bluuebunny/crossref_metadata_2025_split huggingface dataset:
A robust method for generating, quantifying and testing large amounts ofEscherichia colipersisters
Authors: Vedelaar Silke R. , Radzikowski Jakub L. , Heinemann Matthias 
Published: July 2020

AbstractBacteria can exhibit phenotypes, which makes them tolerant against antibiotics. However, often only a few cells of a bacterial population show such so-called persister phenotype, which makes it difficult to study this health-threatening phenotype. We recently found that certain abrupt nutrient-shifts generateE. colipopulations that consist of almost only antibiotic tolerant persister cells. Such nearly homogeneous persister cell populations enable assessment with population-averaging experimental methods, such as high-throughput methods. In this paper, we provide a detailed protocol of how to generate such large fraction of tolerant cells using the nutrient-switch approach. Furthermore, we describe how to determine the fraction of cells that enter the tolerant state upon a sudden nutrient shift and describe a new way to assess antibiotic tolerance with flow cytometry. We envision that these methods facilitate research into the important and exciting phenotype of bacterial cells.
Sexually divergent development of depression-related brain networks during healthy human adolescence
Authors: Dorfschmidt L. , Bethlehem R.A.I. , Seidlitz J. , Váša F. , White S.R. , Romero-García R. , Kitzbichler M.G. , Aruldass A. , Morgan S.E. , Goodyer I.M. , Fonagy P. , Jones P.B. , Dolan R.J. ,   the NSPN consortium, Harrison N.A. , Vértes P.E. , Bullmore E.T. 
Published: July 2020

AbstractWe hypothesized that there are sexual differences in human brain network development underlying the female > male divergence in adolescent depression. We tested for sex differences in parameters of brain network development (accelerated longitudinal fMRI, N=298 healthy adolescents, each scanned 1 to 3 times). Sexually divergent development of functional connectivity was located in default mode network (DMN), limbic cortex, and subcortical nuclei. Females had a more “disruptive” pattern of development, where weak functional connectivity at age 14 became stronger during adolescence. This fMRI-derived map of divergent adolescent development was co-located with (i) a map of functional dysconnectivity associated with adult major depressive disorder (MDD); and (ii) an adult brain gene expression pattern enriched for genes on the X chromosome, neurodevelopmental genes, and risk genes for MDD. Sexual divergence in disruptive development of DMN, limbic and subcortical functional networks is potentially relevant to the increased risk of depression in adolescent females.
Sleep Identification Enabled by Supervised Training Algorithms (SIESTA): An open-source platform for automatic sleep staging of rodent polysomnographic data
Authors: Caldart Carlos S. , Sanchez Raymond E. A. , Ben-Hamo Miriam , Beck Asad I. , Weil Tenley A. , Perez Jazmine G. , Kalume Franck , Brunton Bingni W. , de la Iglesia Horacio O. 
Published: July 2020

AbstractThe temporal distribution of sleep stages is critical for the study of sleep function, regulation, and disorders in higher vertebrates. This temporal distribution is typically determined polysomnographically. In laboratory rodents, scoring of electrocorticography (ECoG) and electromyography (EMG) recordings is usually performed manually, where 5-10 second epochs are categorized as one of three specific stages: wakefulness, rapid-eye-movement (REM) sleep and non-REM (NREM) sleep. This process is laborious, time-consuming, and particularly impractical for large experimental cohorts with recordings lasting longer than 24 hours.To circumvent this problem, we developed an open-source Python toolkit,Sleep Identification Enabled by Supervised Training Algorithms(SIESTA), that automates the detection of these three main behavioral stages in mice. Our supervised machine learning algorithm extracts features from the ECoG and EMG signals, then automatically scores recordings with a hierarchical classifier based on Bagging Random Forest approaches. We evaluated this approach on data collected from wild-type mice housed under both normal and different lighting conditions, as well as from a mutant mouse line with abnormal sleep phenotypes. To validate its performance on test data, we compared SIESTA with manually scored data and obtained F1scores of 0.92 for wakefulness, 0.81 for REM, and 0.93 for NREM.SIESTA has a user-friendly interface that can be used without coding expertise. To our knowledge, this is the first time that such a strategy has been developed using all open-source and freely available resources, and our aim is that SIESTA becomes a useful tool that facilitates further research of sleep in rodent models.
Self-assembling shell proteins PduA and PduJ have essential and redundant roles in bacterial microcompartment assembly
Authors: Kennedy Nolan W. , Ikonomova Svetlana P. , Lee Marilyn Slininger , Raeder Henry W. , Tullman-Ercek Danielle 
Published: July 2020

AbstractProtein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the survival of enteric bacteria. These structures are increasingly popular with biological engineers due to their potential utility as nanobioreactors or drug delivery vehicles. However, the limited understanding of the assembly mechanism of these bacterial microcompartments hinders efforts to repurpose them for non-native functions. Here, we comprehensively investigate proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment fromSalmonella entericaserovar Typhimurium LT2, one of the most widely studied microcompartment systems. We first demonstrate that two shell proteins, PduA and PduJ, have a high propensity for self-assembly upon overexpression, and we provide a novel method for self-assembly quantification. Using genomic knock-outs and knock-ins, we systematically show that these two proteins play an essential and redundant role in bacterial microcompartment assembly that cannot be compensated by other shell proteins. At least one of the two proteins PduA and PduJ must be present for the bacterial microcompartment shell to assemble. We also demonstrate that assembly-deficient variants of these proteins are unable to rescue microcompartment formation, highlighting the importance of this assembly property. Our work provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.
Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
Authors: Gustafsson Johan , Robinson Jonathan , Nielsen Jens , Pachter Lior 
Published: July 2020

AbstractThe incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays allows for the removal of amplification bias in the estimation of gene abundances. We show that UMIs can also be used to address a problem resulting from incomplete sequencing of amplified molecules in sequencing libraries that can lead to bias in gene abundance estimates. Our method, called BUTTERFLY, is based on a zero truncated negative binomial estimator and is implemented in the kallisto bustools single-cell RNA-seq workflow. We demonstrate its efficacy using a range of datasets and show that it can invert the relative abundance of certain genes in cases of a pooled amplification paradox.
Faunistic study on the freshwater ciliates from Delhi, India
Authors: Abraham Jeeva Susan , Gupta Renu , Somasundaram Sripoorna , Naqvi Ilmas , Maurya Swati , Toteja Ravi , Makhija Seema 
Published: July 2020

AbstractThe ciliated protist communities show richness as well as uniqueness. This is true both for aquatic and soil ciliates. Delhi region lies in the subtropical semi-arid zone wherein the temperatures are highest in May-June and lowest in January. It also receives its monsoonal rainfall during the month of July-August. Thus, the region offers ideal conditions for the growth and proliferation of aquatic living beings. During the past three decades, a series of investigation has been carried out on the freshwater free-living ciliate fauna from fourteen sites at the river Yamuna and different freshwater bodies in Delhi. Samples were brought to the laboratory, ciliates were identified using live-cell observations and silver staining methods. A large number of Spirotrich species and a lower proportion belonging to class Heterotrichea, Litostomaea, Phyllopharyngea, Oligohymenophorea, Prostomatea, and Colpodea were identified. A total of 55 species belonging to 7 classes, 16 orders, 26 families, 40 genera were identified and documented. Ciliate diversity was found to be highest in the water sample from Okhla bird sanctuary (OBS). All ciliate species recorded during the present study have been listed and their general characteristics have been discussed.
Towards a taxonomically unbiased EU Biodiversity Strategy for 2030
Authors: Mammola Stefano , Riccardi Nicoletta , Prié Vincent , Correia Ricardo , Cardoso Pedro , Lopes-Lima Manuel , Sousa Ronaldo 
Published: July 2020

AbstractThrough the Habitats Directive (92/43/EEC) and the LIFE projects financial investments, Europe has been the world’s experimental arena for biological conservation. With an estimated budget of €20 billion/year, the EU Biodiversity Strategy for 2030 has set an ambitious goal of reaching 30% Protected Areas and ensure no deterioration in conservation trends and status of all protected species. We analyzed LIFE projects focused on animals from 1992 to 2018 and we found that investment towards vertebrates has been six times higher than that for invertebrates (€970 vs €150 million), with birds and mammals alone accounting for 72% species and 75% total budget. Budget allocation is primarily explained by species’ popularity. We propose a roadmap to achieve unbiased conservation targets for 2030 and beyond.
UvrD helicase–RNA polymerase interactions are governed by UvrD’s carboxy-terminal Tudor domain
Authors: Kawale Ashish A. , Burmann Björn M. 
Published: July 2020

ABSTRACTAll living organisms have to cope with the constant threat of genome damage by UV light and other toxic reagents. To maintain the integrity of their genomes, organisms developed a variety of DNA repair pathways. One of these, theTranscriptionCoupled DNA-Repair (TCR) pathway, is triggered by stalled RNA Polymerase (RNAP) complexes at DNA damage sites on actively transcribed genes. A recently elucidated bacterial TCR pathway employs the UvrD helicase pulling back stalled RNAP complexes from the damage, stimulating recruitment of the DNA-repair machinery. However, structural and functional aspects of UvrD’s interaction with RNA Polymerase remain elusive. Here we used advanced solution NMR spectroscopy to investigate UvrD’s role within the TCR, identifying that the carboxy-terminal region of the UvrD helicase facilitates RNAP interactions by adopting a Tudor-domain like fold. Subsequently, we functionally analyzed this domain, identifying it as a crucial component for the UvrD–RNAP interaction besides having nucleic-acid affinity.
Ghat: An R package for identifying adaptive polygenic traits
Authors: Mahmoud Medhat , Tost Mila , Ha Ngoc-Thuy , Simianer Henner , Beissinger Timothy 
Published: July 2020

AbstractIdentifying selection on polygenic complex traits in crops and livestock is important for understanding evolution and helps prioritize important characteristics for breeding. The QTL that contribute to polygenic trait variation often exhibit small or infinitesimal effects. This hinders the ability to detect QTL controlling polygenic traits because enormously high statistical power is needed for their detection. Recently, we circumvented this challenge by introducing a method to identify selection on complex traits by evaluating the relationship between genome-wide changes in allele frequency and estimates of effect-size. The approach involves calculating a composite-statistic across all markers that captures this relationship, followed by implementing a linkage disequilibrium-aware permutation test to evaluate if the observed pattern differs from that expected due to drift during evolution and population stratification. In this manuscript, we describe “Ghat”, an R package developed to implement this method to test for selection on polygenic traits. We demonstrate the package by applying it to test for polygenic selection on 15 published European wheat traits including yield, biomass, quality, morphological characteristics, and disease resistance traits. Moreover, we applied Ghat to different simulated populations with different breeding history and genetic architecture. The results highlight the power of Ghat to identify selection on complex traits. The Ghat package is accessible on CRAN, the Comprehensive R Archival Network, and on GitHub.
Sodium Diethyldithiocarbamate antiparasitic activity against differentTrypanosoma cruzistrains: Insights of its biological activity
Authors: de Freitas Oliveira Johny Wysllas , Torres Taffarel Melo , Gonçalves Moreno Cláudia Jassica , Amorim-Carmo Bruno , Damasceno Igor Zumba , Cruz Soares Ana Katarina Menezes , da Silva Barbosa Jefferson , Oliveira Rocha Hugo Alexandre , Silva Marcelo Sousa 
Published: July 2020

AbstractBackgroundChagas disease is caused by the protozoanTrypanosoma cruzi, a neglected tropical disease that affects thousands of people, mainly in Latin America. The drugs currently used in therapy are toxic and have therapeutic limitations during treatment. In addition, the genetic diversity ofT. cruzirepresents an important variable and challenge with regard to the pathogenesis of the infection, the epidemiological profile of the cases, and the therapeutic control of the infection. Sodium diethyldithiocarbamate (DETC) is a compound of high pharmacological versatility acting as metal chelators and producing reactive oxygen species. Thus, the objective of this work is to characterize the antiparasitic action of DETC against different strains and evolutionary forms ofT. cruzi, as well as the characterization of the mechanism of antiparasitic action.Methodology/Principal findingsThe different strains and evolutionary forms ofT. cruziwere grown in LIT medium. To evaluate the antiparasitic activity of DETC, the evolutionary forms epimastigote and trypomastigote ofT. cruziwere used by resazurin reduction methods and by counting under optical microscopy. Different response patterns were obtained between the strains and an IC50of DETC ranging from 9.44 ± 3,181µM to 60.49 ± 7.62 µM. Cell cytotoxicity against cell lines 3T3 and RAW and evaluated by MTT, demonstrated that DETC in high concentration (2222 µM) reduces around 60% the cell capacity of MTT reduction. The antiparasitic activity of DETC has been demonstrated through damage caused in the mitochondria ofT. cruzi, a reduction of up to 80% in the mitochondrial potential of the parasites, as well as through damage caused in the membrane of the parasite.ConclusionIn this study we can conclude that DETC has antiparasitic activity against different genotypes and evolutionary forms ofT. cruzi, representing a promising molecule as a drug for the treatment of Chagas disease.
Mus musculuspopulations in Western Australia lack VKORC1 mutations conferring resistance to first generation anticoagulant rodenticides: Implications for conservation and biosecurity
Authors: Duncan Bridget J.M.L. , Koenders Annette , Burnham Quinton , Lohr Michael T. 
Published: July 2020

AbstractBackgroundHumans routinely attempt to manage pest rodent populations with anticoagulant rodenticides (ARs). We require information on resistance to ARs within rodent populations to have effective eradication programs that minimise exposure in non-target species. Mutations to the VKORC1 gene have been shown to confer resistance in rodents with high proportions of resistance in mice found in all European populations tested. We screened mutations inMus musculuswithin Western Australia, by sampling populations from the capital city (Perth) and a remote island (Browse Island). These are the first Australian mouse populations screened for resistance using this method. Additionally, the mitochondrial D-loop of house mice was sequenced to explore population genetic structure, identify the origin of Western Australian mice, and to elucidate whether resistance was linked to certain haplotypes.ResultsNo resistance-related VKORC1 mutations were detected in either house mouse population. A genetic introgression in the intronic sequence of the VKORC1 gene of Browse Island house mouse was detected which is thought to have originated through hybridisation with the Algerian mouse (Mus spretus). Analysis of the mitochondrial D-loop reported two haplotypes in the house mouse population of Perth, and two haplotypes in the population of Browse Island.ConclusionsBoth house mouse populations exhibited no genetic resistance to ARs, in spite of free use of ARs in Western Australia. Therefore weaker anticoagulant rodenticides can be employed in pest control and eradication attempts, which will result in reduced negative impacts on non-target species. Biosecurity measures must be in place to avoid introduction of resistant house mice, and new house mouse subspecies to Western Australia.
Identification of oxygen-independent pathways for pyridine-nucleotide and Coenzyme-A synthesis in anaerobic fungi by expression of candidate genes in yeast
Authors: Perli Thomas , Vos Aurin M. , Bouwknegt Jonna , Dekker Wijb J. C. , Wiersma Sanne J. , Mooiman Christiaan , Ortiz-Merino Raúl A. , Daran Jean-Marc , Pronk Jack T. 
Published: July 2020

AbstractNeocallimastigomycetes are rare examples of strictly anaerobic eukaryotes. This study investigates how these anaerobic fungi bypass reactions involved in synthesis of pyridine nucleotide cofactors and coenzyme A that, in canonical fungal pathways, require molecular oxygen. Analysis of Neocallimastigomycete proteomes identified a candidate L-aspartate-decarboxylase (AdcA), and L-aspartate oxidase (NadB) and quinolinate synthase (NadA), constituting putative oxygen-independent bypasses for coenzyme A synthesis and pyridine nucleotide cofactor synthesis, respectively. The corresponding gene sequences indicated acquisition by ancient horizontal gene transfer event involving bacterial donors. To test whether these enzymes suffice to bypass corresponding oxygen-requiring reactions, they were introduced intofms1Δandbna2Δ Sacharomyces cerevisiaestrains. Expression ofnadAandnadB, andadcAfrom the NeocallimastigomycetesPiromyces finnisandNeocallimastix californiae, respectively, conferred cofactor prototrophy under aerobic and anaerobic conditions. This study simulates how horizontal gene transfer can drive eukaryotic adaptation to anaerobiosis, and provides a basis for elimination of auxotrophic requirements in anaerobic industrial applications of yeasts and fungi.
A simple and rapid method for isolating high-quality RNA from kenaf containing high polysaccharide and polyphenol contents
Authors: Liao Xiaofang , Li Hongwei , Khan Aziz , Zhao Yanhong , Hou Wenhuan , Tang Xingfu , Akhtar Kashif , Zhou Ruiyang 
Published: July 2020

AbstractThe isolation of high-quality RNA from kenaf is crucial for genetic and molecular biology studies. However, high levels of polysaccharide and polyphenol compounds in kenaf tissues could irreversibly bind to and coprecipitate with RNA, which complicates RNA extraction. In the present study, we proposed a simplified, time-saving and low-cost extraction method for isolating high quantities of high-quality RNA from several different kenaf tissues. RNA quality was measured for yield and purity, and the proposed protocol yielded high quantities of RNA (10.1-12.9 μg/g·FW). Spectrophotometric analysis showed that A260/280ratios of RNA samples were in the range of 2.11 to 2.13, and A260/230ratios were in the range of 2.04-2.24, indicating that the RNA samples were free of polyphenols, polysaccharides, and protein contaminants after isolation. The method of RNA extraction presented here was superior to the conventional CTAB method in terms of RNA isolation efficiency and was more sample-adaptable and cost-effective than commercial kits. Furthermore, to confirm downstream amenability, the high-quality RNA obtained from this method was successfully used for RT-PCR, real-time RT-PCR and Northern blot analysis. We provide an efficient and low-cost method for extracting high quantities of high-quality RNA from plants that are rich in polyphenols and polysaccharides, and this method was also validated for the isolation of high-quality RNA from other plants.
Neuronal autophagy regulates presynaptic neurotransmission by controlling the axonal endoplasmic reticulum
Authors: Kuijpers Marijn , Kochlamazashvili Gaga , Stumpf Alexander , Puchkov Dmytro , Lucht Max Thomas , Krause Eberhard , Schmitz Dietmar , Haucke Volker 
Published: July 2020

SUMMARYInformation processing in the brain is encoded as electrical impulses in neurons that are relayed from the presynaptic compartment to postsynaptic neurons by regulated neurotransmitter release. Neurons are known to rely on autophagy for the removal of defective proteins or organelles to maintain synaptic neurotransmission and to counteract neurodegeneration. In spite of its importance for neuronal health, the physiological substrates of neuronal autophagy in the absence of proteotoxic challenge have remained largely elusive. We use knockout mice conditionally lacking the essential autophagy protein ATG5 and quantitative proteomics to demonstrate that loss of neuronal autophagy causes the selective accumulation of tubular endoplasmic reticulum (ER) in axons, resulting in increased excitatory neurotransmission and compromised postnatal viabilityin vivo. The gain in excitatory neurotransmission is shown to be a consequence of elevated calcium release from ER stores via ryanodine receptors accumulated in axons and at presynaptic sites. We propose a model in which neuronal autophagy controls axonal ER calcium stores to regulate neurotransmission in healthy neurons and in the brain.
A Sample Covariance-Based Approach For Spatial Binary Data
Authors: Zarmehri Sahar , Hanks Ephraim M. , Lin Lin 
Published: July 2020

AbstractThe field of landscape genetics enables the study of infectious disease dynamics by connecting the landscape features with evolutionary changes. Quantifying genetic correlation across space is helpful in providing insight into the rate of spread of an infectious disease. We investigate two genetic patterns in spatially referenced single-nucleotide polymorphisms (SNPs): isolation by distance and isolation by resistance. We model the data using a Generalized Linear Mixed effect Model (GLMM) with spatially referenced random effects and provide a novel approach for estimating parameters in spatial GLMMs. In this approach, we use the links between binary probit models and bivariate normal probabilities to directly compute the model-based covariance function for spatial binary data. Parameter estimation is based on minimizing sum of squared distance between the elements of sample covariance and model-based covariance matrices. We analyze data includingBrucella AbortusSNPs from spatially referenced hosts in the Greater Yellowstone Ecosystem (GYE).