bluuebunny/crossref_metadata_2025_split huggingface dataset:
Air and surface measurements of SARS-CoV-2 inside a bus during normal operation
Authors: Di Carlo Piero , Chiacchiaretta Piero , Sinjari Bruna , Aruffo Eleonora , Stuppia Liborio , De Laurenzi Vincenzo , Di Tomo Pamela , Pelusi Letizia , Potenza Francesca , Veronese Angelo , Vecchiet Jacopo , Falasca Katia , Ucciferri Claudio 
Published: June 2020

AbstractTransmission pathways of SARS-CoV-2 are through aerosol, droplet and touching infected material. Indoor locations are more likely environments for the diffusion of the virus contagion among people, but direct detection of SARS-CoV-2 in air or on surfaces is quite sparse, especially regarding public transport. In fact, an important demand is to know how and if it is safe to use them. To understand the possible spreading of COVID-19 inside a city bus during normal operation and the effectiveness of the protective measures adopted for transportation, we analysed the air and the surfaces most usually touched by passengers. The measurements were carried out across the last week of the lockdown and the first week when gradually all the travel restrictions were removed.
Validation of the Social Responsiveness Scale (SRS) to screen for atypical social behaviors in juvenile macaques
Authors: Balint Z. Kovacs , Raper J. , Michopoulos V. , Howell L.H. , Gunter C. , Bachevalier J. , Sanchez M.M. 
Published: June 2020

AbstractPrimates form strong social bonds and depend on social relationships and networks that provide shared resources and protection critical for survival. Social deficits such as those present in autism spectrum disorder (ASD) and other psychiatric disorders hinder the individual’s functioning in communities. Given that early diagnosis and intervention can improve outcomes and trajectories of ASD, there is a great need for tools to identify early markers for screening/diagnosis, and for translational animal models to uncover biological mechanisms and develop treatments. One of the most widely used screening tools for ASD in children is the Social Responsiveness Scale (SRS), a quantitative measure used to identify individuals with atypical social behaviors. The SRS has been adapted for use in adult rhesus monkeys (Macaca mulatta) –a species very close to humans in terms of social behavior, brain anatomy/connectivity and development– but has not yet been validated or adapted for a necessary downward extension to younger ages matching those for ASD diagnosis in children. The goal of the present study was to adapt and validate the adult macaque SRS (mSRS) in juvenile macaques with age equivalent to 4-6 yr old human children. Expert primate coders modified the mSRS to adapt it to rate atypical social behaviors in juvenile macaques living in complex social groups at the Yerkes National Primate Research Center. Construct and face validity of this juvenile mSRS (jmSRS) was determined based on well-established and operationalized measures of social and non-social behaviors in this species using traditional behavioral observations. We found that the jmSRS identifies variability in social responsiveness of juvenile rhesus monkeys and shows strong construct/predictive validity, as well as sensitivity to detect atypical social behaviors in young male and female macaques across social status. Thus, the jmSRS provides a promising tool for translational research on macaque models of children social disorders.
Inferring cellular trajectories from scRNA-seq using Pseudocell Tracer
Authors: Reiman Derek , Xu Heping , Sonin Andrew , Chen Dianyu , Singh Harinder , Khan Aly A. 
Published: June 2020

ABSTRACTSingle cell RNA sequencing (scRNA-seq) can be used to infer a temporal ordering of dynamic cellular states. Current methods for the inference of cellular trajectories rely on unbiased dimensionality reduction techniques. However, such biologically agnostic ordering can prove difficult for modeling complex developmental or differentiation processes. The cellular heterogeneity of dynamic biological compartments can result in sparse sampling of key intermediate cell states. This scenario is especially pronounced in dynamic immune responses of innate and adaptive immune cells. To overcome these limitations, we develop a supervised machine learning framework, called Pseudocell Tracer, which infers trajectories in pseudospace rather than in pseudotime. The method uses a supervised encoder, trained with adjacent biological information, to project scRNA-seq data into a low-dimensional cellular state space. Then a generative adversarial network (GAN) is used to simulate pesudocells at regular intervals along a virtual cell-state axis. We demonstrate the utility of Pseudocell Tracer by modeling B cells undergoing immunoglobulin class switch recombination (CSR) during a prototypic antigen-induced antibody response. Our results reveal an ordering of key transcription factors regulating CSR, including the concomitant induction ofNfkb1andStat6prior to the upregulation ofBach2expression. Furthermore, the expression dynamics of genes encoding cytokine receptors point to the existence of a regulatory mechanism that reinforces IL-4 signaling to direct CSR to the IgG1 isotype.
Epigenetic regulations follow cell cycle progression during differentiation of human pluripotent stem cells
Authors: Madrigal Pedro , Pauklin Siim , Goh Kim Jee , Grandy Rodrigo , Osnato Anna , Ortmann Daniel , Brown Stephanie , Vallier Ludovic 
Published: June 2020

AbstractMost mammalian stem cells undergo cellular division during their differentiation to produce daughter cells with a new cellular identity. However, the cascade of epigenetic events and molecular mechanisms occurring between successive cell divisions upon differentiation have not yet been described in detail due to technical limitations. Here, we address this question by taking advantage of the Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) reporter to develop a culture system allowing the differentiation of human Embryonic Stem Cells (hESCs) synchronised for their cell cycle. Using this approach, we have assessed the epigenome and transcriptome dynamics during the first two divisions leading to definitive endoderm. We first observed that transcription of key markers of differentiation occurs before division suggesting that differentiation is initiated during the progression of cell cycle. Furthermore, ATAC-seq shows a major decrease in chromatin accessibility after pluripotency exit indicating that the first event of differentiation is the inhibition of alternative cell fate. In addition, using digital genomic footprinting we identified novel cell cycle-specific transcription factors with regulatory potential in endoderm specification. Of particular interest, Activator protein 1 (AP-1) controlled p38/MAPK signalling seems to be necessary for blocking endoderm shifting cell fate toward mesoderm lineage. Finally, histone modifications analyses suggest a temporal order between different marks. We can also conclude that enhancers are dynamically and rapidly established / decommissioned between different cell cycle upon differentiation. Overall, these data not only reveal key the successive interplays between epigenetic modifications during differentiation but also provide a valuable resource to investigate novel mechanisms in germ layer specification.
Charge Interactions in a Highly Charge-depleted Protein
Authors: Hervø-Hansen Stefan , Højgaard Casper , Johansson Kristoffer Enøe , Wang Yong , Wahni Khadija , Young David , Messens Joris , Teilum Kaare , Lindorff-Larsen Kresten , Winther Jakob Rahr 
Published: June 2020

ABSTRACTInteractions between charged residues are difficult to study because of the complex network of interactions found in most proteins. We have designed a purposely simple system to investigate this problem by systematically introducing individual and pairs of charged and titratable residues in a protein otherwise free of such residues. We used constant pH molecular dynamics simulations, NMR spectroscopy, and thermodynamic double mutant cycles to probe the structure and energetics of the interaction between the charged residues. We found that the partial burial of surface charges contributes to a shift in pKavalue, causing an aspartate to titrate in the neutral pH range. Additionally, the interaction between pairs of residues was found to be highly context dependent, with some pairs having no apparent preferential interaction, while other pairs would engage in coupled titration forming a highly stabilized salt bridge. We find good agreement between experiments and simulations, and use the simulations to rationalize our observations and to provide a detailed mechanistic understanding of the electrostatic interactions.SignificanceElectrostatic forces are important for protein folding and are favored targets of protein engineering. However, despite the many advances in the field of protein electrostatics, the prediction of changes in protein structure and function upon introduction or removal of titratable residues is still complicated. In order to provide a basic understanding of protein electrostatics we here characterize a highly charge-depleted protein and its titratable variants by a combination of NMR spectroscopy and constant pH molecular dynamics simulations. Our investigations reveal how strongly interacting residues engaged in salt bridging, can be characterized. Furthermore, our study may also enrich and facilitate the understanding of dehydration of salt-bridges and its potential effect on protein stability.
Illuminating a Phytochrome Paradigm – a Light-Activated Phosphatase in Two-Component Signaling Uncovered
Authors: Multamäki Elina , Nanekar Rahul , Morozov Dmitry , Lievonen Topias , Golonka David , Yuan Wahlgren Weixiao , Stucki-Buchli Brigitte , Rossi Jari , Hytönen Vesa P. , Westenhoff Sebastian , Ihalainen Janne A. , Möglich Andreas , Takala Heikki 
Published: June 2020

ABSTRACTBacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome fromDeinococcus radiodurans(DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome fromAgrobacterium fabrum(AgP1). Whereas AgP1 acts as a conventional histidine kinase, we identify DrBphP as a light-sensitive phosphatase. While AgP1 binds its cognate response regulator only transiently, DrBphP does so strongly, which is rationalized at the structural level. Our data pinpoint two key residues affecting the balance between kinase and phosphatase activities, which immediately bears on photoreception and two-component signaling. The opposing output activities in two highly similar bacteriophytochromes inform the use of light-controllable histidine kinases and phosphatases for optogenetics.
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges
Authors: Turoňová Beata , Sikora Mateusz , Schürmann Christoph , Hagen Wim J. H. , Welsch Sonja , Blanc Florian E. C. , von Bülow Sören , Gecht Michael , Bagola Katrin , Hörner Cindy , van Zandbergen Ger , Mosalaganti Shyamal , Schwarz Andre , Covino Roberto , Mühlebach Michael D. , Hummer Gerhard , Locker Jacomine Krijnse , Beck Martin 
Published: June 2020

AbstractThe spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the major focus for vaccine development. We combine cryo electron tomography, subtomogram averaging and molecular dynamics simulations to structurally analyze Sin situ. Compared to recombinant S, the viral S is more heavily glycosylated and occurs predominantly in a closed pre-fusion conformation. We show that the stalk domain of S contains three hinges that give the globular domain unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and the development of safe vaccines. The large scale tomography data set of SARS-CoV-2 used for this study is therefore sufficient to resolve structural features to below 5 Ångstrom, and is publicly available at EMPIAR-10453.
Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p
Authors: Tong Yaojun , Sun Nuo , Wang Xiangming , Wei Qi , Zhang Yu , Huang Ren , Pu Yingying , Dai Huanqin , Ren Biao , Pei Gang , Song Fuhang , Zhu Guoliang , Wang Xinye , Xia Xuekui , Chen Xiangyin , Jiang Lan , Zhang Jingyu , Ouyang Liming , Zhang Buchang , Jiang Yuanying , Liu Xueting , Calderone Richard , Bai Fan , Zhang Lixin , Alterovitz Gil 
Published: June 2020

AbstractClinical use of antimicrobials faces great challenges from the emergence of multidrug resistant (MDR) pathogens. The overexpression of drug efflux pumps is one of the major contributors to MDR. It is considered as a promising approach to overcome MDR by reversing the function of drug efflux pumps. In the life-threatening fungal pathogenCandida albicans, the major facilitator superfamily (MFS) transporter Mdr1p can excrete many structurally unrelated antifungals, leading to multidrug resistance. Here we report a counterintuitive case of reversing multidrug resistance inC. albicansby using a natural product berberine to hijack the overexpressed Mdr1p for its own importation. Moreover, we illustrate that the imported berberine accumulates in mitochondria, and compromises the mitochondrial function by impairing mitochondrial membrane potential and mitochondrial Complex I. It results in the selective elimination of Mdr1p overexpressedC. albicanscells. Furthermore, we show that berberine treatment can prolong the mean survival time (MST) of mice with a blood-borne dissemination of Mdr1p overexpressed multidrug resistant candidiasis. This study provided a potential direction of novel anti-MDR drug discovery by screening for multidrug efflux pump converters.
Requirement for PKC Epsilon in Kras-Driven Lung Tumorigenesis
Authors: Garg Rachana , Cooke Mariana , Wang Shaofei , Benavides Fernando , Abba Martin C. , Cicchini Michelle , Feldser David M. , Kazanietz Marcelo G. 
Published: June 2020

ABSTRACTNon-small cell lung cancer (NSCLC), the most frequent subtype of lung cancer, remains a highly lethal malignancy and one of the leading causes of cancer deaths worldwide. Mutant KRAS is the prevailing oncogenic driver of lung adenocarcinoma, the most common histological form of NSCLC. In this study, we examined the role of PKCε, an oncogenic kinase highly expressed in NSCLC and other cancers, in KRAS-driven tumorigenesis. Notably, database analysis revealed an association between PKCε expression and poor outcome in lung adenocarcinoma patients specifically having KRAS mutation. By generating a PKCε-deficient, conditionally activatable allele of oncogenicKras(LSL-KrasG12D;PKCε−/−mice) we were able to demonstrate the requirement of PKCε forKras-driven lung tumorigenesisin vivo, which is consistent with the impaired transformed growth observed in PKCε-deficient KRAS-dependent NSCLC cells. Moreover, PKCε-knockout mice were found to be less susceptible to lung tumorigenesis induced by benzo[a]pyrene, a carcinogen that induces mutations inKras. Mechanistic analysis using RNA-Seq revealed little overlapping for PKCε and KRAS in the control of genes/biological pathways relevant in NSCLC, suggesting that a permissive role of PKCε inKRAS-driven lung tumorigenesis may involve non-redundant mechanisms. Our results thus highlight the relevance and potential of targeting PKCε for lung cancer therapeutics.
Modification of cell wall polysaccharide spatially controls cell division inStreptococcus mutans
Authors: Zamakhaeva Svetlana , Chaton Catherine T. , Rush Jeffrey S. , Castro Sowmya Ajay , Yarawsky Alexander E. , Herr Andrew B. , van Sorge Nina M. , Dorfmueller Helge C. , Frolenkov Gregory I. , Korotkov Konstantin V. , Korotkova Natalia 
Published: June 2020

AbstractBacterial cell division is driven by a tubulin homolog FtsZ, which assembles into the Z-ring structure leading to the recruitment of the cell division machinery. In ovoid-shaped Gram-positive bacteria, such as streptococci, MapZ guides Z-ring positioning at cell equators through an, as yet, unknown mechanism. The cell wall of the important dental pathogenStreptococcus mutansis composed of peptidoglycan decorated with SerotypecCarbohydrates (SCCs). Here, we show that an immature form of SCC, lacking the recently identified glycerol phosphate (GroP) modification, coordinates Z-ring positioning. Pulldown assays usingS. mutanscell wall combined with binding affinity analysis identified the major cell separation autolysin, AtlA, as an SCC binding protein. Importantly, AtlA binding to mature SCC is attenuated due to GroP modification. Using fluorescently-labeled AtlA, we mapped SCC distribution on the streptococcal surface to reveal that GroP-deficient immature SCCs are exclusively present at the cell poles and equators. Moreover, the equatorial GroP-deficient SCCs co-localize with MapZ throughout theS. mutanscell cycle. Consequently, in GroP-deficient mutant bacteria, proper AtlA localization is abrogated resulting in dysregulated cellular autolysis. In addition, these mutants display morphological abnormalities associated with MapZ mislocalization leading to Z-ring misplacement. Altogether, our data support a model in which GroP-deficient immature SCCs spatially coordinate the localization of AtlA and MapZ. This mechanism ensures cell separation by AtlA at poles and Z-ring alignment with the cell equator.Graphical abstract
The structure and diversity of strain level variation in vaginal bacteria
Authors: Tortelli Brett A. , Lewis Amanda L. , Fay Justin C. 
Published: June 2020

AbstractThe vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core-genomes for six species of vaginal bacteria:G. vaginalis,L. crispatus,L. iners,L. jensenii,L. gasseri, andA. vaginae. Despite inhabiting the same environment, strain diversity and structure varies across species. All species exceptL. inersare characterized by multiple distinct groups of strains. Even so, strain diversity is lower in theLactobacillusspecies, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain level variation provides both the motivation and means of testing whether strain level differences contribute to the function and health consequences of the vaginal microbiome.Data SummaryAll vaginal metagenomic sequence data generated for this project can be found on the Sequence Read Archive under BioProject PRJNA639592.
Phantom histories of misspecified pasts
Authors: Platt Alexander , Harris Daniel N. 
Published: June 2020

AbstractThe observation that even a tiny sample of genome sequences from a natural population contains a plethora of information about the history of the population has enticed researchers to use these data to fit complex demographic histories and make detailed inference about the changes a population has experienced through time. Unfortunately, the standard assumptions required to make these inferences are often violated by natural populations in such ways as to produce specious results. This paper examines two phenomena of particular concern: when a sample is drawn from a single sub-population of a larger meta-population these models infer a spurious recent population decline, and when a genome contains loci under weak or recessive purifying selection these models infer a spurious recent population expansion.
Non-canonical activation of the ER stress sensor ATF6 byLegionella pneumophilaeffectors
Authors: Ibe Nnejiuwa U. , Mukherjee Shaeri 
Published: June 2020

AbstractThe intracellular bacterial pathogenLegionella pneumophila(L.p.) secretes ~330 effector proteins into the host cell to sculpt an Endoplasmic Reticulum (ER)-derived replicative niche. We previously reported fiveL.p.effectors that inhibit IRE1, a key sensor of the homeostatic unfolded protein response (UPR) pathway. In this study, we discovered a subset ofL.p.toxins that selectively activate the UPR sensor ATF6, resulting in its cleavage, nuclear translocation and target gene transcription without affecting other UPR sensors such as PERK. In a deviation from the conventional model, thisL.p. dependent activation of ATF6 does not require its transport to the Golgi or its cleavage by the S1P/S2P proteases. We believe that our findings highlight the unique regulatory control thatL.p. exerts upon the three UPR sensors and expand the repertoire of bacterial proteins that selectively perturb host homeostatic pathways.
A cytosine-to-uracil change within the programmed -1 ribosomal frameshift signal of SARS-CoV-2 results in structural similarities with the MERS-CoV signal
Authors: Fourmy Dominique , Yoshizawa Satoko 
Published: June 2020

ABSTRACTThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the ongoing COVID-19 pandemic, like many other viruses, uses programmed ribosomal frameshifting (PRF) to enable synthesis of multiple proteins from its compact genome. In independent analyses, we evaluated the PRF regions of all SARS-CoV-2 sequences available in GenBank and from the Global Initiative on Sharing All Influenza Data for variations. Of the 5,156 and 27,153 sequences analyzed, respectively, the PRF regions were identical in 95.7% and 97.2% of isolates. The most common change from the reference sequence was from C to U at position 13,536, which lies in the three-stemmed pseudoknot known to stimulate frameshifting. With the conversion of the G13493-C13536Watson-Crick pair to G-U, the SARS-CoV-2 PRF closely resembles its counterpart in the Middle East respiratory syndrome coronavirus. The occurrence of this change increased from 0.5 to 3% during the period of March to May 2020.
Insights into the successful breeding of Hawksbill sea turtles (Eretmochelys imbricata) from a long-term captive breeding program
Authors: Maggeni Ruth , Feeney William E 
Published: June 2020

AbstractSea turtle populations are declining and evidence-based methods for supporting their populations are required. Captive breeding and release programs can be effective, offering the opportunity to supplement nature populations; however, sea turtles require specific conditions to successfully breed. Here, we present insights gained from a 16 year Hawksbill sea turtle (Eretmochelys imbricata) captive breeding program that was conducted at the Underwater Observatory Marine Park, Eilat, Israel, between 1982-1997. As the first program of its kind for the Hawksbill sea turtle, insights were gained largely through trial-and-error and word of mouth advice. The key insight gained during this program was the critical importance of pre-breeding separation of the sexes; turtles did not breed prior to pre-breeding separation being implemented, but it became predictably regular once it was. Over the course of the program, 161 two-three years old hatchlings were introduced to the Red Sea, which was enabled largely as a result of pre-breeding separation being implemented.