bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscale Dynamics of Cellulase TrCel7A Digesting Cellulose
Authors: Haviland Zachary K. , Nong Daguan , Vasquez Kuntz Kate L. , Starr Thomas J. , Ma Dengbo , Tien Ming , Anderson Charles T. , Hancock William O. 
Published: February 2021

AbstractUnderstanding how cellulases catalyze the digestion of lignocellulose is a major goal of bioenergy research. Cel7A fromTrichoderma reeseiis a model exoglucanase that degrades cellulose strands from their reducing ends by processively cleaving individual cellobiose units. Despite being one of the most studied cellulases, the binding and hydrolysis mechanisms of Cel7A are still debated. We used single-molecule tracking to analyze the dynamics of 11,116 quantum dot-labeledTrCel7A binding to and moving processively along immobilizedGluconoacetobactercellulose. Enzyme molecules were localized with a spatial precision of a few nanometers and followed for hundreds of seconds. Most enzymes bound into a static state and dissociated without detectable movement. Processive enzymes moved an average distance of 39 nm at an average speed of 3.2 nm/s. Static binding episodes preceding and following processive runs were of similar duration to static binding events that lacked any processive movement. Transient jumps of >20 nm were observed, but no diffusive behavior indicative of a diffusive search of the enzyme for a free cellulose strand end was observed. These data were integrated into a three-state model in whichTrCel7A molecules can bind from solution into either a static or a processive state, and can reversibly switch between static and processive states before dissociating. From these results, we conclude that the rate-limiting step for cellulose degradation by Cel7A is the transition out of the static state either by dissociation from the cellulose surface or initiation of a processive run.
Investigating the chemolithoautotrophic and formate metabolism ofNitrospira moscoviensisby constraint-based metabolic modeling and13C-tracer analysis
Authors: Lawson Christopher E. , Mundinger Aniela B. , Koch Hanna , Jacobson Tyler B. , Weathersby Coty A. , Jetten Mike S. M. , Pabst Martin , Amador-Noguez Daniel , Noguera Daniel R. , McMahon Katherine , Lücker Sebastian 
Published: February 2021

AbstractNitrite-oxidizing bacteria belonging to the genusNitrospiramediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment. While these organisms have recently been shown to exhibit metabolic flexibility beyond their chemolithoautotrophic lifestyle, including the use of simple organic compounds to fuel their energy metabolism, the metabolic networks controlling their autotrophic and mixotrophic growth remain poorly understood. Here, we reconstructed a genome-scale metabolic model forNitrospira moscoviensis(iNmo686) and used constraint-based analysis to evaluate the metabolic networks controlling autotrophic and formatotrophic growth on nitrite and formate, respectively. Subsequently, proteomic analysis and13C-tracer experiments with bicarbonate and formate coupled to metabolomic analysis were performed to experimentally validate model predictions. Our findings support thatN. moscoviensisuses the reductive tricarboxylic acid cycle for CO2fixation. We also show thatN. moscoviensiscan indirectly use formate as a carbon source by oxidizing it first to CO2followed by reassimilation, rather than direct incorporation via the reductive glycine pathway. Our study offers the first measurements ofNitrospira’s in vivocentral carbon metabolism and provides a quantitative tool that can be used for understanding and predicting their metabolic processes.ImportanceNitrospiraare globally abundant nitrifying bacteria in soil and aquatic ecosystems and wastewater treatment plants, where they control the oxidation of nitrite to nitrate. Despite their critical contribution to nitrogen cycling across diverse environments, detailed understanding of their metabolic network and prediction of their function under different environmental conditions remains a major challenge. Here, we provide the first constraint-based metabolic model ofN. moscoviensisrepresenting the ubiquitousNitrospiralineage II and subsequently validate this model using proteomics and13C-tracers combined with intracellular metabolomic analysis. The resulting genome-scale model will serve as a knowledge base ofNitrospirametabolism and lays the foundation for quantitative systems biology studies of these globally important nitrite- oxidizing bacteria.
SARS-CoV-2 serostatus of healthcare worker in the Austrian state Vorarlberg between June 2020 and January 2021
Authors: Atzl Michele , Muendlein Axel , Winder Thomas , Fraunberger Peter , Brandtner Eva-Maria , Geiger Kathrin , Klausberger Miriam , Duerkop Mark , Sprenger Lukas , Mutschlechner Beatrix , Volgger Andreas , Benda Magdalena , Severgnini Luciano , Jaeger Johannes B. , Drexel Heinz , Lang Alois , Leiherer Andreas 
Published: February 2021

AbstractBackgroundAustria, and particularly its westernmost federal state Vorarlberg, developed an extremely high COVID-19 incidence rate in November 2020. Health care workers (HCW) may be at higher risk of contracting the disease within the working environment and therefore the seroprevalence in this population is of particular interest. Here, we analyzed SARS-CoV-2-specific antibody response in Vorarlberg HCW in a prospective cohort study.MethodsA total of 395 HCW have been tested at three different time points for the prevalence of anti-SARS-CoV-2 IgG antibodies specific for NP and RBD. Enrollment started in June 2020 (t1), two months after the end of the first wave. Re-testing took place between October to November at the beginning of the second wave (t2), and again at the end of the second wave in January 2021 (t3).ResultsAt t1, 3% of HCW showed a strong IgG-specific responses to either NP or RBD. At t2, the rate increased to 4%, and after the second wave in January 2021, 14% had a strong response, which was assessed to be stable for up to ten months. The amount of HCW with anti-SARS-CoV-2 IgG antibodies was 38% higher than the number of infections found by RT-PCR.ConclusionWe found low numbers of SARS-CoV-2-seropositive HCW in a hotspot setting after the first wave but a very high increase during the second massive wave. Though the seroprevalence in HCW was comparable to the general population. Our findings offer support for the routine application of serological testing in management of the ongoing COVID-19 pandemic.Main summaryA relatively low percentage of 3% SARS-CoV-2 seropositive HCW with strong IgG-specific antibody responses was found in the Austrian federal state Vorarlberg after the first wave increasing to 14% after the second massive wave lasting until January 2021.
Evaluation of VIDAS® diagnostic assay prototypes detecting dengue virus NS1 antigen and anti-dengue virus IgM and IgG antibodies
Authors: Somlor Somphavanh , Brossault Ludovic , Grandadam Marc 
Published: February 2021

AbstractDengue is a serious tropical disease caused by the mosquito-borne dengue virus (DENV). Performant, rapid and easy-to-use assays are needed for the accurate diagnosis of acute DENV infection. We evaluated the performance of three prototype assays developed for the VIDAS® automated platform to detect dengue NS1 antigen and anti-dengue IgM and IgG antibodies. Positive and negative agreement with competitor enzyme-linked immunosorbent assays (ELISA) and rapid diagnostic tests (RDT) was evaluated in 91 Lao patients (57 adults, 34 children) with acute DENV infection. The VIDAS® NS1 assay showed the best overall agreement (95.6%) with the competitor NS1 ELISA. Both VIDAS® NS1 and NS1 ELISA assays also demonstrated high sensitivity relative to DENV RNA RT-PCR set as gold standard (85.7% and 83.9%, respectively). In contrast, NS1 RDT was less sensitive relative to DENV RNA RT-PCR (72.7%). The overall agreement of VIDAS® IgM and IgG assays with the competitor assays was moderate (72.5% for IgM ELISA, 76.9% for IgG ELISA, and 68.7% for IgM and IgG RDT). In most analyses, test agreements of the VIDAS® assays were comparable in adults and children. Altogether, the VIDAS® dengue prototypes performed very well and appear to be suitable for routine detection of dengue NS1 antigen and anti-dengue IgM/IgG antibodies.
The aversive value of pain in human decision-making
Authors: Slimani Hocine , Rainville Pierre , Roy Mathieu 
Published: February 2021

AbstractAccording to basic utilitarian principles, people should try to maximize rewards and minimize pain. Here, participants were put in a situation where monetary rewards were paired to electric shocks spanning between pain detection and tolerance thresholds. Monetary offers ranged linearly from $0 to $5 or $10 in Group1 and 2, respectively, and exponentially from $0 to $5 in Group3. The value of pain increased quadratically as a function of the anticipated pain intensity. While increasing the range of monetary offers increased the price requested to accept pain, skewing the distribution of rewards encouraged profit maximization. Participants scoring higher on harm avoidance and lower on persistence scales requested more money to accept pain. Accepting highly painful offers slowed decisions regardless of the value of the concurrent reward. Altogether, pain-related decisions are highly relative to the local range of available rewards and may be under the control of more automatic avoidance mechanisms.
Training-induced bioenergetic improvement in human skeletal muscle is associated with non-stoichiometric changes in the mitochondrial proteome without reorganization of respiratory chain content
Authors: Granata Cesare , Caruana Nikeisha J. , Botella Javier , Jamnick Nicholas A. , Huynh Kevin , Kuang Jujiao , Janssen Hans A. , Reljic Boris , Mellett Natalie A. , Laskowski Adrienne , Stait Tegan L. , Frazier Ann E. , Coughlan Melinda T. , Meikle Peter J. , Thorburn David R. , Stroud David A. , Bishop David J. 
Published: February 2021

SUMMARYMitochondrial defects are implicated in multiple diseases and aging. Exercise training is an accessible and inexpensive therapeutic intervention improving mitochondrial bioenergetics and quality of life. By combining a multi-omics approach with biochemical andin siliconormalization, we removed the bias arising from the training-induced increase in human skeletal muscle mitochondrial content to unearth an intricate and previously undemonstrated network of differentially prioritized mitochondrial adaptations. We show that changes in hundreds of transcripts, proteins, and lipids are not stoichiometrically linked to the increase in mitochondrial content. We demonstrate that enhancing electron flow to oxidative phosphorylation (OXPHOS) is more important to improve ATP generation than increasing the abundance of the OXPHOS machinery, and that training-induced supercomplex formation does not confer enhancements in mitochondrial bioenergetics. Our study provides a new analytical approach allowing unbiased and in-depth investigations of training-induced mitochondrial adaptations, challenging our current understanding and calling for careful reinterpretation of previous findings.
QTLs for potato tuber resistance toDickeya solaniare located on chromosomes II and IV
Authors: Lebecka Renata , Śliwka Jadwiga , Grupa-Urbańska Anna , Szajko Katarzyna , Marczewski Waldemar 
Published: February 2021

AbstractSoft rot is a bacterial disease that causes heavy losses in potato production worldwide. The goal of this study was to identify quantitative trait loci (QTLs) for potato tuber resistance to bacteriumDickeya solaniand for tuber starch content to study the relationship between these traits. A highly resistant diploid hybrid of potato was crossed with a susceptible hybrid to generate the F1 mapping population. Tubers that were wound-inoculated with bacteria were evaluated for disease severity expressed as the mean weight of rotted tubers, and disease incidence measured as the proportion of rotten tubers. Diversity array technology (DArTseq™) was used for genetic map construction and QTLs analysis. The most prominent QTLs for disease severity and incidence were identified in overlapping regions on potato chromosome IV and explained 22.4% and 22.9% of the phenotypic variance, respectively. The second QTL for disease severity was mapped to chromosome II and explained 16.5% of the variance. QTLs for starch content were detected on chromosomes III, V, VI, VII, VIII, IX, XI, and XII in regions different than the QTLs for soft rot resistance. Two strong and reproducible QTLs for resistance toDickeya solanion potato chromosomes IV and II might be useful for further study of candidate genes and marker development in potato breeding programs. The relationship between tuber resistance to bacteria and the starch content in potato tubers was not confirmed by QTL mapping, which makes the selection of genotypes highly resistant to soft rot with a desirable starch content feasible.
Inhibition of SARS-CoV-2 infection in human cardiomyocytes by targeting the Sigma-1 receptor disrupts cytoskeleton architecture and contractility
Authors: Salerno José Alexandre , Torquato Thayana , Temerozo Jairo R. , Goto-Silva Livia , Mendes Mayara , Sacramento Carolina Q. , Fintelman-Rodrigues Natalia , Vitoria Gabriela , Souza Leticia , Ornelas Isis , Veríssimo Carla , Karmirian Karina , Pedrosa Carolina , Dias Suelen da Silva Gomes , Soares Vinicius Cardoso , Aragão Luiz Guilherme HS , Puig-Pijuan Teresa , Salazar Vinícius W. , Dariolli Rafael , Biagi Diogo , Furtado Daniel Rodrigues , Borges Helena L. , Bozza Patrícia , Guimarães Marília Zaluar , Souza Thiago Moreno L. , Rehen Stevens K. 
Published: February 2021

ABSTRACTHeart dysfunction, represented by conditions such as myocarditis and arrhythmia, has been reported in COVID-19 patients. Therapeutic strategies focused on the cardiovascular system, however, remain scarce. The Sigma-1 receptor (S1R) has been recently proposed as a therapeutic target because its inhibition reduces SARS-CoV-2 replication. To investigate the role of S1R in SARS-CoV-2 infection in the heart, we used human cardiomyocytes derived from induced pluripotent stem cells (hiPSC-CM) as an experimental model. Here we show that the S1R antagonist NE-100 decreases SARS-CoV-2 infection and viral replication in hiPSC-CMs. Also, NE-100 reduces cytokine release and cell death associated with infection. Because S1R is involved in cardiac physiology, we investigated the effects of NE-100 in cardiomyocyte morphology and function. We show that NE-100 compromises cytoskeleton integrity and reduces beating frequency, causing contractile impairment. These results show that targeting S1R to challenge SARS-CoV-2 infection may be a useful therapeutic strategy but its detrimental effects in vivo on cardiac function should not be ignored.
Recovery of small plasmid sequences via Oxford Nanopore sequencing
Authors: Wick Ryan R. , Judd Louise M. , Wyres Kelly L. , Holt Kathryn E. 
Published: February 2021

AbstractOxford Nanopore Technologies (ONT) sequencing platforms currently offer two approaches to whole-genome native-DNA library preparation: ligation and rapid. In this study, we compared these two approaches for bacterial whole-genome sequencing, with a specific aim of assessing their ability to recover small plasmid sequences. To do so, we sequenced DNA from seven plasmid-rich bacterial isolates in three different ways: ONT ligation, ONT rapid and Illumina. Using the Illumina read depths to approximate true plasmid abundance, we found that small plasmids (<20 kbp) were underrepresented in ONT ligation read sets (by a mean factor of ∼4) but were not underrepresented in ONT rapid read sets. This effect correlated with plasmid size, with the smallest plasmids being the most underrepresented in ONT ligation read sets. We also found lower rates of chimeric reads in the rapid read sets relative to ligation read sets. These results show that when small plasmid recovery is important, ONT rapid library preparations are preferable to ligation-based protocols.Impact statementResearchers who use Oxford Nanopore Technologies (ONT) platforms to sequence bacterial genomes can currently choose from two library preparation methods. The first is a ligation-based approach, which uses ligase to attach sequencing adapters to the ends of DNA molecules. The second is a rapid approach, which uses a transposase enzyme to cleave DNA and attach adapters in a single step. There are advantages to each preparation, for example ligation can produce better yields but rapid is a simpler procedure. Our study reveals another advantage of rapid preparations: they are more effective at sequencing small plasmids. We show that sequencing of ligation-based libraries yields fewer reads derived from small plasmids, making such plasmids harder to detect in bacterial genomes. Since small plasmids can contain clinically relevant genes, including antimicrobial resistance (AMR) or virulence determinants, their exclusion could lead to unreliable conclusions that have serious consequences for AMR surveillance and prediction. We therefore recommend that researchers performing ONT-only sequencing of bacterial genomes should consider using rapid preparations whenever small plasmid recovery is important.Data summarySupplementary figures, tables, data and code can be found at:github.com/rrwick/Small-plasmid-Nanopore
Automatic segmentation and cardiac mechanics analysis of evolving zebrafish using deep-learning
Authors: Zhang Bohan , Pas Kristofor , Ijaseun Toluwani , Cao Hung , Fei Peng , Lee Juhyun 
Published: February 2021

AbstractObjectiveIn the study of early cardiac development, it is important to acquire accurate volume changes of the heart chambers. Although advanced imaging techniques, such as light-sheet fluorescent microscopy (LSFM), provide an accurate procedure for analyzing the structure of the heart, rapid and robust segmentation is required to reduce laborious time and accurately quantify developmental cardiac mechanics.MethodsThe traditional biomedical analysis involving segmentation of the intracardiac volume is usually carried out manually, presenting bottlenecks due to enormous data volume at high axial resolution. Our advanced deep-learning techniques provide a robust method to segment the volume within a few minutes. Our U-net based segmentation adopted manually segmented intracardiac volume changes as training data and produced the other LSFM zebrafish cardiac motion images automatically.ResultsThree cardiac cycles from 2 days post fertilization (dpf) to 5 dpf were successfully segmented by our U-net based network providing volume changes over time. In addition to understanding the cardiac function for each of the two chambers, the ventricle and atrium were separated by 3D erode morphology methods. Therefore, cardiac mechanical properties were measured rapidly and demonstrated incremental volume changes of both chambers separately. Interestingly, stroke volume (SV) remains similar in the atrium while that of the ventricle increases SV gradually.ConclusionOur U-net based segmentation provides a delicate method to segment the intricate inner volume of zebrafish heart during development; thus providing an accurate, robust and efficient algorithm to accelerate cardiac research by bypassing the labor-intensive task as well as improving the consistency in the results.
IL-32 is a metabolic regulator promoting survival and proliferation of malignant plasma cells
Authors: Aass Kristin Roseth , Mjelle Robin , Kastnes Martin H. , Tryggestad Synne S. , van den Brink Luca M. , Westhrin Marita , Zahoor Muhammad , Moen Siv H. , Buene Glenn , Misund Kristine , Sponaas Anne-Marit , Ma Qianli , Sundan Anders , Groen Richard WJ , Slørdahl Tobias S. , Waage Anders , Standal Therese 
Published: February 2021

AbstractIL-32 is a non-classical cytokine expressed in cancers, inflammatory diseases and infections. IL-32 can have both extracellular and intracellular functions, and its receptor is not identified. We here demonstrate that endogenously expressed, intracellular IL-32 binds to components of the mitochondrial respiratory chain and promotes oxidative phosphorylation. Knocking out IL-32 in malignant plasma cells significantly reduced survival and proliferationin vitroandin vivo. High throughput transcriptomic and MS-metabolomic profiling of IL-32 KO cells revealed that loss of IL-32 leads to profound perturbations in metabolic pathways, with accumulation of lipids, pyruvate precursors and citrate, indicative of reduced mitochondrial function. IL-32 is expressed in a subgroup of multiple myeloma patients with an inferior prognosis. Primary myeloma cells expressing IL-32 were characterized by a plasma cell gene signature associated with immune activation, proliferation and oxidative phosphorylation. We propose a novel concept for regulation of metabolism by an intracellular cytokine and identify IL-32 as an endogenous growth and survival factor for malignant plasma cells. IL-32 is a potential prognostic biomarker and a treatment target in multiple myeloma.
Annealing of focused ion beam damage in gold microcrystals: an in situ Bragg coherent X-ray diffraction imaging study
Authors: Yang David , Phillips Nicholas W. , Song Kay , Harder Ross J. , Cha Wonsuk , Hofmann Felix 
Published: February 2021

Focused ion beam (FIB) techniques are commonly used to machine, analyse and image materials at the micro- and nanoscale. However, FIB modifies the integrity of the sample by creating defects that cause lattice distortions. Methods have been developed to reduce FIB-induced strain; however, these protocols need to be evaluated for their effectiveness. Here, non-destructive Bragg coherent X-ray diffraction imaging is used to study the in situ annealing of FIB-milled gold microcrystals. Two non-collinear reflections are simultaneously measured for two different crystals during a single annealing cycle, demonstrating the ability to reliably track the location of multiple Bragg peaks during thermal annealing. The thermal lattice expansion of each crystal is used to calculate the local temperature. This is compared with thermocouple readings, which are shown to be substantially affected by thermal resistance. To evaluate the annealing process, each reflection is analysed by considering facet area evolution, cross-correlation maps of the displacement field and binarized morphology, and average strain plots. The crystal's strain and morphology evolve with increasing temperature, which is likely to be caused by the diffusion of gallium in gold below ∼280°C and the self-diffusion of gold above ∼280°C. The majority of FIB-induced strains are removed by 380–410°C, depending on which reflection is being considered. These observations highlight the importance of measuring multiple reflections to unambiguously interpret material behaviour.