bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 Entry Protein TMPRSS2 and Its Homologue, TMPRSS4 Adopts Structural Fold Similar to Blood Coagulation and Complement Pathway Related Proteins
Authors: Muley Vijaykumar Yogesh , Singh Amit , Gruber Karl , Varela-Echavarría Alfredo 
Published: April 2021

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes TMPRSS2 receptor to enter target human cells and subsequently causes coronavirus disease 19 (COVID-19). TMPRSS2 belongs to the type II serine proteases of subfamily TMPRSS, which is characterized by the presence of the serine-protease domain. TMPRSS4 is another TMPRSS member, which has a domain architecture similar to TMPRSS2. TMPRSS2 and TMPRSS4 have been shown to be involved in SARS-CoV-2 infection. However, their normal physiological roles have not been explored in detail. In this study, we analyzed the amino acid sequences and predicted 3D structures of TMPRSS2 and TMPRSS4 to understand their functional aspects at the protein domain level. Our results suggest that these proteins are likely to have common functions based on their conserved domain organization. Furthermore, we show that the predicted 3D structure of their serine protease domain has significant similarity to that of plasminogen which dissolves blood clot, and of other blood coagulation related proteins. Additionally, molecular docking analyses of inhibitors of four blood coagulation and anticoagulation factors show the same high specificity to TMPRSS2 and TMPRSS4 3D structures. Hence, our observations are consistent with the blood coagulopathy observed in COVID-19 patients and their predicted functions based on the sequence and structural analyses offer avenues to understand better and explore therapeutic approaches for this disease.
Sequential single cell transcriptional and protein marker profiling reveals TIGIT as a marker of CD19 CAR-T cell dysfunction in patients with non-Hodgkin’s lymphoma
Authors: Jackson Zachary , Hong Changjin , Schauner Robert , Dropulic Boro , Caimi Paolo F. , de Lima Marcos , Gupta Kalpana , Reese Jane S. , Hwang Tae Hyun , Wald David N. 
Published: April 2021

AbstractChimeric antigen receptor T cell (CAR-T cell) therapy is known to produce durable remissions in the treatment of CD19+relapsed/refractory B cell malignancies. Nonetheless, a significant portion of patients receiving the therapy experience poor outcomes in the acute response for unknown reasons. Given the decreased expansion and persistence of CD8 CAR-T cells in poor outcome groups, this failure may be attributed to CAR-T cell dysfunction. However, a comparison of the post-infusion transcriptional profiles and phenotypes between CAR-T cells of poor and favorable response groups has not been performed. Here, we employed single cell RNA sequencing and protein surface marker profiling of serial CAR-T cell blood samples from patients with CD19+relapsed/refractory non-Hodgkin’s lymphoma (NHL) to reveal CAR-T cell evolution, identify biomarkers of response, and test for evidence of exhaustion in CAR-T cells of poor responders. At the transcriptional and protein levels, we note the evolution of a majority of CAR-T cells toward a non-proliferative and highly-differentiated state. In poor outcome patients, we observed a more marked enrichment of an exhaustion profile as compared to favorable outcome patients. Lastly, we identified the checkpoint receptor TIGIT (T cell immunoreceptor with Ig and ITIM domains) as a novel prognostic biomarker and potential driver of CAR-T cell exhaustion. Altogether, we provide evidence of CAR-T cell dysfunction marked by TIGIT expression driving poor response in NHL patients.
Subcellular Organization of Viral Particles During Maturation of Nucleus-Forming Jumbo Phage
Authors: Chaikeeratisak Vorrapon , Khanna Kanika , Nguyen Katrina T. , Egan MacKennon E. , Enustun Eray , Armbruster Emily , Pogliano Kit , Villa Elizabeth , Pogliano Joe 
Published: April 2021

SummaryMany eukaryotic viruses assemble mature particles within distinct subcellular compartments, but bacteriophages were long assumed to assemble randomly throughout the host cell cytoplasm. Here we visualized the subcellular location of viral particles formed during replication ofPseudomonasnucleus-forming jumbo phages and discovered that they assemble a unique structure inside cells we term phage bouquets. We show that after capsids complete DNA packaging at the surface of the phage nucleus, tails assemble and attach to the capsids, and these particles accumulate to form bouquets at specific subcellular locations. In these bouquets, the viral particles are arranged in a spherical pattern with tails oriented inward and the heads outwards. Localized at fixed distances on either side of the phage nucleus, bouquets grow in size and number over time as new phage particles are added. In the presence of mutations that cause the phage nucleus to be mispositioned away from its typical position at the midcell, bouquets still localize at the same fixed distance from the nucleus, suggesting an active mechanism for their formation and positioning. These results mark the discovery of a pathway for organizing mature viral particles inside bacteria and demonstrate that nucleus-forming jumbo phage, like most eukaryotic viruses, are highly spatially organized during all stages of their lytic cycle.
Mathematical model of the multi-amino acid multi-transporter system predicts uptake flux in CHO cells
Authors: Sreejan Ashley , Gadgil Mugdha , Gadgil Chetan J. 
Published: April 2021

AbstractChinese hamster ovary (CHO) cells express several amino acid (AA) transporters including uniporters and exchangers. Each transporter transports multiple AAs, making prediction of the effect of changed medium composition or transporter levels on individual AA transport rate challenging. A general kinetic model and a simplified analytical expression for the uptake rate is presented. A CHO cell-specific AA transport model, to our knowledge the first such network model for any cell type, is constructed. The model is validated by its prediction of reported uptake flux and amino acid inter-dependencies from experiments that were not used in model construction or parameter estimation. The model defines theoretical conditions for synergistic/repressive effect on the uptake rates of other AAs upon external addition of one AA. This model will help formulate testable hypotheses of the effect of process changes on AA initial uptake, and serve as the AA transport component of kinetic models for cellular metabolism.
Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages
Authors: Ullrich Sebastian , Arnan Carme , Pulido-Quetglas Carlos , Nurtdinov Ramil , Esteban Alexandre , Blanco-Fernandez Joan , Aparicio-Prat Estel , Johnson Rory , Pérez-Lluch Sílvia , Guigó Roderic 
Published: April 2021

ABSTRACTCRISPR-Cas9 screening libraries have arisen as a powerful tool to identify both protein coding (pc) and non-coding genes playing a role along different processes. In particular, the usage of a nuclease active Cas9 coupled to a single gRNA has proven to efficiently impair the expression of pc-genes by generating deleterious frameshifts. Here, we first demonstrate that the usage of a second gRNA targeting the same gene synergistically enhances the capacity of the CRISPR-Cas9 system to knock out pc-genes. We next take advantage of our paired-guide (pgRNA) system to design a library to simultaneously target 874 pc-genes and 166 lncRNAs which are known to change expression during the transdifferentiation from pre-B cells to macrophages. We show that this system is able to identify known players in this process, and also predicts 26 potential novel ones, of which we select four for deeper characterization. Two of these,FURINandNFE2, code for proteins related to cell differentiation and macrophage function; the other two,LINC02432andMIR3945HG, are lncRNAs associated with cancerous and infectious diseases, respectively. The CRISPR-Cas9 coupled to pgRNAs system is, therefore, a suitable tool to target simultaneously pc-genes and lncRNAs for genomic perturbation assays.
JAFFAL: Detecting fusion genes with long read transcriptome sequencing
Authors: Davidson Nadia M. , Chen Ying , Sadras Teresa , Ryland Georgina L. , Blombery Piers , Ekert Paul G. , Göke Jonathan , Oshlack Alicia 
Published: April 2021

AbstractMassively parallel short read transcriptome sequencing has greatly expanded our knowledge of fusion genes which are drivers of tumor initiation and progression. In cancer, many fusions are also important diagnostic markers and targets for therapy. Long read transcriptome sequencing allows the full length of fusion transcripts to be discovered, however, this data has a high rate of errors and fusion finding algorithms designed for short reads do not work. While numerous fusion finding algorithms now exist for short read RNA sequencing data, there are few methods to detect fusions using third generation or long read sequencing data. Fusion finding in long read sequencing will allow the discovery of the full isoform structure of fusion genes.Here we present JAFFAL, a method to identify fusions from long-read transcriptome sequencing. We validated JAFFAL using simulation, cell line and patient data from Nanopore and PacBio. We show that fusions can be accurately detected in long read data with JAFFAL, providing better accuracy than other long read fusion finders and with similar performance as state-of-the-art methods applied to short read data. By comparing Nanopore transcriptome sequencing protocols we find that numerous chimeric molecules are generated during cDNA library preparation that are absent when RNA is sequenced directly. We demonstrate that JAFFAL enables fusions to be detected at the level of individual cells, when applied to long read single cell sequencing. Moreover, we demonstrate JAFFAL can identify fusions spanning three genes, highlighting the utility of long reads to characterise the transcriptional products of complex structural rearrangements with unprecedented resolution. JAFFAL is open source and available as part of the JAFFA package athttps://github.com/Oshlack/JAFFA/wiki.
Construction of a neural network energy function for protein physics
Authors: Yang Huan , Xiong Zhaoping , Zonta Francesco 
Published: April 2021

AbstractClassical potentials are widely used to describe protein physics, due to their simplicity and accuracy, but they are continuously challenged as real applications become more demanding with time. Deep neural networks could help generating alternative ways of describing protein physics. Here we propose an unsupervised learning method to derive a neural network energy function for proteins. The energy function is a probability density model learned from plenty of 3D local structures which have been extensively explored by evolution. We tested this model on a few applications (assessment of protein structures, protein dynamics and protein sequence design), showing that the neural network can correctly recognize patterns in protein structures. In other words, the neural network learned some aspects of protein physics from experimental data.
Neutrophil transit time and localization within the megakaryocyte define morphologically distinct forms of emperipolesis
Authors: Huang Frank Y. , Cunin Pierre , Radtke Felix A. , Grieshaber-Bouyer Ricardo , Nigrovic Peter A. 
Published: April 2021

AbstractIn emperipolesis, neutrophils transit through megakaryocytes, but it is unknown whether this interaction represents a single type of cell-in-cell interaction or a set of distinct processes. Using anin vitromodel of murine emperipolesis, we characterized neutrophils entering megakaryocytes using live-cell spinning disk microscopy and electron microscopy. Approximately half of neutrophils exited the megakaryocyte rapidly, typically in 10 minutes or less, displaying ameboid morphology as they passed through the host cell (fast emperipolesis). The remaining neutrophils assumed a sessile morphology, most remaining within the megakaryocyte for at least 60 minutes (slow emperipolesis). These neutrophils typically localized near the megakaryocyte nucleus. By ultrastructural assessment, all internalized neutrophils remained morphologically intact. Most neutrophils resided within emperisomes, but some could be visualized exiting the emperisome into the cell cytoplasm. Neutrophils in the cytoplasm assumed close contact with the platelet-forming demarcation membrane system or with the perinuclear endoplasmic reticulum, as confirmed by immunofluorescence microscopy. Together, these findings reveal that megakaryocyte emperipolesis reflects at least two processes, fast and slow emperipolesis, each with its own characteristic transit time, morphology, and intracellular localization, suggesting distinct functions.Key PointsNeutrophil passage through megakaryocytes, termed emperipolesis, diverges into fast and slow forms that differ in transit time, morphology, and intracellular localizationDuring emperipolesis, neutrophils can reside in vacuoles (emperisomes) or escape into the cell cytoplasm to assume positions near the megakaryocyte’s demarcation membrane system, endoplasmic reticulum, or nucleus.
Mitochondrial unfolded protein response transcription factor ATFS-1 increases resistance to exogenous stressors through upregulation of multiple stress response pathways
Authors: Soo Sonja K. , Traa Annika , Mistry Meeta , Van Raamsdonk Jeremy M. 
Published: April 2021

AbstractThe mitochondrial unfolded protein response (mitoUPR) is an evolutionarily conserved pathway that responds to various insults to the mitochondria through transcriptional changes that restore mitochondrial homeostasis in order to facilitate cell survival. Gene expression changes resulting from the activation of the mitoUPR are mediated by the transcription factor ATFS-1/ATF-5. To further define the mechanisms through which the mitoUPR protects the cell during mitochondrial dysfunction, we characterized the role of ATFS-1 in responding to organismal stress. We found that activation of ATFS-1 is sufficient to cause upregulation of genes involved in multiple stress response pathways, including the DAF-16-mediated stress response pathway, the SKN-1-mediated oxidative stress response pathway, the HIF-mediated hypoxia response pathway, the p38-mediated innate immune response pathway, and antioxidant genes. Moreover, ATFS-1 is required for the upregulation of stress response genes after exposure to exogenous stressors, especially oxidative stress and bacterial pathogens. Constitutive activation of ATFS-1 increases resistance to multiple acute exogenous stressors, while disruption ofatfs-1decreases stress resistance. Although ATFS-1-dependent genes are upregulated in multiple long-lived mutants, constitutive activation of ATFS-1 in wild-type animals results in decreased lifespan. Overall, our work demonstrates that ATFS-1 serves a vital role in organismal survival of acute stresses through its ability to activate multiple stress response pathways, but that chronic ATFS-1 activation is detrimental for longevity.
Partial resistance to HDAC inhibitors in FAPs of dystrophic muscles at late stages of disease is associated to epigenetic and transcriptional features of cellular senescence
Authors: Consalvi S. , Tucciarone L. , Macrì E. , De Bardi M. , Picozza M. , Salvatori I. , Renzini A. , Valente S. , Mai A. , Moresi V. , Puri P.L. 
Published: April 2021

AbstractPharmacological treatment of Duchenne Muscular Dystrophy (DMD) with histone deacetylase inhibitors (HDACi) is currently being tested in clinical trials. Pre-clinical studies performed in mdx mice - the mouse model of DMD - have shown that HDACi promote compensatory muscle regeneration, while inhibiting fibro-adipogenic degeneration, by targeting fibro-adipogenic progenitors (FAPs); however, these beneficial effects are restricted to early stages of disease progression. We show here that FAPs from late stage mdx mice exhibit epigenetic and transcriptional features of senescence that could not be fully reversed by HDACi. In particular, genome-wide increase in H3K9/14 acetylation at gene promoters of Senescence Associated Secretory Phenotype (SASP) genes was associated with their upregulation in late stage mdx FAPs. Treatment with the HDACi Trichostatin A (TSA) could inhibit SASP gene activation in FAPs, by decreasing H3K9/14 acetylation. Conversely, combinatorial decrease of H3K27 and/or H3K9/14 acetylation at promoters of genes required for cycle activation and progression was associated with their downregulation in FAPs from late stage mdx mice. However, these epigenetic and transcriptional alterations could not be reversed by TSA, due to a general resistance exhibited by FAPs from late stage mdx mice to HDACi-induced H3K9/14 hyperacetylation. Overall, this data reveal that disease-associated features of senescence develop in FAPs of DMD muscle through epigenetically distinct and pharmacologically dissociable events, and suggests that HDACi might at least retain anti- fibrotic and inflammatory activity at late stages of DMD, by repressing FAP-derived SASP.
De novo identification of universal cell mechanics gene signatures
Authors: Urbanska Marta , Ge Yan , Winzi Maria , Abuhattum Shada , Ali Syed Shafat , Herbig Maik , Kräter Martin , Toepfner Nicole , Durgan Joanne , Florey Oliver , Dori Martina , Calegari Federico , Lolo Fidel-Nicolás , del Pozo Miguel Á. , Taubenberger Anna , Cannistraci Carlo V. , Guck Jochen 
Published: April 2021

AbstractCell mechanical properties determine many physiological functions, such as cell fate specification, migration, or circulation through vasculature. Identifying factors that govern the mechanical properties is therefore a subject of great interest. Here we present a mechanomics approach for establishing links between single-cell mechanical phenotype changes and the genes involved in driving them. We combine mechanical characterization of cells across a variety of mouse and human systems with machine learning-based discriminative network analysis of associated transcriptomic profiles to infer a conserved network module of five genes with putative roles in cell mechanics regulation. We validate in silico that the identified gene markers are universal, trustworthy and specific to the mechanical phenotype across the studied mouse and human systems, and demonstrate experimentally that a selected target,CAV1, changes the mechanical phenotype of cells accordingly when silenced or overexpressed. Our data-driven approach paves the way towards engineering cell mechanical properties on demand to explore their impact on physiological and pathological cell functions.
Synthesising the multiple impacts of climatic variability on community responses to climate change
Authors: Terry J. Christopher D. , O’Sullivan Jacob D. , Rossberg Axel G. 
Published: April 2021

AbstractRecent developments in understanding and predicting species responses to climate change have emphasised the importance of both environmental variability and consideration of the wider biotic community. However, to date, the interaction between the two has received less attention. Both theoretical and empirical results suggest that the combined effect of environmental variability and interspecific interactions can have strong impacts on existing range limits. Here we explore how competitive interactions and temporal variability can interact with the potential to strongly influence range shift dynamics. We highlight the need to understand these between-process interactions in order to predict how species will respond to global change. In particular, future research will need to move from evaluating possibilities to quantifying their impact. We emphasise the value and utility of empirically parameterised models to determine the direction and relative importance of these forces in natural systems.
Secondary Structure Prediction for RNA Sequences Including N6-methyladenosine
Authors: Kierzek Elzbieta , Zhang Xiaoju , Watson Richard M. , Kierzek Ryszard , Mathews David H. 
Published: April 2021

AbstractThere is increasing interest in the roles played by covalently modified nucleotides in mRNAs and non-coding RNAs. New high-throughput sequencing technologies localize these modifications to exact nucleotide positions. There has been, however, and inability to account for these modifications in secondary structure prediction because of a lack of software tools for handling modifications and a lack of thermodynamic parameters for modifications. Here, we report that we solved these issues for N6-methyladenosine (m6A), for the first time allowing secondary structure prediction for a nucleotide alphabet of A, C, G, U, and m6A. We revised the RNAstructure software package to work with any user-defined alphabet of nucleotides. We also developed a set of nearest neighbor parameters for helices and loops containing m6A, using a set of 45 optical melting experiments. Interestingly, N6-methylation decreases the folding stability of structures with adenosines in the middle of a helix, has little effect on the folding stability of adenosines at the ends of helices, and stabilizes the folding stability for structures with unpaired adenosines stacked on the end of a helix. The parameters were tested against an additional two melting experiments, including a consensus sequence for methylation and an m6A dangling end. The utility of the new software was tested using predictions of the structure of a molecular switch in the MALAT1 lncRNA, for which a conformation change is triggered by methylation. Additionally, human transcriptome-wide calculations for the effect of N6-methylation on the probability of an adenosine being buried in a helix compare favorably with PARS structure mapping data. Now users of RNAstructure are able to develop hypothesis for structure-function relationships for RNAs with m6A, including conformational switching triggered by methylation.
Characterization of methylation profiles in spontaneous preterm birth placental villous tissue
Authors: Brockway Heather M , Wilson Samantha L , Kallapur Suhas G , Buhimschi Catalin S , Muglia Louis J , Jones Helen N 
Published: April 2021

AbstractPreterm birth is a global public health crisis which results in significant neonatal and maternal mortality. Yet little is known regarding the molecular mechanisms of idiopathic spontaneous preterm birth, and we have few diagnostic markers for adequate assessment of placental development and function. Previous studies of placental pathology and our transcriptomics studies suggest a role for placental maturity in idiopathic spontaneous preterm birth. It is known that placental DNA methylation changes over gestation. We hypothesized that if placental hypermaturity is present in our samples, we would observe a unique idiopathic spontaneous preterm birth DNA methylation profile potentially driving the gene expression differences we previously identified in our placental samples. Our results indicate the idiopathic spontaneous preterm birth DNA methylation pattern mimics the term birth methylation pattern suggesting hypermaturity. Only seven significant differentially methylated regions fitting the idiopathic spontaneous preterm birth specific (relative to the controls) profile were identified, indicating unusually high similarity in DNA methylation between idiopathic spontaneous preterm birth and term birth samples. We identified an additional 1,718 significantly methylated regions in our gestational age matched controls were the idiopathic spontaneous preterm birth DNA methylation pattern mimics the term birth methylation pattern, again indicating a striking level of similarity between the idiopathic spontaneous preterm birth and term birth samples. Pathway analysis of these regions revealed differences in genes within the WNT and Cadherin signaling pathways, both of which are essential in placental development and maturation. Taken together, these data demonstrate that the idiopathic spontaneous preterm birth samples are molecularly more mature than expected given their respective gestational age which likely impacts birth timing.