reveals a previously unappreciated role for Notch in reactivation. We propose that activated Notch cooperates with Rta in a promoter-specific manner that is partially programmed by Rta’s ability to redistribute RBP-Jk DNA binding to the virus during reactivation.
GSearch: Ultra-Fast and Scalable Microbial Genome Search by Combining K-mer Hashing with Hierarchical Navigable Small World Graphs
Authors: Zhao Jianshu , Both Jean Pierre , Rodriguez-R Luis M. , Konstantinidis Konstantinos T. 
Published: October 2022

AbstractGenome search and/or classification is a key step in microbiome studies and has recently become more challenging due to the increasing number of available (reference) genomes and the fact that traditional methods do not scale well with large databases. By combining k-mer hashing-based probabilistic data structures (e.g., (Prob/Super/Densified)-MinHash or SetSketch) to estimate genomic distance, with a graph-based nearest neighbor search algorithm (called Hierarchical Navigable Small World Graphs, or HNSW), we created a new data structure and developed an associated computer program, GSearch, that is orders of magnitude faster than alternative tools while maintaining high accuracy and low memory usage. For example, GSearch can identify/classify 8,000 query genomes against all available microbial or viral genomes (n=∼318,000 or ∼3,000,000) within a few minutes on a personal laptop, using only ∼6GB of memory or less (e.g., 2.5G via SetSketch). Notably, GSearch will be even faster compared to other tools with even larger database size due to O(log(N)) time complexity and will scale well with billions of database genomes based on a database splitting strategy. Further, GSearch implements a three-step classification pipeline that accounts for the degree of novelty of query genomes relative to the database genome to maximize specificity and sensitivity. Therefore, GSearch solves a major bottleneck of microbiome studies that require genome search and/or classification of microbial or viral genomes. GSearch is available at:https://github.com/jean-pierreBoth/gsearch
Transcriptomics reveals amygdala neuron regulation by fasting and ghrelin thereby promoting feeding
Authors: Peters Christian , He Songwei , Fermani Federica , Lim Hansol , Mayer Christian , Klein Rüdiger 
Published: October 2022

SUMMARYThe central amygdala (CeA) consists of numerous genetically-defined inhibitory neurons that control defensive and appetitive behaviors including feeding. Transcriptomic signatures of cell types and their links to function remain poorly understood. Using single-nucleus RNA-sequencing, we describe nine CeA cell clusters, of which four are mostly associated with appetitive and two with aversive behaviors. To analyze the activation mechanism of appetitive CeA neurons, we characterized Serotonin receptor 2a (Htr2a)-expressing neurons (CeAHtr2a) that comprise three appetitive clusters and were previously shown to promote feeding. In vivo calcium imaging revealed that CeAHtr2aneurons are activated by fasting, the hormone ghrelin, and the presence of food. Moreover, these neurons are required for the orexigenic effects of ghrelin. Appetitive CeA neurons responsive to fasting and ghrelin project to the parabrachial nucleus (PBN) causing inhibition of target PBN neurons. These results illustrate how the transcriptomic diversification of CeA neurons relates to fasting and hormone-regulated feeding behavior.HighlightsTranscriptomics reveals four appetitive, two aversive and three unknown CeA clustersGhrelin and fasting activate CeAHtr2aneurons comprising three appetitive clustersGhrelin’s orexigenic effects require the activity of appetitive CeA neuronsCeA→PBN inhibition is necessary for ghrelin/fasting induced feeding
Blood and site of disease inflammatory profiles differ in HIV-1-infected pericardial tuberculosis patients
Authors: Mutavhatsindi Hygon , Du Bruyn Elsa , Ruzive Sheena , Howlett Patrick , Sher Alan , Mayer-Barber Katrin D. , Barber Daniel L. , Ntsekhe Mpiko , Wilkinson Robert J. , Riou Catherine 
Published: October 2022

AbstractObjectivesTo better understand the pathogenesis of pericardial tuberculosis (PCTB), we sought to characterize the systemic inflammatory profile in HIV-1-infected participants with latent TB infection (LTBI), pulmonary TB (PTB) and PCTB.MethodsUsing Luminex, we measured 39 analytes in pericardial fluid (PCF) and paired plasma from 18 PCTB participants, and plasma from 16 LTBI and 20 PTB. Follow-up plasma samples were also obtained from PTB and PCTB participants. HLA-DR expression on Mtb-specific CD4 T cells was measured in baseline samples using flow cytometry.ResultsAssessment of the overall systemic inflammatory profile by principal component analysis showed that the inflammatory profile of active TB participants was distinct from the LTBI group, while PTB patients could not be distinguished from those with PCTB. In the LTBI group, 12 analytes showed a positive association with plasma HIV-1 viral load, and most of these associations were lost in the diseased groups. When comparing the inflammatory profile between PCF and paired blood, we found that the concentrations of most analytes (24/39) were elevated at site of disease. However, the inflammatory profile in PCF partially mirrored inflammatory events in the blood. After TB treatment completion, the overall plasma inflammatory profile reverted to those observed in the LTBI group. Lastly, HLA-DR expression showed the best performance for TB diagnosis compared to previously described biosignatures built from soluble markers.ConclusionOur results describe the inflammatory profile associated with PTB and PCTB and emphasize the potential role of HLA-DR as a promising biomarker for TB diagnosis.
Loss of altruism in the social amoebaDictyostelium discoideumis associated with the G protein-coupled receptorgrlG
Authors: Walker Laura M. , Sherpa Rintsen N. , Ivaturi Sindhuri , Brock Debra A. , Walker Jason R. , Strassmann Joan E. , Queller David C. 
Published: October 2022

AbstractAggregative multicellularity relies on cooperation among individual cells to form a multicellular body. InDictyostelium discoideumthis cooperation is maintained by high relatedness. Previous work showed that experimental evolution under low-relatedness resulted in an increase of cheaters (cells that contribute proportionally more to spores than to the sterile stalk) and that many clones completely lost cooperation and the ability to form fruiting bodies. Here, we investigate the genomic changes underlying the evolution of the cheating phenotype using whole-genome sequencing and variant analysis of these previously evolvedD. discoideumlines. We identified 38 single nucleotide polymorphisms in 29 genes, none of which have been previously implicated in cheating. Each gene has one variant except for the G protein-coupled receptorgrlG, which has at least one variant in over half of the lines. Upon identifying the parallel evolution ofgrlG, we screened additional clones to investigate the correlation between variants in the gene and the loss of cooperation (identified by the inability to form a fruiting body). We found that variants in the 5’ half ofgrlGthat impact the signal peptide or extracellular binding domain are significantly associated with the loss of cooperation (non-fruiting); the association was not significant in the 3’ half of the gene. This suggests that the loss ofgrlGwas adaptive under low-relatedness and that the 5’ half of the gene in particular is important for cooperation and multicellular development. This confirms the importance of high relatedness in the evolution of altruism in the social amoebaD. discoideum.