bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Proteinase Activated Receptor (PAR) cleaving enzymes in human osteoarthritis knee joint synovial fluids
Authors: Chandrabalan Arundhasa , Firth Andrew , Litchfield Robert B , Appleton C Thomas , Getgood Alan , Ramachandran Rithwik 
Published: October 2020

ABSTRACTObjectiveOsteoarthritis (OA) is the most prevalent joint disorder with incidence increasing worldwide. Mechanistic insights into OA pathophysiology are still evolving and there are currently no disease-modifying OA drugs available. It is well established that an increase in proteolytic enzyme activity is linked to progressive degradation of the cartilage in OA. Proteolytic enzymes can also trigger inflammation through activation of a family of G-protein coupled receptors (GPCRs) called the Proteinase Activated Receptors (PARs). Here we sought to characterize the PAR activating enzyme repertoire in human OA knee joint fluids.MethodsHuman knee joint synovial fluids derived from twenty-five OA patients and four healthy donors were screened for PAR cleavage activity using novel genetically encoded human PAR biosensor expressing cells. The class or type of enzymes cleaving the PARs was further characterized using enzyme-selective inhibitors and enzyme-specific fluorogenic substrates.ResultsActivity of PAR1, PAR2 and PAR4 activating enzymes were identified at substantially different levels in OA patients relative to healthy knee joint synovial fluids. Using enzyme class or type selective inhibitors and fluorogenic substrates we found that serine proteinases, including thrombin-like enzymes, trypsin-like enzymes, and matrix metalloproteinases are the major PAR activating enzymes present in the OA knee synovial fluids.ConclusionsMultiple enzymes activating PAR1, PAR2 and PAR4 are present in OA joint fluids. PAR signalling can trigger pro-inflammatory responses and targeting PARs has been proposed as a therapeutic approach in OA. Knowledge of the PAR activators present in the human knee joint will guide study of relevant signaling events and enable future development of novel PAR targeted therapies for OA and other inflammatory joint diseases.
Time-resolved single-cell RNAseq profiling identifies a novelFabp5-expressing subpopulation of inflammatory myeloid cells in chronic spinal cord injury
Authors: Hamel Regan , Peruzzotti-Jametti Luca , Ridley Katherine , Testa Veronica , Yu Bryan , Rowitch David , Marioni John C. , Pluchino Stefano 
Published: October 2020

AbstractInnate immune responses following spinal cord injury (SCI) participate in early secondary pathogenesis and wound healing events. Here, we used time-resolved scRNAseq to map transcriptional profiles of SC tissue-resident and infiltrating myeloid cells post-SCI.Our work identifies a novel subpopulation ofFabp5+inflammatory myeloid cells, comprising both resident and infiltrating cells and displaying a delayed cytotoxic profile at the lesion epicentre, which may serve as a target for future therapeutics.
The interaction of physical structure and nutrient loading drives ecosystem change in a large tropical lake over 40 years
Authors: Fadum Jemma M. , Hall Ed K. 
Published: October 2020

AbstractMany lakes across the world are entering novel states and experiencing altered biogeochemical cycling due to local anthropogenic stressors. In the tropics, understanding the drivers of these changes can be difficult due to a lack of documented historic conditions or an absence of continuous monitoring that can distinguish between intra- and inter-annual variation. Over the last forty years (1980-2020), Lake Yojoa (Honduras) has experienced increased watershed development as well as the introduction of a large net-pen Tilapia farm, resulting in a dramatic reduction in seasonal water clarity, increased trophic state and altered nutrient dynamics, shifting Lake Yojoa from an oligotrophic (low productivity) to mesotrophic (moderate productivity) ecosystem. To assess the changes that have occurred in Lake Yojoa as well as putative drivers for those changes, we compared Secchi depth (water clarity), dissolved inorganic nitrogen (DIN), and total phosphorus (TP) concentrations at continuous semi-monthly intervals for the three years between 1979-1983 and again at continuous 16-day intervals for 2018-2020. Between those two periods we observed the loss of a clear water phase that previously occurred in the months when the water column was fully mixed. Seasonal peaks in DIN coincident with mixing suggest that an enhanced accumulation of ammonium in the hypolimnion (the bottom layer of a stratified lake) during stratification, and release to the epilimnion (the top layer of a stratified lake) with mixing maintains high algal abundance and subsequently low secchi depth during what was previously the clear water phase. This interaction of nutrient loading and Lake Yojoa’s monomictic stratification regime illustrates a key phenomenon in how physical water column structure and nutrients interact in tropical monomictic lakes. This work highlights the need to consider nutrient dynamics of warm anoxic hypolimnions, not just surface water nutrient concentrations, to understand environmental change in these societally important but understudied ecosystems.
Preclinical study of DNA vaccines targeting SARS-CoV-2
Authors: Hayashi Hiroki , Sun Jiao , Yanagida Yuka , Otera Takako , Kubota-Kotetsu Ritsuko , Shioda Tatsuo , Ono Chikako , Matsuura Yoshiharu , Arase Hisashi , Yoshida Shota , Nakamaru Ryo , Ide Ryoko , Tenma Akiko , Kawabata Sotaro , Ehara Takako , Sakaguchi Makoto , Tomioka Hideki , Shimamura Munehisa , Okamoto Sachiko , Amaishi Yasunori , Chono Hideto , Mineno Junichi , Komatsuno Takano , Saito Yoshimi , Rakugi Hiromi , Morishita Ryuichi , Nakagami Hironori 
Published: October 2020

AbstractTo fight against the worldwide COVID-19 pandemic, the development of an effective and safe vaccine against SARS-CoV-2 is required. As potential pandemic vaccines, DNA/RNA vaccines, viral vector vaccines and protein-based vaccines have been rapidly developed to prevent pandemic spread worldwide. In this study, we designed plasmid DNA vaccine targeting the SARS-CoV-2 Spike glycoprotein (S protein) as pandemic vaccine, and the humoral, cellular, and functional immune responses were characterized to support proceeding to initial human clinical trials. After intramuscular injection of DNA vaccine encoding S protein with alum adjuvant (three times at 2-week intervals), the humoral immunoreaction, as assessed by anti-S protein or anti-receptor-binding domain (RBD) antibody titers, and the cellular immunoreaction, as assessed by antigen-induced IFNγ expression, were up-regulated. In IgG subclass analysis, IgG2b was induced as the main subclass. Based on these analyses, DNA vaccine with alum adjuvant preferentially induced Th1-type T cell polarization. We confirmed the neutralizing action of DNA vaccine-induced antibodies via two different methods, a binding assay of RBD recombinant protein with angiotensin-converting enzyme 2 (ACE2), a receptor of SARS-CoV-2, and pseudovirus assay. Further B cell epitope mapping analysis using a peptide array showed that most vaccine-induced antibodies recognized the S2 and RBD subunits, but not the S1 subunit. In conclusion, DNA vaccine targeting the spike glycoprotein of SARS-CoV-2 might be an effective and safe approach to combat the COVID-19 pandemic.
Dual RNA-Seq analysis ofin vitroinfection multiplicity inChlamydia-infected epithelial cells
Authors: Hayward Regan J. , Humphrys Michael S. , Huston Wilhelmina M. , Myers Garry S.A. 
Published: October 2020

AbstractDual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq toChlamydia trachomatisinfected epithelial cells to examine transcriptomic responses from both organisms. We compared two time points post infection (1 and 24 hours), three multiplicity of infection (MOI) ratios (0.1, 1 and 10) and two RNA depletion methods (rRNA and polyA). Capture of bacterial-specific RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI. However, under these conditions, host RNA capture was negatively impacted. Although it is tempting to use high infection rates, the implications on host cell survival, the potential reduced length of infection cycles and real world applicability should be considered. This data highlights the delicate nature of balancing host-pathogen RNA capture and will assist future transcriptomic-based studies to achieve more specific and relevant infection-related biological insights.
HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation
Authors: Kumamoto Soichiro , Nishiyama Atsuya , Chiba Yoshie , Miyashita Ryota , Konishi Chieko , Azuma Yoshiaki , Nakanishi Makoto 
Published: October 2020

ABSTRACTDNA Ligase 1 (LIG1) is known as the major DNA ligase responsible for Okazaki fragment joining. Recent studies have implicated LIG3 complexed with XRCC1 as an alternative player in Okazaki fragment joining in cases where LIG1 is not functional, although the underlying mechanisms are largely unknown. Here, using a cell-free system derived fromXenopusegg extracts, we demonstrated the essential role of PARP1-HPF1 in LIG3-dependent Okazaki fragment joining. We found that Okazaki fragments were eventually ligated even in the absence of LIG1, employing in its place LIG3-XRCC1 which was recruited onto chromatins. Concomitantly, LIG1 deficiency induces ADP-ribosylation of histone H3 in a PARP1-HPF1-dependent manner. The depletion of PARP1 or HPF1 resulted in a failure to recruit LIG3 onto chromatin and a subsequent failure in Okazaki fragment joining in LIG1-depleted extracts. Importantly, Okazaki fragments were not ligated at all when LIG1 and XRCC1 were co-depleted. Our results suggest that a unique form of ADP-ribosylation signalling promotes the recruitment of LIG3 on chromatins and its mediation of Okazaki fragment joining as a backup system for LIG1 perturbation.
Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16s rDNA amplicon sequencing
Authors: Serrana Joeselle M. , Watanabe Kozo 
Published: October 2020

ABSTRACTSequential membrane filtration as a pre-processing step for the isolation of microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques, e.g., 16s rDNA amplicon sequencing. Here, we assessed the impact of pre-processing sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size membrane filters) for 16s rDNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the quality and quantity of extracted DNA and PCR amplicons between the two methods. Although we found a significant difference in raw and quality-filtered reads, read abundance after bioinformatics processing (i.e., denoising and the chimeric-read filtering steps) were not significantly different. These results suggest that read abundance after these read processing steps were not influenced by sediment processing or lack thereof. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods’ absolute read abundance. More so at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). Accordingly, the diversity estimates and community composition were not significantly different between the non- and pre-processed samples. We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition. We also suggest the inclusion of sequential filters (i.e., pre- and mid-filters) in the community profiling, given the additional taxa not detected from the non-processed and the final collection filter. Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.
Explainable Machine Learning Approach to Predict and Explain the Relationship between Task-based fMRI and Individual Differences in Cognition
Authors: Pat Narun , Wang Yue , Bartonicek Adam , Candia Julián , Stringaris Argyris 
Published: October 2020

AbstractDespite decades of costly research, we still cannot accurately predict individual differences in cognition from task-based fMRI. Moreover, aiming for methods with higher prediction is not sufficient. To understand brain-cognition relationships, we need to explain how these methods draw brain information to make the prediction. Here we applied an explainable machine-learning (ML) framework to predict cognition from task-based fMRI during the n-back working-memory task, using data from the Adolescent Brain Cognitive Development (n=3,989). We compared nine predictive algorithms in their ability to predict 12 cognitive abilities. We found better out-of-sample prediction from ML algorithms over the mass-univariate and OLS multiple regression. Among ML algorithms, Elastic Net, a linear and additive algorithm, performed either similar to or better than non-linear and interactive algorithms. We explained how these algorithms drew information, using SHapley Additive explanation, eNetXplorer, Accumulated Local Effects and Friedman’s H-statistic. These explainers demonstrated benefits of ML over the OLS multiple regression. For example, ML provided some consistency in variable importance with a previous study (Sripada et al. 2020) and consistency with the mass-univariate approach in the directionality of brain-cognition relationships at different regions. Accordingly, our explainable-ML framework predicted cognition from task-based fMRI with boosted prediction and explainability over standard methodologies.
Gait variability is affected more by peripheral artery disease than by vascular occlusion
Authors: Rahman Hafizur , Pipinos Iraklis I. , Johanning Jason M. , Myers Sara A. 
Published: October 2020

AbstractBackgroundPatients with peripheral artery disease (PAD) have altered gait variability from the first step they take, well before the onset of claudication pain. The mechanisms underlying these gait alterations are poorly understood.AimsThis study sought to isolate the effect of reduced blood flow on gait variability by comparing healthy older controls and patients with PAD. We also determined the diagnostic value of gait variability parameters to identify the presence of PAD.MethodsThirty healthy older controls and thirty patients with PAD walked on a treadmill at their self-selected speed in rested (normal walking for controls; pain free for PAD) and reduced blood flow (post vascular occlusion with thigh tourniquet for controls; pain for PAD) conditions. Gait variability was assessed using the largest Lyapunov exponent, approximate entropy, standard deviation, and coefficient of variation of ankle, knee, and hip joints range of motion. Receiver operating characteristics curve analyses of the rested condition were performed to determine the optimal cut-off values for separating individuals with PAD from those without PAD.Results and DiscussionPatients with PAD have increased amount of variability for knee and hip ranges of motion compared with healthy older group. Comparing for conditions, reduced blood flow demonstrated increased amount of variability compared with rested blood flow. Significant interactions between group and condition occurred at the ankle for Lyapunov exponent, approximate entropy, and coefficient of variation. A combination of gait variability parameters correctly identifies PAD disease 70% of the time or more.ConclusionsGait variability is affected both by PAD and by the mechanical induction of reduced blood flow.
Widespread occurrence of the droplet state of proteins in the human proteome
Authors: Hardenberg Maarten , Horvath Attila , Ambrus Viktor , Fuxreiter Monika , Vendruscolo Michele 
Published: October 2020

AbstractA wide range of proteins have been reported to condensate into a dense liquid phase, forming a reversible droplet state. Failure in the control of the droplet state can lead to the formation of the more stable amyloid state, which is often disease-related. These observations prompt the question of how many proteins can undergo liquid-liquid phase separation. Here, in order to address this problem, we discuss the biophysical principles underlying the droplet state of proteins by analyzing current evidence for droplet-driver and droplet-client proteins. Based on the concept that the droplet state is stabilized by the large conformational entropy associated with non-specific side-chain interactions, we develop the FuzDrop method to predict droplet-promoting regions and proteins, which can spontaneously phase separate. We use this approach to carry out a proteome-level study to rank proteins according to their propensity to form the droplet state, spontaneously or via partner interactions. Our results lead to the conclusion that the droplet state could be, at least transiently, accessible to most proteins under conditions found in the cellular environment.SignificanceLiquid-liquid phase separation of proteins results in biomolecular condensates, which contribute to the organisation of cellular matter into membraneless organelles. It is still unclear, however, whether these condensates represent a common state of proteins. Here, based on biophysical principles driving phase separation, we report a proteome-wide ranking of proteins according to their propensity to condensate into a droplet state. We analyze two mechanisms for droplet formation - driver proteins can spontaneously phase separate, while client proteins require additional components. We conclude that the droplet state, as the native and amyloid states, is a fundamental state of proteins, with most proteins expected to be capable of undergoing liquid-liquid phase separation via either of these two mechanisms.
Context dependent activation and repression of enhancers by Hunchback binding sites inDrosophilaembryo
Authors: Ceolin Stefano , Hanf Monika , Schnepf Max , Unnerstall Ulrich , Jung Christophe , Gaul Ulrike 
Published: October 2020

ABSTRACTHunchback (Hb) is considered a context-dependent transcription factor, able to activate or repress different enhancers duringDrosophilaembryo segmentation. The mechanism driving the contextdependent activity of Hb is however not well understood. Here we measure the activity of a large set of 20 synthetic enhancers that we design to elucidate the effect of Hb binding sites inDrosophilasegmentation. We obtain quantitative data on the spatiotemporal dynamics of activity of all synthetic enhancersin-vivo, by using a quantitative and sensitive reporter system we recently developed. Our data reveal the dual role of Hb binding sites in segmentation enhancers: on the one hand, Hb act as a typical short range repressor by binding to its cognate sequences; on the other hand, we report a novel effect of a sequence containing multiple Hb binding sites, which is able to increase enhancer activity independently from Hb binding. This sequence, which contains multiple Poly-dA stretches, increases the activity of enhancers driven by different activators, possibly by disfavoring nucleosome occupancy.AUTHOR SUMMARYThe control of gene expression is a fundamental process that allows cells to respond to external stimuli and take on various identities in complex organisms. Enhancers are DNA sequences that play a key role in this process. In the simplest model of an enhancer, small parts of its sequence can be specifically bound by proteins called transcription factors and the occupancy pattern of these proteins on the enhancer determines the expression level of a specific gene. In this research work we have studied enhancers in the context of the development of a fruit fly embryo. We have built synthetic enhancer sequences containing binding sites for a few specific factors and measured their activity in living embryos using fluorescence microscopy. Our results revealed that binding sites for a particular protein, Hunchback, are able to influence the activity of the enhancer even independently from Hunchback binding to them. This discovery might help to explain the complex effects that have been observed when studying Hunchback binding sites in natural enhancers.
Nanoscopic Structural Fluctuations of Disassembling Microtubules Revealed by Label-Free Super-Resolution Microscopy
Authors: Vala Milan , Bujak Łukasz , Marín Antonio García , Holanová Kristýna , Henrichs Verena , Braun Marcus , Lánský Zdeněk , Piliarik Marek 
Published: October 2020

AbstractMicrotubules are cytoskeletal polymers of tubulin dimers assembled into protofilaments that constitute nanotubes undergoing periods of assembly and disassembly. Static electron micrographs suggest a structural transition of straight protofilaments into curved ones occurring at the tips of disassembling microtubules. However, these structural transitions have never been observed and the process of microtubule disassembly thus remains unclear. Here, a label-free optical microscopy capable of selective imaging of the transient structural changes of protofilaments at the tip of a disassembling microtubule is introduced. Upon induced disassembly, the transition of ordered protofilaments into a disordered conformation is resolved at the tip of the microtubule. Imaging the unbinding of individual tubulin oligomers from the microtubule tip reveals transient pauses and relapses in the disassembly, concurrent with enrichment of ordered protofilament segments at the microtubule tip. These findings show that microtubule disassembly is a discrete process and suggest a mechanism of switching from the disassembly to the assembly phase.
GWAS analysis combined with QTL mapping identifyCPT3andABHas genes underlying dolichol accumulation in Arabidopsis
Authors: Gawarecka Katarzyna , Siwinska Joanna , Poznanski Jaroslaw , Onysk Agnieszka , Surowiecki Przemyslaw , Surmacz Liliana , Ahn Ji Hoon , Korte Arthur , Swiezewska Ewa , Ihnatowicz Anna 
Published: October 2020

ABSTRACTDolichols (Dols), ubiquitous components of living organisms, are indispensable for cell survival. In plants, as well as other eukaryotes, Dols are crucial for posttranslational protein glycosylation, aberration of which leads to fatal metabolic disorders in humans. Until now, the regulatory mechanisms underlying Dol accumulation remain elusive. In this report, we have analyzed the natural variation of the accumulation of Dols and six other isoprenoids between 120Arabidopsis thalianaaccessions. Subsequently, by combining QTL and GWAS approaches, we have identified several candidate genes involved in the accumulation of Dols, polyprenols, plastoquinone, and phytosterols. The role of two genes implicated in the accumulation of major Dols in Arabidopsis – the AT2G17570 gene encoding a long searched forcis-prenyltransferase (CPT3) and the AT1G52460 gene encoding an alpha-beta hydrolase (ABH) – is experimentally confirmed. These data will help to generate Dol-enriched plants which might serve as a remedy for Dol-deficiency in humans.