bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation epigenetically regulates gene expression inBurkholderia cenocepacia
Authors: Vandenbussche Ian , Sass Andrea , Pinto-Carbó Marta , Mannweiler Olga , Eberl Leo , Coenye Tom 
Published: February 2020

AbstractRespiratory tract infections by the opportunistic pathogenBurkholderia cenocepaciaoften lead to severe lung damage in cystic fibrosis (CF) patients. New insights in how to tackle these infections might emerge from the field of epigenetics, as DNA methylation has shown to be an important regulator of gene expression. The present study focused on two DNA methyltransferases (MTases) inB. cenocepaciastrains J2315 and K56-2, and their role in regulating gene expression.In silicopredicted DNA MTase genes BCAL3494 and BCAM0992 were deleted in both strains, and the phenotypes of the resulting deletion mutants were studied: deletion mutant ΔBCAL3494 showed changes in biofilm structure and cell aggregation, ΔBCAM0992 was less motile.B. cenocepaciawild type cultures treated with sinefungin, a known DNA MTase inhibitor, exhibited the same phenotype as DNA MTase deletion mutants. Single-Molecule Real-Time sequencing was used to characterize the methylome ofB. cenocepacia, including methylation at the origin of replication, and motifs CACAG and GTWWAC were identified as targets of BCAL3494 and BCAM0992, respectively. All genes with methylated motifs in their putative promoter region were identified and qPCR experiments showed an upregulation of several genes, including biofilm and motility related genes, in MTase deletion mutants with unmethylated motifs, explaining the observed phenotypes in these mutants. In summary, our data confirm that DNA methylation plays an important role in regulating the expression ofB. cenocepaciagenes involved in biofilm formation and motility.ImportanceCF patients diagnosed withB. cenocepaciainfections often experience rapid deterioration of lung function, known ascepacia syndrome. B. cenocepaciahas a large multi-replicon genome and a lot remains to be learned about regulation of gene expression in this organism. From studies in other (model) organisms, it is known that epigenetic changes through DNA methylation play an important role in this regulation. The identification ofB. cenocepaciagenes of which the expression is regulated by DNA methylation and identification of the regulatory systems involved in this methylation are likely to lead to new insights in how to tackleB. cenocepaciainfections in CF patients.
Red-light (670 nm) therapy reduces mechanical sensitivity and neuronal cell death, and alters glial responses following spinal cord injury in rats
Authors: Hu Di , Moalem-Taylor Gila , Potas Jason R 
Published: February 2020

AbstractIndividuals with spinal cord injury (SCI) often develop debilitating neuropathic pain, which may be driven by neuronal damage and neuroinflammation. We have previously demonstrated that treatment using 670 nm (red) light irradiation alters microglia/macrophage responses and alleviates mechanical hypersensitivity at 7-days post-injury. Here, we investigated the effect of red-light on the development of mechanical hypersensitivity, neuronal markers, and glial response in the subacute stage (days 1-7) following SCI. Wistar rats were subjected to a mild T10 hemi-contusion SCI or sham surgery followed by daily red-light treatment (30 min/day; 670 nm LED; 35mW/cm2) or sham treatment. Mechanical sensitivity of the rat dorsum was assessed from 1-day post-injury and repeated every second day. Spinal cords were collected at 1, 3, 5 and 7-days post-injury for analysis of myelination, neurofilament protein NF200 expression, neuronal cell death, reactive astrocytes (GFAP+ cells), interleukin1β (IL1β) expression, and inducible nitric oxide synthase (iNOS) production in IBA1+microglia/macrophages. Red-light treatment significantly reduced the cumulative mechanical sensitivity and the hypersensitivity incidence following SCI. This effect was accompanied by significantly reduced neuronal cell death, reduced astrocyte activation and reduced iNOS expression in IBA1+cells at the level of the injury. However, myelin and NF200 immunoreactivity and IL1β expression in GFAP+and IBA1+cells were not altered by red-light treatment. Thus, red-light therapy may represent a useful non-pharmacological approach for treating pain during the subacute period after SCI by decreasing neuronal loss and modulating the inflammatory glial response.
Creating outbred and inbred populations of haplodiploid mites to measure adaptive responses in the lab
Authors: Godinho Diogo P. , Cruz Miguel A. , de la Masselière Maud Charlery , Teodoro-Paulo Jéssica , Eira Cátia , Fragata Inês , Rodrigues Leonor R. , Zélé Flore , Magalhães Sara 
Published: February 2020

AbstractLaboratory studies are often criticized for not being representative of processes occurring in natural populations. This can be partially mitigated by using lab populations that capture large amounts of variation. Additionally, many studies addressing adaptation of organisms to their environment are done with laboratory populations, using quantitative genetics or experimental evolution methodologies. Such studies rely on populations that are either highly outbred or inbred. However, the methodology underlying the generation of such biological resources are usually not explicitly documented.Given their small size, short generation time, amenability to laboratory experimentation and knowledge of their ecological interactions, haplodiploid spider mites are becoming a widely used model organism. Here, we describe the creation of outbred populations of two species of spider mites,Tetranychus urticaeandT. evansi, obtained by performing controlled crosses between individuals from field-collected populations. Subsequently, from the outbred population ofT. evansi, we derived inbred lines, by performing several generations of sib-mating. These can be used to measure broad-sense heritability as well as correlations among traits. Finally, we outline an experimental evolution protocol that can be widely used in other systems. Sharing these biological resources with other laboratories and combining them with the available powerful genetic tools forT. urticae(and other species) will allow consistent and comparable studies that greatly contribute to our understanding of ecological and evolutionary processes.
SimpylCellCounter: An Automated Solution for Quantifying Cells in Brain Tissue
Authors: Bal Aneesh , Maureira Fidel , Arguello Amy A. 
Published: February 2020

ABSTRACTRationale & ObjectiveManual quantification of activated cells can provide valuable information about stimuli-induced changes within brain regions; however, this analysis remains time intensive. Therefore, we created SimpylCellCounter (SCC), an automated method to quantify cells that express Cfos protein, an index of neuronal activity, in brain tissue and benchmarked it against two widely-used methods: OpenColonyFormingUnit (OCFU) and ImageJ Edge Detection Macro (IMJM).MethodsIn Experiment 1, manually-obtained counts were compared to those detected via OCFU, IMJM and SCC. The absolute error in counts (manualversusautomated method) was calculated, and error types were categorized as false positives or negatives. In Experiment 2, performance analytics of OCFU, IMJM and SCC were compared. In Experiment 3, SCC performed analysis on images it was not trained on, to assess its general utility.Results & ConclusionsWe found SCC to be highly accurate and efficient in quantifying both cells with circular morphologies and those expressing Cfos. Additionally, SCC utilizes a new approach for counting overlapping cells with a pretrained convolutional neural network classifier. The current study demonstrates that SCC is a novel, automated tool to quantify cells in brain tissue, complementing current, open-sourced quantification methods designed to detect cellsin vitro.
The costs of competition: high social status males experience accelerated epigenetic aging in wild baboons
Authors: Anderson Jordan A. , Johnston Rachel A. , Lea Amanda J. , Campos Fernando A. , Voyles Tawni N. , Akinyi Mercy Y. , Alberts Susan C. , Archie Elizabeth A. , Tung Jenny 
Published: February 2020

AbstractAging, for virtually all life, is inescapable. However, within populations, biological aging rates vary. Understanding sources of variation in this process is central to understanding the biodemography of natural populations. We constructed a DNA methylation-based age predictor for an intensively studied wild baboon population in Kenya. Consistent with findings in humans, the resulting “epigenetic clock” closely tracks chronological age, but individuals are predicted to be somewhat older or younger than their known ages. Surprisingly, these deviations are not explained by the strongest predictors of lifespan in this population, early adversity and social integration. Instead, they are best predicted by male dominance rank: high-ranking males are predicted to be older than their true ages, and epigenetic age tracks changes in rank over time. Our results argue that achieving high rank for male baboons—the best predictor of reproductive success—imposes costs consistent with a “live fast, die young” life history strategy.
Specialized DNA structures act as genomic beacons for integration by evolutionarily diverse retroviruses
Authors: Kohio Hinissan P. , Ajoge Hannah O. , Coleman Macon D. , Ndashimye Emmanuel , Gibson Richard M. , Arts Eric J. , Barr Stephen D. 
Published: February 2020

ABSTRACTRetroviral integration site targeting is not random and plays a critical role in expression and long-term survival of the integrated provirus. To better understand the genomic environment surrounding retroviral integration sites, we performed an extensive comparative analysis of new and previously published integration site data from evolutionarily diverse retroviruses from seven genera, including different HIV-1 subtypes. We showed that evolutionarily divergent retroviruses exhibited distinct integration site profiles with strong preferences for non-canonical B-form DNA (non-B DNA). Whereas all lentiviruses and most retroviruses integrate within or near genes and non-B DNA, MMTV and ERV integration sites were highly enriched in heterochromatin and transcription-silencing non-B DNA features (e.g. G4, triplex and Z-DNA). Compared toin vitro-derived HIV-1 integration sites,in vivo-derived sites are significantly more enriched in transcriptionally silent regions of the genome and transcription-silencing non-B DNA features. Integration sites from individuals infected with HIV-1 subtype A, C or D viruses exhibited different preferences for non-B DNA and were more enriched in transcriptionally active regions of the genome compared to subtype B virus. In addition, we identified several integration site hotspots shared between different HIV-1 subtypes with specific non-B DNA sequence motifs present at these hotspots. Together, these data highlight important similarities and differences in retroviral integration site targeting and provides new insight into how retroviruses integrate into genomes for long-term survival.Graphical AbstractSchematic comparing integration site profiles from evolutionarily diverse retroviruses. Upper left, heatmaps showing the fold-enrichment (blue) and fold-depletion (red) of integration sites near non-B DNA features (lower left). Lower right, circa plot showing integration site hotspots shared between HIV-1 subtype A, B, C and D virus.
Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming
Authors: Guo Xue , Gao Qun , Yuan Mengting , Wang Gangsheng , Zhou Xishu , Feng Jiajie , Shi Zhou , Hale Lauren , Wu Linwei , Zhou Aifen , Tian Renmao , Liu Feifei , Wu Bo , Chen Lijun , Jung Chang Gyo , Niu Shuli , Li Dejun , Xu Xia , Jiang Lifen , Escalas Arthur , Wu Liyou , He Zhili , Van Nostrand Joy D. , Ning Daliang , Liu Xueduan , Yang Yunfeng , Schuur Edward. A.G. , Konstantinidis Konstantinos T. , Cole James R. , Penton C. Ryan , Luo Yiqi , Tiedje James M. , Zhou Jizhong 
Published: February 2020

AbstractSoil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. Despite intensive studies for two decades, the magnitude, direction, and duration of such feedbacks are uncertain, and their underlying microbial mechanisms are still poorly understood. Here we examined the responses of soil respiration and microbial community structure to long-term experimental warming in a temperate grassland ecosystem. Our results indicated that the temperature sensitivity of soil microbial respiration (i.e.,Q10) persistently decreased by 12.0±3.7% across 7 years of warming. Integrated metagenomic and functional analyses showed that microbial community adaptation played critical roles in regulating respiratory acclimation. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improved the modeling performance of soil microbial respiration by 5–19%, compared to the traditional non-microbial model. Model parametric uncertainty was also reduced by 55–71% when gene abundances were used. In addition, our modeling analyses suggested that decreased temperature sensitivity could lead to considerably less heterotrophic respiration (11.6±7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.
Complete reconstruction of the unbinding pathway of an anticancer drug by conventional unbiased molecular dynamics simulation
Authors: Sohraby Farzin , Moghadam Mostafa Javaheri , Aliyar Masoud , Aryapour Hassan 
Published: February 2020

AbstractUnderstanding the details of unbinding mechanism of small molecule drugs is an inseparable part of rational drug design. Reconstruction of the unbinding pathway of small molecule drugs, todays, can be achieved through molecular dynamics simulations. Nonetheless, simulating a process in which a drug unbinds from its receptor demands lots of time, mostly up to several milliseconds. This amount of time is neither reasonable nor affordable; therefore, many researchers utilize various biases that there are still many doubts about their trustworthiness. In this work we have utilized short-run simulations, replicas, to make such time-consuming process cost effective. By replicating those snapshots of the trajectories which, after careful analyses, were selected as potential candidates we increased our system’s efficiency considerably. As a matter of fact, we have implemented a sort of human bias, inspecting trajectories visually, to achieve multiple unbinding events. We would like to call this stratagem, replicating of potent snapshots, “rational sampling” as it is, in fact, benefiting from human logic. In our case, an anticancer drug, the dasatinib, completely unbounded from its target protein, c-Src kinase, in only 392.6 ns, and this was gained without applying any internal biases and potentials which can increase error level. Thus, we achieved important structural details that can alter our viewpoint as well as assist drug designers.
Enzyme Kinetics and Inhibition Parameters of Human Leukocyte Glucosylceramidase
Authors: Karataş Mesut , Doğan Şenol , Spahiu Emrulla , Ašić Adna , Bešić Larisa , Turan Yusuf 
Published: February 2020

AbstractGlucosylceramidase (GCase) is a lysosomal enzyme that catalyzes the cleavage of β-glucosidic linkage of glucocerebroside (GC) into glucose and ceramide; thereby, plays an essential function in the degradation of complex lipids and the turnover of cellular membranes.The growing list of 460 mutations in the gene coding for it—glucosylceramidase beta acid 1 (GBA1)—is reported to abolish its catalytic activity and decrease its enzyme stability, associating it with severe health conditions such as Gaucher disease (GD), Parkinson Disease and Dementia with Lewy bodies.Although the three-dimensional structure of wild type glucosylceramidase is elucidated, little is known about its features in human cells. Moreover, alternative sources of GCase that prove to be effective in the treatment of diseases with enzyme treatment therapies, impose the need for simple and cost-effective procedures to study the enzyme behaviour. This work, for the first time, shows a well established, yet simple, cost- and time-efficient protocol for the study of GCase enzyme in human leukocytes by the artificial substrate PNPG. Characterization of the enzyme in human leukocytes for activation parameters (optimal pH, Km, and Vmax) and enzyme inhibition, was done. The results indicate that the optimum pH of GCase enzyme with PNPG is 5.1. The Kmand Vmaxvalues were 12.6mM and 333 U/mg, respectively. Gluconolactone successfully inhibits GCase in a competitive manner, with a Kivalue of 0.023 mM and IC50of 0.047 mM. Glucose inhibition was uncompetitive with a Kiof 1.94 mM and IC50of 55.3 mM. This is the first report for the inhibitory effect of glucose, δ-gluconolactone on leukocyte GCase activity.
Brainrender: a python-based software for visualizing anatomically registered data
Authors: Claudi F. , Tyson A. L. , Petrucco L. , Margrie T.W. , Portugues R. , Branco T. 
Published: February 2020

AbstractThe recent development of high-resolution three-dimensional (3D) digital brain atlases and high-throughput brain wide imaging techniques has fueled the generation of large datasets that can be registered to a common reference frame. This registration facilitates integrating data from different sources and resolutions to assemble rich multidimensional datasets. Generating insights from these new types of datasets depends critically on the ability to easily visualize and explore the data in an interactive manner. This is, however, a challenging task. Currently available software is dedicated to single atlases, model species or data types, and generating 3D renderings that merge anatomically registered data from diverse sources requires extensive development and programming skills. To address this challenge, we have developedbrainrender: a generic, open-source Python package for simultaneous and interactive visualization of multidimensional datasets registered to brain atlases.Brainrenderhas been designed to facilitate the creation of complex custom renderings and can be used programmatically or through a graphical user interface. It can easily render different data types in the same visualization, including user-generated data, and enables seamless use of different brain atlases using the same code base. In addition,brainrendergenerates high-quality visualizations that can be used interactively and exported as high-resolution figures and animated videos. By facilitating the visualization of anatomically registered data,brainrendershould accelerate the analysis, interpretation, and dissemination of brain-wide multidimensional data.
A zebrafish functional genomics model to investigate the role of human A20 variantsin vivo
Authors: Cultrone Daniele , Zammit W. Nathan , Self Eleanor , Postert Benno , Han Jeremy ZR , Bailey Jacqueline , Warren Joanna , Croucher David R , Kikuchi Kazu , Bogdanovic Ozren , Chtanova Tatyana , Hesselson Daniel , Grey Shane T. 
Published: February 2020

SUMMARYGermline loss-of-function variation inTNFAIP3, encoding A20, has been implicated in a wide variety of autoinflammatory and autoimmune conditions, with acquired somatic missense mutations linked to cancer progression. Furthermore, human sequence data reveals that the A20 locus contains ~400 non-synonymous coding variants which are largely uncharacterised. The growing number of A20 coding variants with unknown function, but potential clinical impact, poses a challenge to traditional mouse-based approaches. Here we report the development of a novel functional genomics approach that utilises the new A20-deficient zebrafish (Danio rerio) model to investigate the impact ofTNFAIP3genetic variantsin vivo. Similar to A20-deficient mice, A20-deficient zebrafish are hyper-responsive to inflammatory triggers and exhibit spontaneous early lethality. While ectopic addition of human A20 rescued A20-null zebrafish from lethality, missense mutations at two conserved A20 residues, S381A and C243Y reversed this protective effect. Ser381 represents a phosphorylation site important for enhancing A20 activity that is abrogated by its mutation to alanine, or by a C243Y mutation that associates with human autoimmune disease. These data reveal an evolutionarily conserved role for A20, but also demonstrate how a zebrafish functional genomics pipeline can be utilized to investigate thein vivosignificance of medically relevant TNFAIP3 gene variants. This approach could be utilised to investigate genetic variation for other conserved genes.
Mapping proteolytic neo-N termini at the surface of living cells
Authors: Weeks Amy M. , Byrnes James R. , Lui Irene , Wells James A. 
Published: February 2020

AbstractN terminomics is a powerful strategy for profiling proteolytic neo-N termini, but its application to cell surface proteolysis has been limited by the low relative abundance of plasma membrane proteins. Here we apply plasma membrane-targeted subtiligase variants to efficiently and specifically capture cell surface N termini in live cells. Using this approach, we sequenced 807 cell surface N termini and quantified changes in their abundance in response to stimuli that induce proteolytic remodeling of the cell surface proteome. This technology will facilitate greater understanding of extracellular protease biology and reveal neo-N termini biomarkers and targets in disease.
The transition from primary colorectal cancer to isolated peritoneal malignancy is associated with a hypermutant, hypermethylated state
Authors: Hallam Sally , Stockton Joanne , Bryer Claire , Whalley Celina , Pestinger Valerie , Youssef Haney , Beggs Andrew D 
Published: February 2020

ABSTRACTColoretcal Peritoneal metastases (CPM) develop in 15% of colorectal cancers. Cytoreductive surgery and heated intraperitoneal chemotherapy (CRS & HIPEC) is the current standard of care in selected patients with limited resectable CPM. Despite selection using known prognostic factors survival is varied and morbidity and mortality are relatively high. There is a need to improve patient selection and a paucity of research concerning the biology of isolated CPM. We aimed to determine the biology associated with transition from primary CRC to CPM and poor prognosis CPM, to identify those suitable for treatment with CRS & HIPEC and to identify targets for existing repurposed or novel treatment strategies. A cohort of patients with CPM treated with CRS & HIPEC was recruited and divided according to prognosis. Molecular profiling of the transcriptome, epigenome and genome of CPM and matched primary CRC was performed.CPM were characterised by frequent Wnt/ β catenin negative regulator mutations, mismatch repair mutations and resulting high tumour mutational burden and dysregulation of methylation suggested by frequent TET2 mutations and mutations suggesting an immune evasive phenotype. Several novel therapies could be targeted to these frequent mutations including porcupine inhibitors, immune checkpoint inhibitors and methylation inhibitors. Here we show the molecular features associated with CPM development and with poor prognosis. Potential applications include improving patient selection for treatment and in the development of novel and personalised treatments.NOVELTY AND IMPACTColorectal peritoneal metastasis (CPM) are associated with limited and variable survival despite patient selection using known prognostic factors and optimal currently available treatments. There is a paucity of research concerning the biology of CPM. This study describes the biological landscape of CPM and the molecular features associated with CPM development, conferring poor prognosis and has identified that the majority of CPM develop a hypermutant phenotype that may be suitable for treatment with anti-PD1/CTLA4 immunotherapy.