bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of methanogen community to elevation of cathode potentials in the presence of magnetite
Authors: Gao Kailin , Wang Xin , Huang Junjie , Xia Xingxuan , Lu Yahai 
Published: November 2020

ABSTRACTElectromethanogenesis refers to the process where methanogens utilize electrons derived from cathodes for the reduction of CO2to CH4. Setting of low cathode potentials is essential for this process. In this study, we test if magnetite, an iron oxide mineral widespread in environment, can facilitate the adaption of methanogen community to the elevation of cathode potentials in electrochemical reactors. Two-chamber electrochemical reactors were constructed with inoculants obtained from a paddy field soil. We elevated cathode potentials stepwise from the initial −0.6 V vs standard hydrogen electrode (SHE) to −0.5 V and then to −0.4 V over the 120 days acclimation. Only weak current consumption and CH4production were observed in the reactors without magnetite. But biocathodes were firmly developed and significant current consumption and CH4production were recorded in the magnetite reactors. The robustness of electro-activity in the magnetite reactors was not affected with the elevation of cathode potentials from −0.6 V to −0.4 V. But, the current consumption and CH4production were virtually halted in the reactors without magnetite when cathode potential was elevated to −0.4 V. Methanogens related toMethanospirillumwere enriched on cathode surface of the magnetite reactors at −0.4 V, whileMethanosarcinarelatively dominated in the reactors without magnetite.Methanobacteriumalso increased in the magnetite reactors but stayed off electrodes in the culture medium at −0.4 V. Apparently, magnetite greatly facilitates the development of biocathodes, and it appears that with the aid of magnetiteMethanospirillumspp. can adapt to high cathode potentials performing the efficient electromethanogenesis.IMPORTANCEConverting CO2to CH4through bioelectrochemistry is a promising approach for development of green energy biotechnology. This process however requires setting the low cathode potentials, which takes cost. In this study, we test if magnetite, a conductive iron mineral, can facilitate the adaption of methanogens to the elevation of cathode potentials. In the two-chamber reactors constructed using inoculants obtained from a paddy field soil, biocathodes were firmly developed in the presence of magnetite, whereas only weak electro-activity was observed in the reactors without magnetite. The elevation of cathode potentials did not affect the robustness of electro-activity in the magnetite reactors over the 120 days acclimation.Methanospirillumwas identified as the key methanogens associated with cathode surface during the operation at relatively high potentials. The findings reported in this study shed a new light on the adaption of methanogen community to the elevated cathode potentials in the presence of magnetite.
Environment-driven reprogramming of gamete DNA methylation occurs during maturation and is transmitted intergenerationally in salmon
Authors: Wellband Kyle , Roth David , Linnansaari Tommi , Curry R. Allen , Bernatchez Louis 
Published: November 2020

AbstractAn epigenetic basis for transgenerational plasticity is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally-induced intergenerational effects, but solely in the context of early life environmental differences. Using whole genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.
Conservation of glutathione S-transferase mRNA and protein sequences similar to human and horse Alpha class GST A3-3 across dog, goat, and opossum species
Authors: Hubert Shawna M. , Samollow Paul B. , Lindström Helena , Mannervik Bengt , Ing Nancy H. 
Published: November 2020

AbstractRecently, the glutathione S-transferase A3-3 (GST A3-3) homodimeric enzyme was identified as the most efficient enzyme that catalyzes isomerization of the precursors of testosterone, estradiol, and progesterone in the gonads of humans and horses. However, the presence of GST A3-3 orthologs with equally high ketosteroid isomerase activity has not been verified in other mammalian species, even though pig and cattle homologs have been cloned and studied. IdentifyingGSTA3genes is a challenge because of multipleGSTAgene duplications (12 in the human genome), so few genomes have a correspondingGSTA3gene annotated. To improve our understanding ofGSTA3gene products and their functions across diverse mammalian species, we cloned homologs of the horse and humanGSTA3mRNAs from the testes of a dog, goat, and gray short-tailed opossum, with those current genomes lackingGSTA3gene annotations. The resultant novelGSTA3mRNA and inferred protein sequences had a high level of conservation with humanGSTA3mRNA and protein sequences (≥ 70% and ≥ 64% identities, respectively). Sequence conservation was also apparent for the 13 residues of the “H-site” in the 222 amino acid GSTA3 protein that is known to interact with the steroid substrates. Modeling predicted that the dog GSTA3-3 is a more active ketosteroid isomerase than the goat or opossum enzymes. Our results help us understand the active sites of mammalian GST A3-3 enzymes, and their inhibitors may be useful for reducing steroidogenesis for medical purposes, such as fertility control or treatment of steroid-dependent diseases.
Comprehensive benchmarking of single cell RNA sequencing technologies for characterizing cellular perturbation
Authors: Karen Verboom , Assefa Alemu T , Yigit Nurten , Anckaert Jasper , Vandamme Niels , Rombaut Dries , Saeys Yvan , Thas Olivier , Speleman Frank , Durinck Kaat , Vandesompele Jo 
Published: November 2020

ABSTRACTTechnological advances in transcriptome sequencing of single cells continues to provide an unprecedented view on tissue composition and cellular heterogeneity. While several studies have compared different single cell RNA-seq methods with respect to data quality and their ability to distinguish cell subpopulations, none of these studies investigated the heterogeneity of the cellular transcriptional response upon a chemical perturbation. In this study, we evaluated the transcriptional response of NGP neuroblastoma cells upon nutlin-3 treatment using the C1, ddSeq and Chromium single cell systems. These devices and library preparation methods are representative for the wide variety of platforms, ranging from microfluid chips to droplet-based systems and from full transcript sequencing to 3-prime end sequencing. In parallel, we used bulk RNA-seq for molecular characterization of the transcriptional response. Two complementary metrics to evaluate performance were applied: the first is the number and identity of differentially expressed genes as defined in consensus by two statistical models, and the second is the enrichment analysis of biological signals. Where relevant, to make the data more comparable, we downsampled sequencing library size, selected cell subpopulations based on specific RNA abundance features, or created pseudobulk samples. While the C1 detects the highest number of genes per cell and better resembles bulk RNA-seq, the Chromium identifies most differentially expressed genes, albeit still substantially fewer than bulk RNA-seq. Gene set enrichment analyses reveals that detection of a limited set of the most abundant genes in single cell RNA-seq experiments is sufficient for molecular phenotyping. Finally, single cell RNA-seq reveals a heterogeneous response of NGP neuroblastoma cells upon nutlin-3 treatment, revealing putative late-responder or resistant cells, both undetected in bulk RNA-seq experiments.
Reversed upper glycolysis and rapid activation of oxidative pentose phosphate pathway supports the oxidative burst in neutrophils
Authors: Britt Emily C. , Fan Jing 
Published: November 2020

AbstractNeutrophils are abundant white blood cells at the frontline of innate immunity. Upon stimulation, neutrophils rapidly activate effector functions such as the oxidative burst and neutrophil extracellular traps (NETs) to eliminate pathogens. However, little is known about how neutrophil metabolism powers these functions. Our metabolomic analysis on primary human neutrophils revealed that neutrophil metabolism is rapidly rewired upon pro-inflammatory activation, with particularly profound changes observed in glycolysis and the pentose phosphate pathway (PPP). We found that the stimulation-induced changes in PPP were specifically coupled with the oxidative burst. The oxidative burst requires a large amount of NADPH to fuel superoxide production via NADPH Oxidase (NOX). Isotopic tracing studies revealed that in order to maximize the NADPH yield from glucose metabolism, neutrophils quickly adopt near complete pentose cycle during the oxidative burst. In this metabolic mode, all glucose is shunted into the oxidative PPP, and the resulting pentose-phosphate is recycled back to glucose-6-phosphate, which then re-enters the oxidative PPP. To enable this recycling, net flux through the upper glycolytic enzyme glucose-6-phosphate isomerase (GPI) is completely reversed. This allows oxidative PPP flux in neutrophils to reach greater than two-fold of the glucose uptake rate, far exceeding other known mammalian cells and tissues. Intriguingly, the adoption of this striking metabolic mode is completely dependent on an increased demand for NADPH associated with the oxidative burst, as inhibition of NOX resets stimulated neutrophils to use glycolysis-dominant glucose metabolism, with oxidative PPP flux accounting for less than 10% of glucose metabolism. Together, these data demonstrated that neutrophils have remarkable metabolic flexibility that is essential to enable the rapid activation of their effector functions.Graphic Abstract
3D segmentation of perivascular spaces on T1-weighted 3 Tesla MR images with a convolutional autoencoder and a U-shaped neural network
Authors: Boutinaud Philippe , Tsuchida Ami , Laurent Alexandre , Adonias Filipa , Hanifehlou Zahra , Nozais Victor , Verrecchia Violaine , Lampe Leonie , Zhang Junyi , Zhu Yi-Cheng , Tzourio Christophe , Mazoyer Bernard , Joliot Marc 
Published: November 2020

AbstractWe implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance imaging (MRI) data from a large database of 1,832 healthy young adults. An important feature of this approach is the ability to learn from relatively sparse data, which gives the present algorithm a major advantage over other DL algorithms. Here, we trained the algorithm with 40 T1-weighted MRI datasets in which all “visible” PVSs were manually annotated by an experienced operator. After learning, performance was assessed using another set of 10 MRI scans from the same database in which PVSs were also traced by the same operator and were checked by consensus with another experienced operator. The Sorensen-Dice coefficients for PVS voxel detection in DWM (resp. BG) were 0.51 (resp. 0.66), and 0.64 (resp. 0.71) for PVS cluster detection (volume threshold of 0.5 within a range of 0 to 1). Dice values above 0.90 could be reached for detecting PVSs larger than 10 mm3and 0.95 for PVSs larger than 15 mm3. We then applied the trained algorithm to the rest of the database (1,782 individuals). The individual PVS load provided by the algorithm showed a high agreement with a semi-quantitative visual rating done by an independent expert rater, both for DWM and for BG. Finally, we applied the trained algorithm to an age-matched sample from another MRI database acquired using a different scanner. We obtained a very similar distribution of PVS load, demonstrating the interoperability of this algorithm.
Model-based integration of citizen-science data from disparate sources increases the precision of bird population trends
Authors: Hertzog Lionel R , Frank Claudia , Klimek Sebastian , Röder Norbert , Böhner Hannah GS , Kamp Johannes 
Published: November 2020

AbstractAimTimely and accurate information on population trends is a prerequisite for effective biodiversity conservation. Structured biodiversity monitoring programs have been shown to track population trends reliably, but require large financial and time investment. The data assembled in a large and growing number of online databases are less structured and suffer from bias, but the number of observations is much higher compared to structured monitoring programs. Model-based integration of data from these disparate sources could capitalize on their respective strengths.LocationGermany.MethodsAbundance data for 26 farmland bird species were gathered from the standardized Common Breeding Bird Survey (CBBS) and three online databases that varied with regard to their degree of survey standardization. Population trends were estimated with a benchmark model that included only CBBS data, and five Bayesian hierarchical models integrating all data sources in different combinations. Across models, we compared consistency and precision of the predicted population trends, and the accuracy of the models. Bird species body mass, prevalence in the dataset and abundance were tested as potential predictors of the explored quantities.ResultsConsistency in predicted annual abundance indices was generally high especially when comparing the benchmark models to the integrated models without unstructured data. The accuracy of the estimated population changes was higher in the hierarchical models compared to the benchmark model but this was not related to data-integration. Precision of the predicted population trends increased as more data sources were integrated.Main conclusionsModel-based integration of data from different sources can lead to improved precision of bird population trend estimates. This opens up new opportunities for conservation managers to identify declining populations earlier. Integrating data from online databases could substantially increase sample size and thus allowing to derive trends for currently not well-monitored species, especially at sub-national scales.
Pediatric glioblastoma - unlike normal cells - are sensitive to the combination of vorinostat and olaparib and to its downstream effector - phosphorylated eIF2α
Authors: Eytan Karin , Versano Ziv , Leitner Moshe , Paglin Shoshana , Toren Amos , Yalon Michal 
Published: November 2020

AbstractCurrent therapies offer only a short relief for patients with pediatric glioblastoma (PED-GBM). Therefore, expanding treatment options for this fatal disease is of utmost importance. We found that PED-GBM cell lines, originated from diffuse intrinsic pontine glioma expressing H3K27M mutation (DIPG), or from hemispheric glioma expressing H3G34R mutation, are sensitive to combinations of histone deacetylase and PARP-1 inhibitors (vorinostat with either olaparib or veliparib). These combinations led to an enhanced decrease in their survival, and to increased phosphorylation of eIF2α. Experiments with the S51D phosphomimetic variant of eIF2α and with brain-penetrating inhibitors of phosphorylated eIF2α (p-eIF2α) dephospohrylation, salubrinal and raphin1, showed that increased eIF2α phosphorylation diminished PED-GBM cell survival and sensitized them to PARP-1 inhibitors as well as to ionizing irradiation, which is the main treatment modality in these patients. PED-GBM cells were also remarkably more sensitive to combination of vorinostat and PARP-1 inhibitors and to salubrinal and raphin1 than normal human astrocytes and fibroblasts.Importantly, although the overall effect of increased eIF2α phosphorylation was a reduced survival of PED-GBM cells, it also increased the cellular level of MTH1, an enzyme that protects treated cells against the incorporation of oxidized nucleotides into nucleic acids, resulting in an enhanced decrease in cell survival in response to the combination of salubrinal and MTH1 inhibitor, TH588.Our results indicate that combinations of the FDA approved drugs, vorinostat and either veliparib or olaparib, could potentially be included in PED-GBM treatment protocols and that the effect of salubrinal and raphin1 on PED-GBM survival warrants further evaluation.
Grandmother’s chemical legacy of pesticide exposure: bi-generational effects and acclimation in a model invertebrate
Authors: Poulsen Rikke , De Fine Licht Henrik H. , Hansen Martin , Cedergreen Nina 
Published: November 2020

AbstractMan-made chemicals are a significant contributor to the ongoing deterioration of ecosystems. Currently, risk assessment of these chemicals is based on observations in a single generation of animals, despite potential adverse intergenerational effects. Here, we investigate the effect of the fungicide prochloraz across three generations ofDaphnia magna.We studied both the effects of continuous exposure over all generations and the effects of first-generation (F0) exposure on two subsequent, non-exposed, generations. Effects at different levels of biological organization were monitored. Acclimation to prochloraz was found after continuous exposure. Following F0-exposure, non-exposed F1-offspring showed no significant effects. However, in the F2 animals, several parameters differed significantly from controls. A direct association between grandmaternal effects and toxic mode of action of prochloraz was found, showing that chemicals can be harmful not only to the exposed generation, but also to subsequent generations and that effects may even skip a generation.
High temperature cycles result in maternal transmission and dengue infection differences between Wolbachia strains in Aedes aegypti
Authors: Mancini Maria Vittoria , Ant Thomas H. , Herd Christie S. , Gingell Daniel D. , Murdochy Shivan M. , Mararo Enock , Sinkins Steven P. 
Published: November 2020

AbstractEnvironmental factors play a crucial role in the population dynamics of arthropod endosymbionts, and therefore in the deployment of Wolbachia symbionts for the control of dengue arboviruses. The potential of Wolbachia to invade, persist and block virus transmission depends in part on its intracellular density. Several recent studies have highlighted the importance of larval rearing temperature in modulating Wolbachia densities in adults, suggesting that elevated temperatures can severely impact some strains, while having little effect on others. The effect of a replicated tropical heat cycle on Wolbachia density and levels of virus blocking was assessed using Aedes aegypti lines carrying strains wMel and wAlbB, two Wolbachia strains currently used for dengue control. Impacts on intracellular density, maternal transmission fidelity and dengue inhibition capacity were observed for wMel. In contrast wAlbB-carrying Ae. aegypti maintained a relatively constant intracellular density at high temperatures and conserved its capacity to inhibit dengue. Following larval heat treatment, wMel showed a degree of density recovery in aging adults, although this was compromised by elevated air temperatures. When choosing the Wolbachia strain to be used in a dengue control programme it is important to consider the effects of environmental temperatures on invasiveness and virus inhibition.Author summaryIn the past decades, dengue incidence has dramatically increased all over the world. An emerging dengue control strategy utilizes Ae. aegypti mosquitoes artificially transinfected with the bacterial symbiont Wolbachia, with the ultimate aim of replacing wild mosquito populations. Wolbachia is transmitted from mother to offspring and is able to interfere with virus transmission within the mosquito vector. However, the rearing temperature of mosquito larvae is known to impact on some Wolbachia strains. In this study, we compared the effects of a temperature cycle mimicking natural breeding sites in tropical climates on two Wolbachia strains, currently used for open field trials. We observed that the strain wMel was susceptible to high larval rearing temperatures, while the strain wAlbB resulted to be more stable. These results underlines the importance of understanding the impact of environmental factors on released mosquitoes, in order to ensure the most efficient strategy for dengue control.
The effect of ischaemic postconditioning on mucosal integrity and function in equine jejunal ischaemia
Authors: Verhaar Nicole , Breves Gerhard , Hewicker-Trautwein Marion , Pfarrer Christiane , Rohn Karl , Burmester Marion , Schnepel Nadine , Neudeck Stephan , Twele Lara , Kaestner Sabine 
Published: November 2020

SummaryBackgroundIschaemic postconditioning (IPoC) has been shown to ameliorate ischaemia reperfusion injury in different species and tissues.ObjectivesTo assess the feasibility of IPoC in equine small intestinal ischaemia and to assess its effect on histomorphology, electrophysiology and paracellular permeability.Study designrandomized controlled terminal in vivo experimentMethodsExperimental jejunal ischaemia was induced for 90 min in horses under general anaesthesia. In the control group (C; n=7), the jejunum was reperfused without further intervention. In the postconditioning group (P; n=7), IPoC was implemented by clamping the mesenterial vessels after ischaemia. This was followed by 120 minutes of reperfusion in both groups. Intestinal microperfusion and oxygenation was measured during IPoC using spectrophotometry and Doppler fluxmetry. Histomorphology and histomorphometry of the intestinal mucosa were assessed. Furthermore, electrophysiological variables and unidirectional fluxrates of 3H-mannitol were determined in Ussing chambers. Western Blot analysis was performed to determine the tight junction protein levels of Claudin-1, Claudin-2 and Occludin in the intestinal mucosa. Comparisons between the groups and time points were performed using a two-way repeated measures ANOVA or non-parametric statistical tests for the ordinal and not normally distributed data (significance p<0.05).ResultsPostconditioning significantly reduced intestinal microperfusion during all clamping cycles, yet affected tissue oxygenation only during the first cycle. After reperfusion, group IPoC showed significantly less mucosal villus denudation (mean difference 21.5 %, p=0.02) and decreased mucosal-to-serosal fluxrates (mean difference 15.2 nM/cm2/h, p=0.007) compared to group C. There were no significant differences between the groups for the other tested variables.Main limitationssmall sample size, long term effects were not investigated.ConclusionsFollowing ischaemic postconditioning, the intestinal mucosa demonstrated significantly less villus denudation and paracellular permeability compared to the untreated control group, possibly indicating a protective effect of IPoC on ischaemia reperfusion injury.