bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trophectoderm differentiation to invasive syncytiotrophoblast is induced by endometrial epithelial cells during human embryo implantation
Authors: Ruane Peter T , Garner Terence , Parsons Lydia , Babbington Phoebe A , Kimber Susan J , Stevens Adam , Westwood Melissa , Brison Daniel R , Aplin John D 
Published: October 2020

AbstractAt implantation, trophoblast derived from the trophectoderm of the blastocyst-stage embryo invades the endometrium to establish pregnancy. To understand how embryos breach the endometrial epithelium, we modelled human implantation using blastocysts or trophoblast stem cell spheroids cultured with endometrial epithelial cells (EEC). Blastocyst invasion of the EEC layer was initiated by multinuclear syncytiotrophoblast. Spheroids also invaded the epithelium with syncytiotrophoblast, and EEC induced upregulation of syncytiotrophoblast markers. Modelling implantation in silico using blastocyst and EEC transcriptomes revealed gene networks that exhibited greater connectivity and organisation in trophectoderm of the polar region of the embryonic axis. However, gene ontologies and machine learning suggested that EEC drives syncytiotrophoblast differentiation in polar and mural trophectoderm. This is the first evidence for endometrial epithelium-induced trophectoderm differentiation to invasive syncytiotrophoblast as the cellular mechanism of embryonic breaching of the endometrium in humans, with implications for reproductive medicine and our understanding of human embryonic development.
Structural basis for recruitment of the CHK1 DNA damage kinase by the CLASPIN scaffold protein
Authors: Day Matthew , Morris Sarah P. , Houghton-Gisby Jack , Oliver Antony W. , Pearl Laurence H. 
Published: October 2020

ABSTRACTCHK1 is a protein kinase that functions downstream of activated ATR to phosphorylate multiple targets as part of intra-S and G2/M DNA damage checkpoints. Its role in allowing cells to survive replicative stress has made it an important target for anti-cancer drug discovery. Activation of CHK1 by ATR depends on their mutual interaction with CLASPIN – a natively unstructured protein that interacts with CHK1 through a cluster of phosphorylation sites in its C-terminal half. We have now determined the crystal structure of the kinase domain of CHK1 bound to a high-affinity motif from CLASPIN. Our data show that CLASPIN engages a conserved site on CHK1 adjacent to the substrate-binding cleft, involved in phosphate sensing in other kinases. The CLASPIN motif is not phosphorylated by CHK1, nor does it affect phosphorylation of a CDC25 substrate peptide, suggesting that it functions purely as a scaffold for CHK1 activation by ATR.
Human hypertrophic cardiomyopathy mutation R712L suppresses the working stroke of cardiac myosin and can be rescued by omecamtiv mecarbil
Authors: Snoberger Aaron , Barua Bipasha , Atherton Jennifer L. , Shuman Henry , Forgacs Eva , Goldman Yale E. , Winkelmann Donald A. , Ostap E. Michael 
Published: October 2020

AbstractHypertrophic cardiomyopathies (HCMs) are the leading cause of acute cardiac failure in young individuals. Over 300 mutations throughout β-cardiac myosin, including in the motor domain, are associated with HCM. A β-cardiac myosin motor mutation (R712L) leads to a severe form of HCM. Actin-gliding motility of R712L-myosin is inhibited, despite near normal ATPase kinetics. By optical trapping, the working stroke of R712L-myosin was decreased 4-fold, but actin-attachment durations were normal. A prevalent hypothesis that HCM mutants are hypercontractile is thus not universal. R712 is adjacent to the binding site of the heart failure drug omecamtiv mecarbil (OM). OM suppresses the working stroke of normal β-cardiac myosin, but remarkably, OM rescues the R712L-myosin working stroke. Using a flow chamber to interrogate a single molecule during buffer exchange, we found OM rescue to be reversible. Thus, the R712L mutation uncouples lever arm rotation from ATPase activity and this inhibition is rescued by OM.
Fine scale sampling unveils diazotroph patchiness in the South Pacific Ocean
Authors: Benavides Mar , Conradt Louis , Bonnet Sophie , Berman-Frank Ilana , Barrillon Stéphanie , Petrenko Anne , Doglioli Andrea M. 
Published: October 2020

AbstractDiazotrophs are important contributors to reactive nitrogen availability in the ocean. Oceanographic cruise data accumulated along decades has revealed a heterogeneous distribution of diazotroph species at regional to global scales. However, the role of dynamic fine scale structures in distributing diazotrophs is not well understood. This is due to typical insufficient spatiotemporal resolution sampling and the lack of detailed physical studies in parallel. Here we show the distribution of five groups of diazotrophs in the South Pacific at an unprecedented resolution of 7-16 km. We find a patchy distribution of diazotrophs, with each group being differently affected by parameters describing fine scale structures. The observed variability could not have been revealed with a lower resolution sampling, highlighting the need to consider fine scale physics to resolve the distribution of diazotrophs in the ocean.
Abstract neural choice signals during action-linked decisions
Authors: Sandhaeger Florian , Omejc Nina , Pape Anna-Antonia , Siegel Markus 
Published: October 2020

AbstractHumans can make abstract choices independent of motor actions. However, in laboratory tasks, choices are typically reported with an associated action. Consequentially, knowledge about the neural representation of abstract choices is sparse, and choices are often thought to evolve as motor intentions. Here, we show that in the human brain, perceptual choices are represented in an abstract, motor-independent manner, even when they are directly linked to an action. We measured MEG signals while participants made choices with known or unknown motor response mapping. Using multivariate decoding, we quantified stimulus, perceptual choice and motor response information with distinct cortical distributions. Choice representations were invariant to whether the response mapping was known during stimulus presentation, and they occupied distinct representational spaces from both stimulus and motor signals. Furthermore, their strength predicted decision confidence and accuracy, as expected from an internal decision variable. Our results uncover abstract neural choice signals that generalize to action-linked decisions, suggesting a general role of an abstract choice stage in human decision-making.
LRRK2-dependent Rab GTPase phosphorylation in response to endolysosomal damage depends on macrophage differentiation
Authors: Herbst Susanne , Gutierrez Maximiliano G. 
Published: October 2020

AbstractThe Parkinson’s Disease (PD) kinase LRRK2 is highly expressed in immune cells such as macrophages. In these cells, LRRK2 regulates innate immune pathways and it is activated after membrane damage leading to the phosphorylation of the Rab GTPases Rab8A and Rab10. Due to their wide-range of functions in immunity and tissue remodelling, macrophagesin vivoare phenotypically heterogeneous.In vitrosystems are used to differentiate these cells into diverse macrophage subsets to mimic the populations observedin vivo. M-CSF and GM-CSF differentiated human blood monocytes are often used to generate monocyte-derived macrophages as a model for tissue macrophages. However, how LRRK2 is activated in different macrophage subsets after membrane damage is unknown.Here, we report that bone marrow derived macrophages and human monocyte-derived macrophages differentiated with either M-CSF or GM-CSF show different levels of LRRK2 activation after membrane damage. Notably, the membrane damaging agent LLOMe triggered LRRK2-dependent Rab8A and Rab10 phosphorylation primarily in GM-CSF differentiated macrophages. Moreover, LRRK2 and Rab8A were recruited to damaged endolysosomes in GM-CSF differentiated macrophages. Strikingly, GM-CSF differentiated macrophages recruited significantly more CHMP4B and Galectin-3 into damaged endolysosomes. These results suggest that LRRK2-regulated pathways of endolysosomal membrane damage and repair differ between macrophage subsets.
A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion
Authors: Yu Alvin , Pak Alexander J. , He Peng , Monje-Galvan Viviana , Casalino Lorenzo , Gaieb Zied , Dommer Abigail C. , Amaro Rommie E. , Voth Gregory A. 
Published: October 2020

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely “bottom-up” coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.Significance StatementThis study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions.
The TRIM9/TRIM67 neuronal interactome reveals novel activators of morphogenesis
Authors: Menon Shalini , Goldfarb Dennis , Ho Tsungyo , Cloer Erica W. , Boyer Nicholas P. , Hardie Christopher , Bock Andrew J. , Johnson Emma C. , Anil Joel , Major M. Ben , Gupton Stephanie L. 
Published: October 2020

ABSTRACTTRIM9 and TRIM67 are neuronally-enriched E3 ubiquitin ligases essential for appropriate morphogenesis of cortical and hippocampal neurons and fidelitous responses to the axon guidance cue netrin-1. Deletion of murineTrim9orTrim67results in neuroanatomical defects and striking behavioral deficits, particularly in spatial learning and memory. TRIM9 and TRIM67 interact with cytoskeletal and exocytic proteins, but the full interactome is not known. Here we performed the unbiased proximity-dependent biotin identification (BioID) approach to define TRIM9 and TRIM67 protein-protein proximity network in developing cortical neurons and identified neuronal putative TRIM interaction partners. Candidates included cytoskeletal regulators, cytosolic protein transporters, exocytosis and endocytosis regulators, and proteins necessary for synaptic regulation. A subset of high priority candidates was validated, including Myo16, Coro1A, SNAP47, ExoC1, GRIP1, PRG-1, and KIF1A. For a subset of validated candidates, we utilized TIRF microscopy to demonstrate dynamic colocalization with TRIM proteins at the axonal periphery, including at the tips of filopodia. Further analysis demonstrated the RNAi-based knockdown of the unconventional myosin Myo16 in cortical neurons altered axonal branching patterns in a TRIM9 and netrin-1 dependent manner. Future analysis of other validated candidates will likely identify novel proteins and mechanisms by which TRIM9 and TRIM67 regulate neuronal form and function.
Accurate Microbiome Sequencing with Synthetic Long Read Sequencing
Authors: Chung Nico , Van Goethem Marc W. , Preston Melanie A. , Lhota Filip , Cerna Leona , Garcia-Pichel Ferran , Fernandes Vanessa , Giraldo-Silva Ana , Kim Hee Shin , Hurowitz Evan , Balamotis Michael , Wu Indira , Ben-Yehezkel Tuval 
Published: October 2020

AbstractThe microbiome plays a central role in biochemical cycling and nutrient turnover of most ecosystems. Because it can comprise myriad microbial prokaryotes, eukaryotes and viruses, microbiome characterization requires high-throughput sequencing to attain an accurate identification and quantification of such co-existing microbial populations. Short-read next-generation-sequencing (srNGS) revolutionized the study of microbiomes and remains the most widely used approach, yet read lengths spanning only a few of the nine hypervariable regions of the 16S rRNA gene limit phylogenetic resolution leading to misclassification or failure to classify in a high percentage of cases. Here we evaluate a synthetic long-read (SLR) NGS approach for full-length 16S rRNA gene sequencing that is high-throughput, highly accurate and low-cost. The sequencing approach is amenable to highly multiplexed sequencing and provides microbiome sequence data that surpasses existing short and long-read modalities in terms of accuracy and phylogenetic resolution. We validated this commercially-available technology, termed LoopSeq, by characterizing the microbial composition of well-established mock microbiome communities and diverse real-world samples. SLR sequencing revealed differences in aquatic community complexity associated with environmental gradients, resolved species-level community composition of uterine lavage from subjects with histories of misconception and accurately detected strain differences, multiple copies of the 16S rRNA in a single strain’s genome, as well as low-level contamination in soil cyanobacterial cultures. This approach has implications for widespread adoption of high-resolution, accurate long-read microbiome sequencing as it is generated on popular short read sequencing platforms without the need for additional infrastructure.
Safe and effective two-in-one replicon-and-VLP minispike vaccine for COVID-19
Authors: Hennrich Alexandru A. , Banda Dominic H. , Oberhuber Martina , Schopf Anika , Pfaffinger Verena , Wittwer Kevin , Sawatsky Bevan , Riedel Christiane , Pfaller Christian K. , Conzelmann Karl-Klaus 
Published: October 2020

SummaryThe large SARS-CoV-2 spike (S) protein is the main target of current COVID-19 vaccine candidates but can induce non-neutralizing antibodies, which may cause vaccination-induced complications or enhancement of COVID-19 disease. Besides, encoding of a functional S in replication-competent virus vector vaccines may result in the emergence of viruses with altered or expanded tropism. Here, we have developed a safe single round rhabdovirus replicon vaccine platform for enhanced presentation of the S receptor-binding domain (RBD). Structure-guided design was employed to build a chimeric minispike comprising the globular RBD linked to a transmembrane stem-anchor sequence derived from rabies virus (RABV) glycoprotein (G). Vesicular stomatitis virus (VSV) and RABV replicons encoding the minispike not only allowed expression of the antigen at the cell surface but also incorporation into the envelope of secreted non-infectious particles, thus combining classic vector-driven antigen expression and particulate virus-like particle (VLP) presentation. A single dose of a prototype replicon vaccine, VSVΔG-minispike-eGFP (G), stimulated high titers of SARS-CoV-2 neutralizing antibodies in mice, equivalent to those found in COVID-19 patients. Boost immunization with the identical replicon further enhanced neutralizing activity. These results demonstrate that rhabdovirus minispike replicons represent effective and safe alternatives to vaccination approaches using replication-competent viruses and/or the entire S antigen.HighlightsSARS-CoV-2 S RBD antigen is preferred over entire S to preclude potential disease enhancing antibodiesconstruction of a chimeric rhabdovirus minispike protein presenting RBD in native conformationconstruction of single round VSV and rabies virus replicon vaccinespresentation of minispike antigen on cells and on noninfectious VLPsstrong induction of SARS-CoV-2 neutralizing antibodies by the VSV replicon/VLP system in vaccinated mice
A Generative Approach toward Precision Antimicrobial Peptide Design
Authors: Ferrell Jonathon B. , Remington Jacob M. , Van Oort Colin M. , Sharafi Mona , Aboushousha Reem , Janssen-Heininger Yvonne , Schneebeli Severin T. , Wargo Matthew J. , Wshah Safwan , Li Jianing 
Published: October 2020

AbstractAs the emergence of bacterial resistance is outpacing the development of new antibiotics, we must find cost-effective and innovative approaches to discover new antibacterial therapeutics. Antimicrobial peptides (AMPs) represent one promising solution to fill this void, since they generally undergo faster development, display rapid onsets of killing, and most importantly, show lower risks of induced resistance. Despite prior success in AMP design with physics- and/or knowledge-based approaches, an efficient approach to precisely design peptides with high activity and selectivity is still lacking. Toward this goal, we have invented a novel approach which utilizes a generative model to predict AMP-like sequences, followed by molecular modeling to rank the candidates. Thus, we can identify peptides with desirable sequences, structures, and potential specific interactions with bacterial membranes. For the proof of concept, we curated a dataset that comprises 500,000 non-AMP peptide sequences and nearly 8,000 labeled AMP sequences to train the generative model. For 12 generated peptides that are cationic and likely helical, we assessed the membrane binding propensity via extensive all-atom molecular simulations. The top six peptides were promoted for synthesis, chemical characterizations, and antibacterial assays, showing various inhibition to bacterial growth. Three peptides were validated with broad-spectrum antibacterial activity. In aggregate, the combination of AMP generator and sophisticated molecular modeling affords enhanced speed and accuracy in AMP design. Our approach and results demonstrate the viability of a generative approach to develop novel AMPs and to help contain the rise of antibiotic resistant microbes.
SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs
Authors: Weingarten-Gabbay Shira , Klaeger Susan , Sarkizova Siranush , Pearlman Leah R. , Chen Da-Yuan , Bauer Matthew R. , Taylor Hannah B. , Conway Hasahn L. , Tomkins-Tinch Christopher H. , Finkel Yaara , Nachshon Aharon , Gentili Matteo , Rivera Keith D. , Keskin Derin B. , Rice Charles M. , Clauser Karl R. , Hacohen Nir , Carr Steven A. , Abelin Jennifer G. , Saeed Mohsan , Sabeti Pardis C. 
Published: October 2020

ABSTRACTT cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class I human leukocyte antigen (HLA-I) can reveal epitopes for recognition by cytotoxic T cells and potential incorporation into vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not captured by current vaccines. Proteomics analyses of infected cells revealed that SARS-CoV-2 may interfere with antigen processing and immune signaling pathways. Based on the endogenously processed and presented viral peptides that we identified, we estimate that a pool of 24 peptides would provide one or more peptides for presentation by at least one HLA allele in 99% of the human population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.
Heat Stress Interferes with Formation of Double-Strand Breaks and Homolog Synapsis inArabidopsis thaliana
Authors: Ning Yingjie , Liu Qingpei , Wang Chong , Qin Erdai , Wu Zhihua , Wang Minghui , Yang Ke , Elesawi Ibrahim Eid , Chen Chunli , Liu Hong , Qin Rui , Liu Bing 
Published: October 2020

AbstractMeiotic recombination (MR) drives novel combination of alleles and contributes to genomic diversity in eukaryotes. In this study, we showed that heat stress (36-38°C) over fertile threshold fully abolished crossover (CO) formation in Arabidopsis. Cytological and genetic studies in wild-type plants, and thesyn1andrad51mutants suggested that heat stress reduces generation of SPO11-dependent double-strand breaks (DSBs). In support, the abundance of recombinase DMC1, which is required for MR-specific DSB repair, was significantly reduced under heat stress. In addition, we showed that high temperatures induced disassembly and/or instability of ASY4-but not SYN1-mediated chromosome axis. At the same time, ASY1-associated lateral element of synaptonemal complex (SC) was partially affected, while the ZYP1-dependent central element of SC was disrupted, indicating that heat stress impairs SC formation. Moreover, quantitative RT-PCR revealed that genes involved in DSB formation; e.g.SPO11-1,PRD1,2and3, were not impacted; however, recombinaseRAD51and chromosome axis factorsASY3andASY4were significantly downregulated under heat stress. Taken together, these findings revealed that heat stress inhibits MR via compromised DSB formation and homolog synapsis, which are possible downstream effects of the impacted chromosome axis. Our study thus provides evidence shedding light on how increase of environmental temperature influences MR in Arabidopsis.
Genome-Wide CRISPR Screen Identifies Non-Canonical NF-κB Signaling as a Potent Regulator of Density-dependent Proliferation
Authors: Fomicheva Maria , Macara Ian G. 
Published: October 2020

ABSTRACTEpithelial cells possess intrinsic mechanisms to maintain an appropriate cell density for normal tissue morphogenesis and homeostasis. Defects in such mechanisms likely contribute to hyperplasia and cancer initiation. To identify genes that regulate the density-dependent proliferation of murine mammary epithelial cells, we developed a fluorescence-activated cell sorting assay based on FUCCI, which marks different stages of the cell cycle with distinct fluorophores. Using this powerful assay, we performed a genome-wide CRISPR/Cas9 knockout screen, selecting for cells that proliferate normally at low density but continue to divide at high density. Unexpectedly, one top hit wasTraf3, a negative regulator of NF-κB signaling that has never previously been linked to density-dependent proliferation. We demonstrate that loss ofTraf3specifically activates non-canonical NF-κB signaling. This in turn triggers an innate immune response and drives cell division independently of known density-dependent proliferation mechanisms, including YAP/TAZ signaling and cyclin kinase inhibitors, by blocking entry into quiescence.