bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanomechanics of negatively supercoiled diaminopurine-substituted DNA
Authors: Salerno Domenico , Mantegazza Francesco , Cassina Valeria , Cristofalo Matteo , Shao Qing , Finzi Laura , Dunlap David 
Published: February 2021

ABSTRACTSingle molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. Since the particular sequence of a DNA segment influences both base stacking and hydrogen bonding, the conformational dynamics of B-to-L transitions should be tunable. To test this idea, DNA with diaminopurine replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded A:T base pairs. Triple hydrogen bonding stiffened the DNA by 30% flexurally. In addition, DAP-substituted DNA formed plectonemes with larger gyres for both B- and L-form helices. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing by DNA stretched and unwound by enzymatic activity. The intramolecular nature and ease of this transition likely prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length indicating it is much more contractile and prone to sharp bends and kinks. However, left-handed DAP DNA was twice as stiff as unmodified L-DNA. Thus, significantly doubly and triply hydrogen bonded segments have very distinct mechanical dynamics at physiological levels of negative supercoiling and tension.
A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets
Authors: Kratzel Annika , Kelly Jenna N. , Brueggemann Yannick , Portmann Jasmine , V’kovski Philip , Todt Daniel , Ebert Nadine , Steinmann Eike , Dijkman Ronald , Zimmer Gert , Pfaender Stephanie , Thiel Volker 
Published: February 2021

SummaryOver the past 20 years, the emergence of three highly pathogenic coronaviruses (CoV) – SARS-CoV, MERS-CoV, and most recently SARS-CoV-2 – has shown that CoVs pose a serious risk to human health and highlighted the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycle. Here, we conducted two independent genome-wide CRISPR/Cas9 knockout screens to identify pan-CoV host factors required for the replication of both endemic and emerging CoVs, including the novel CoV SARS-CoV-2. Strikingly, we found that several autophagy-related genes, including the immunophilin FKBP8, TMEM41B, and MINAR1, were common host factors required for CoV replication. Importantly, inhibition of the immunophilin family with the compounds Tacrolimus, Cyclosporin A, and the non-immunosuppressive derivative Alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures that resemble the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrate that these factors constitute potential targets for therapeutic intervention by clinically approved drugs.
scMoC: Single-Cell Multi-omics clustering
Authors: Eltager Mostafa , Abdelaal Tamim , Mahfouz Ahmed , Reinders Marcel J.T. 
Published: February 2021

AbstractMotivationSingle-cell multi-omics assays simultaneously measure different molecular features from the same cell. A key question is how to benefit from the complementary data available and perform cross-modal clustering of cells.ResultsWe proposeSingle-CellMulti-omicsClustering (scMoC), an approach to identify cell clusters from data with co-measurements of scRNA-seq and scATAC-seq from the same cell. We overcome the high sparsity of the scATAC-seq data by using an imputation strategy that exploits the less-sparse scRNA-seq data available from the same cell. Subsequently, scMoC identifies clusters of cells by merging clusterings derived from both data domains individually. We tested scMoC on datasets generated using different protocols with variable data sparsity levels. We show that, due to its imputation scheme, scMoC 1) is able to generate informative scATAC-seq data due to its RNA guided imputation strategy, and 2) results in integrated clusters based on both RNA and ATAC information that are biologically meaningful either from the RNA or from the ATAC perspective.AvailabilityThe code is freely available at:https://github.com/meltager/scmoc.Supplementary informationSupplementary data are available online.
Effects of substrate stiffness and actin velocity onin silicofibronectin fibril morphometry and mechanics
Authors: Weinberg Seth H. , Saini Navpreet , Lemmon Christopher A. 
Published: February 2021

AbstractAssembly of the extracellular matrix protein fibronectin (FN) into insoluble, viscoelastic fibrils is a critical step during embryonic development and wound healing; misregulation of FN fibril assembly has been implicated in many diseases, including fibrotic diseases and cancer. We have previously developed a computational model of FN fibril assembly that recapitulates the morphometry and mechanics of cell-derived FN fibrils. Here we use this model to probe two important questions: how is FN fibril formation affected by the contractile phenotype of the cell, and how is FN fibril formation affected by the stiffness of the surrounding tissue? We show that FN fibril formation depends strongly on the contractile phenotype of the cell, but only weakly on tissue stiffness. These results are consistent with previous experimental data and provide a better insight into conditions that promote FN fibril assembly. We have also used the model to look at two distinct phenotypes of FN fibrils that we have previously identified; we show that the ratio of the two phenotypes depends on both tissue stiffness and contractile phenotype, with intermediate contractility and high tissue stiffness creating an optimal condition for stably stretched fibrils. Finally, we have investigated how re-stretch of a fibril affects cellular response. We probed how the contractile phenotype of the re-stretching cell affects the mechanics of the fibril; results indicate that the number of myosin motors only weakly affects the cellular response, but increasing actin velocity results in a decrease in the apparent stiffness of the fibril and a decrease in the stably-applied force to the fibril. Taken together, these results give novel insights into the combinatorial effects of tissue stiffness and cell contractility on FN fibril assembly.
Fiber-associatedLachnospiraceaereduce colon tumorigenesis by modulation of the tumor-immune microenvironment
Authors: Almeida Ana S , Tran Tam T T , Ghosh Tarini S. , Ribiere Celine , Foley Cathriona , Azevedo Lisa A , Pellanda Paola , Frei Werner , Hueston Cara M , Kumar Raju , Flemer Burkhardt , Sequeira Inês , O’Riordain Micheal , Shanahan Fergus , O’Toole Paul W. 
Published: February 2021

AbstractPatients with colorectal cancer (CRC) harbor gut microbiomes that differ in structure and function from those of healthy individuals, suggesting this altered microbiome could contribute to tumorigenesis. Despite increasing evidence implicating the gut microbiome in CRC, the collective role of different microbial consortia in CRC carcinogenesis is unclear. We have previously described these consortia as co-abundance groups that co-exist at different abundance levels in the same patient. Here, we report that tumor biopsy tissue from patients with a “high-risk” Pathogen-type microbiome had a different immune transcriptome and immune cell infiltrate from those with a “low-risk”Lachnospiraceae-type microbiome. Transplantation from patients of the two fecal microbiome types into mice with an orthotopic tumor differentially affected tumor growth and the systemic anti-tumor immune response. The differences in tumor volume and immunophenotype between mice receiving the high-risk and the low-risk microbiome correlated with differences in the engrafted human microbial species and predicted microbiome-encoded metabolites in the two groups. Of twelve taxa whose abundance in recipient mice led to increased tumor onset, seven corresponded with differentially abundant taxa in a global dataset of 325 CRC patients versus 310 healthy controls. These data suggest that the enrichment for aLachnospiraceae-type configuration of the gut microbiome may influence colon cancer progression and disease outcome by modulating the local and systemic anti-tumor immune response.Graphical AbstractProposed model of how the high-risk Pathogen and low-riskLachnospiraceaeCAGs differentially modulate the tumor immune response.
A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota
Authors: Sommer Alice J , Peters Annette , Rommel Martina , Cyrys Josef , Grallert Harald , Haller Dirk , Müller Christian L , Bind Marie-Abèle C 
Published: February 2021

AbstractStatistical analysis of microbial genomic data within epidemiological cohort studies holds the promise to assess the influence of environmental exposures on both the host and the host-associated microbiome. The observational character of prospective cohort data and the intricate characteristics of microbiome data make it, however, challenging to discover causal associations between environment and microbiome. Here, we introduce a causal inference framework based on the Rubin Causal Model that can help scientists to investigate such environment-host microbiome relationships, to capitalize on existing, possibly powerful, test statistics, and test plausible sharp null hypotheses. Using data from the German KORA cohort study, we illustrate our framework by designing two hypothetical randomized experiments with interventions of (i) air pollution reduction and (ii) smoking prevention. We study the effects of these interventions on the human gut microbiome by testing shifts in microbial diversity, changes in individual microbial abundances, and microbial network wiring between groups of matched subjects via randomization-based inference. In the smoking prevention scenario, we identify a small interconnected group of taxa worth further scrutiny, including Christensenellaceae and Ruminococcaceae genera, that have been previously associated with blood metabolite changes. These findings demonstrate that our framework may uncover potentially causal links between environmental exposure and the gut microbiome from observational data. We anticipate the present statistical framework to be a good starting point for further discoveries on the role of the gut microbiome in environmental health.
An Adeno-Associated Viral vector encoding Neurotrophin 3 injected into affected forelimb muscles modestly improves sensorimotor function after contusive mid-cervical spinal cord injury
Authors: Sydney Smith Jared D. , Megaro Vanessa , Spejo Aline Barroso , Moon Lawrence D. F. 
Published: February 2021

AbstractTraumatic spinal cord injury (SCI) in humans occurs most frequently in the cervical spine where it can cause substantial sensorimotor impairments to upper limb function. The altered input to spinal circuits below the lesion leads to maladaptive reorganisation which often leads to hyperreflexia in proprioceptive circuits. Neurotrophin 3 (NT3) is growth factor essential for the development of proprioceptive neurons. We have previously shown that following bilateral corticospinal tract axotomy, intramuscular delivery of an Adeno-Associated Viral vector encoding NT3 (AAV-NT3) induces proprioceptive circuit reorganisation linked to functional recovery. To assess its therapeutic effects following a clinically relevant bilateral C5-C6 contusion in rats, AAV-NT3 was injected intramuscularly into the dominant limb 24 hours after injury and forelimb function was assessed over 13 weeks. The injury generated hyperreflexia of a distal forelimb proprioceptive circuit. There was also loss of fine motor skills during reach-and-grasp and walking on a horizontal ladder. Ex vivo magnetic resonance imaging (MRI) revealed atrophy of the spinal cord and white matter disruption throughout the lesion site together with extensive loss of grey matter. Unexpectedly, animals treated with AAV-NT3 had a slightly smaller lesion in the regions close to the epicentre compared to PBS treated animals. Rats treated with AAV-NT3 showed subtly better performance on the horizontal ladder and transient benefits on reach-and-grasp. AAV-NT3 did not normalise hyperreflexia in a treated muscle. The treatment increased the amount of NT3 in treated muscles but, unexpectedly, serum levels were only elevated in a small subset of animals. These results show that this dose and delivery of AAV-NT3 may generate subtle improvements in locomotion but additional treatments will be required to overcome the widespread sensorimotor deficits caused by contusion injury.
Cytotoxic lymphocytes target HIV-1 Gag through granzyme M-mediated cleavage
Authors: Saccon Elisa , Mikaeloff Flora , Ivern Pol Figueras , Végvári Ákos , Sönnerborg Anders , Neogi Ujjwal , van Domselaar Robert 
Published: February 2021

AbstractHIV-1 leads to progression to immunodeficiency and death of individuals who do not receive successful antiretroviral therapy. Initially, the host’s immune response controls the infection, but cannot eliminate the HIV-1 from the host. Cytotoxic lymphocytes are the key effector cells in this response and can mediate crucial antiviral responses through the release of a set of proteases called granzymes towards HIV-1-infected cells. However, little is known about the immunological molecular mechanisms by which granzymes could control HIV-1. Since we noted that HIV-1 subtype C (HIV-1C) Gag with the tetrapeptide insertion PYKE contains a putative granzyme M (GrM) cleavage site (KEPL) that overlaps with the PYKE insertion, we analyzed the proteolytic activity of GrM towards Gag. Immunoblot analysis showed that GrM could cleave Gag proteins from HIV-1B and variants from HIV-1C of which the Gag-PYKE variant was cleaved with extremely high efficiency. The main cleavage site was directly after the insertion after leucine residue 483. GrM-mediated cleavage of Gag was also observed in co-cultures using cytotoxic lymphocytes as effector cells and this cleavage could be inhibited by a GrM inhibitor peptide. Altogether, our data indicate towards a noncytotoxic immunological mechanism by which GrM-positive cytotoxic lymphocytes target the HIV-1 Gag protein within infected cells to potentially control HIV-1 infection. This mechanism could be exploited in new therapeutic strategies to treat HIV-1-infected patients to improve immunological control of the infection.
Pervasive effects ofWolbachiaon host activity
Authors: Hague Michael T.J. , Woods H. Arthur , Cooper Brandon S. 
Published: February 2021

ABSTRACTHeritable symbionts have diverse effects on the physiology, reproduction, and fitness of their hosts. Maternally transmittedWolbachiaare one of the most common endosymbionts in nature, infecting about half of all insect species. We test the hypothesis thatWolbachiaalter host behavior by assessing the effects of 14 differentWolbachiastrains on the locomotor activity of nineDrosophilahost species. We find thatWolbachiaalter the activity of six different host genotypes, including all hosts in our assay infected withwRi-likeWolbachiastrains (wRi,wSuz,wAur), which have rapidly spread amongDrosophilaspecies in only the last 13,000 years. WhileWolbachiaeffects on host activity were common, the direction of these effects varied unpredictability and sometimes depended on host sex. We hypothesize that the prominent effects ofwRi-likeWolbachiamay be explained by patterns ofWolbachiatiter and localization within host somatic tissues, particularly in the central nervous system. Our findings support the view thatWolbachiahave wide-ranging effects on host behavior. The fitness consequences of these behavioral modifications are important for understanding the evolution of host-symbiont interactions, including howWolbachiaspread within host populations.
Pathogen and endophyte assemblages co-vary with beech bark disease progression, tree decline, and regional climate
Authors: Morrison Eric W. , Kasson Matt T. , Heath Jeremy J. , Garnas Jeff R. 
Published: February 2021

AbstractPlant-pathogen interactions are often considered in a pairwise manner with minimal consideration of the impacts of the broader endophytic community on disease progression and/or outcomes for disease agents and hosts. Community interactions may be especially relevant in the context of disease complexes (i.e, interacting or functionally redundant causal agents) and decline diseases (where saprobes and weak pathogens synergize the effects of primary infections and hasten host mortality). Here we describe the bark endophyte communities associated with a widespread decline disease of American beech, beech bark disease (BBD), caused by an invasive scale insect (Cryptococcus fagisuga) and two fungal pathogens,Neonectria faginataandN. ditissima. We show that the two primary fungal disease agents co-occur more broadly than previously understood (35.5% of infected trees), including within the same 1-cm diameter phloem samples. The two species appear to have contrasting associations with climate and stages of tree decline, whereinN. faginatawas associated with warmer andN. ditissimawith cooler temperatures.Neonectria ditissimashowed a positive association with tree crown dieback – no such association was observed forN. faginata. Further, we identify fungal endophytes that may modulate disease progression as entomopathogens, mycoparasites, saprotrophs and/or additional pathogens, includingClonostachys roseaandFusarium babinda. These fungi may alter the trajectory of disease via feedbacks with the primary disease agents or by altering symptom expression or rates of tree decline across the range of BBD.
A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duckAythya fuligula(Tufted Duck)
Authors: Mueller Ralf C , Ellström Patrik , Howe Kerstin , Uliano-Silva Marcela , Kuo Richard I , Miedzinska Katarzyna , Warr Amanda , Fedrigo Olivier , Haase Bettina , Mountcastle Jacquelyn , Chow William , Torrance James , Wood Jonathan , Järhult Josef D , Naguib Mahmoud M , Olsen Björn , Jarvis Erich D , Smith Jacqueline , Eöry Lél , Kraus Robert HS 
Published: February 2021

BackgroundThe tufted duck is a non-model organism that suffers high mortality in highly pathogenic avian influenza out-breaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.ResultsThis study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (cDNA) from brain, ileum, lung, ovary, spleen and testis using Illumina short-read and PacBio long-read sequencing platforms, which was used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies an average of 7.9 isoforms per gene. We also identified 246 small RNA families.ConclusionsThis annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to the avian influenza virus.
Permeant Fluorescent Probes Visualize the Activation of SARM1 and Uncover an Anti-neurodegenerative Drug Candidate
Authors: Li Wan Hua , Huang Ke , Cai Yang , Wang Qian Wen , Zhu Wen Jie , Hou Yun Nan , Wang Sujing , Cao Sheng , Zhao Zhi Ying , Xie Xu Jie , Du Yang , Lee Chi-Sing , Lee Hon Cheung , Zhang Hongmin , Zhao Yong Juan 
Published: February 2021

AbstractSARM1 regulates axonal degeneration through its NAD-metabolizing activity and is a drug target for neurodegenerative disorders. We designed and synthesized fluorescent conjugates of styryl derivative with pyridine to serve as substrates of SARM1, which exhibited large red-shifts after conversion. With the conjugates, SARM1 activation was visualized in live cells following elevation of endogenous NMN or treatment with a cell-permeant NMN-analog. In neurons, imaging documented SARM1 activation preceded vincristine-induced axonal degeneration by hours. Library screening identified a derivative of nisoldipine as a covalent inhibitor of SARM1 that reacted with Cys311 in its Armadillo-domain and blocked its NMN-activation, protecting axons from degeneration. CryoEM showed that SARM1 was locked into an inactive conformation by the inhibitor, uncovering an unsuspected neuroprotective mechanism of dihydropyridines.
Dichotomous regulation of lysosomes by MYC and TFEB controls hematopoietic stem cell fate
Authors: García-Prat Laura , Kaufmann Kerstin B. , Schneiter Florin , Voisin Veronique , Murison Alex , Chen Jocelyn , Chan-Seng-Yue Michelle , Gan Olga I. , McLeod Jessica L. , Smith Sabrina A. , Shoong Michelle C. , Paris Darrien , Pan Kristele , Zeng Andy G.X. , Krivdova Gabriela , Gupta Kinam , Takayanagi Shin-Ichiro , Wagenblast Elvin , Wang Weijia , Lupien Mathieu , Schroeder Timm , Xie Stephanie Z. , Dick John E. 
Published: February 2021

SummaryIt is critical to understand how quiescent long-term hematopoietic stem cells (LT-HSC) sense demand from daily and stress-mediated cues and transition into bioenergetically active progeny to differentiate and meet these cellular needs. Here, we show that lysosomes, which are sophisticated nutrient sensing and signaling centers, are dichotomously regulated by the Transcription Factor EB (TFEB) and MYC to balance catabolic and anabolic processes required for activating LT-HSC and guiding their lineage fate. TFEB-mediated induction of the endolysosomal pathway causes membrane receptor degradation, limiting LT-HSC metabolic and mitogenic activation, which promotes quiescence, self-renewal and governs erythroid-myeloid commitment. By contrast, MYC engages biosynthetic processes while repressing lysosomal catabolism to drive LT-HSC activation. Collectively, our study identifies lysosomes as a central regulatory hub for proper and coordinated stem cell fate determination.