bluuebunny/crossref_metadata_2025_split huggingface dataset:
A role for a conserved kinase in the transcriptional control of methionine biosynthesis inEscherichia coliexperiencing sustained nitrogen starvation
Authors: Switzer Amy , Evangelopoulos Dimitrios , Figueira Rita , de Carvalho Luiz Pedro S. , Brown Daniel R. , Wigneshweraraj Sivaramesh 
Published: January 2018

ABSTRACTThe initial adaptive transcriptional response to nitrogen (N) starvation inEscherichia coliinvolves large-scale alterations to the transcriptome mediated by the transcription activator, NtrC. One of the NtrC-activated genes isyeaG, which encodes a conserved bacterial kinase. Although it is known that YeaG is required for optimal survival under sustained N starvation, the molecular basis by which YeaG benefits N starvedE. coliremains elusive. By combining transcriptomics with targeted metabolomics analyses, we demonstrate that the methionine biosynthesis pathway becomes transcriptionally dysregulated inΔyeaGbacteria experiencing sustained N starvation. This results in the aberrant and energetically costly biosynthesis of methionine and associated metabolites under sustained N starvation with detrimental consequences to cell viability. It appears the activity of the master transcriptional repressor of methionine biosynthesis genes, MetJ, is compromised inΔyeaGbacteria under sustained N starvation, resulting in transcriptional derepression of MetJ-regulated genes. The results suggest that YeaG is a novel regulatory factor and functions as a molecular brake in the transcriptional control of both the NtrC-regulon and methionine biosynthesis genes inE. coliexperiencing sustained N starvation.
Experimental analysis of exome-scale mutational signature of glycidamide, the reactive metabolite of acrylamide
Authors: Zhivagui Maria , Ardin Maude , Ng Alvin W.T. , Churchwell Mona I. , Pandey Manuraj , Villar Stephanie , Cahais Vincent , Robitaille Alexis , Bouaoun Liacine , Heguy Adriana , Guyton Kathryn , Stampfer Martha R. , McKay James , Hollstein Monica , Olivier Magali , Rozen Steven G. , Beland Frederick A. , Korenjak Michael , Zavadil Jiri 
Published: January 2018

AbstractAcrylamide, a probable human carcinogen, is ubiquitously present in the human environment, with sources including heated starchy foods, coffee and cigarette smoke. Humans are also exposed to acrylamide occupationally. Acrylamide is genotoxic, inducing gene mutations and chromosomal aberrations in various experimental settings. Covalent haemoglobin adducts were reported in acrylamide-exposed humans and DNA adducts in experimental systems. The carcinogenicity of acrylamide has been attributed to the effects of glycidamide, its reactive and mutagenic metabolite capable of inducing rodent tumors at various anatomical sites. In order to characterize the pre-mutagenic DNA lesions and global mutation spectra induced by acrylamide and glycidamide, we combined DNA-adduct and whole-exome sequencing analyses in an established exposure-clonal immortalization system based on mouse embryonic fibroblasts. Sequencing and computational analysis revealed a unique mutational signature of glycidamide, characterized by predominant T:A>A:T transversions, followed by T:A>C:G and C:G>A:T mutations exhibiting specific trinucleotide contexts and significant transcription strand bias. Computational interrogation of human cancer genome sequencing data indicated that a combination of the glycidamide signature and an experimental benzo[a]pyrene signature are nearly equivalent to the COSMIC tobacco-smoking related signature 4 in lung adenocarcinomas and squamous cell carcinomas. We found a more variable relationship between the glycidamide‐ and benzo[a]pyrene-signatures and COSMIC signature 4 in liver cancer, indicating more complex exposures in the liver. Our study demonstrates that the controlled experimental characterization of specific genetic damage associated with glycidamide exposure facilitates identifying corresponding patterns in cancer genome data, thereby underscoring how mutation signature laboratory experimentation contributes to the elucidation of cancer causation.A 40-word summaryInnovative experimental approaches identify a novel mutational signature of glycidamide, a metabolite of the probable human carcinogen acrylamide. The results may elucidate the cancer risks associated with exposure to acrylamide, commonly found in tobacco smoke, thermally processed foods and beverages.
Mechanical evolution of DNA double-strand breaks in the nucleosome
Authors: Cleri Fabrizio , Landuzzi Fabio , Blossey Ralf 
Published: January 2018

SummaryDouble strand breaks in the DNA backbone are the most lethal type of defect that can be induced in the cell nucleus by chemical and radiation treatments of cancer. However, little is known about the potentially large differences in the outcomes of damage between free and nucleosomal DNA, leading to corresponding differences in damage repair capability. We performed microsecond-length molecular dynamics computer simulations of nucleosomes including double-strand breaks (DSB) at various sites, to characterize the early stages of the evolution of this important DNA lesion right after its formation. We find that all DSB configurations tend to remain compact, with only the terminal bases interacting with histone proteins; the interacting molecular structures are studied by looking at the essential dynamics of the relevant DNA and histone fragments, and compared to the intact nucleosome, thus exposing key features of the interactions. Moreover, we show that the broken DNA ends at the DSB must overcome a free-energy barrier to detach from the nucleosome core, as measured by means of umbrella sampling of the potential of mean force. Finally, by using state-of-the-art calculation of the covariant mechanical stress at the molecular scale, we demonstrate that, depending on the DNA-core separation distance, the coupled bending and torsional stress stored in the detached DNA can force the free end to either stick back to the nucleosome core surface, or to open up straight, thus making it accessible to damage signalization proteins.
Genetic factors and age are the strongest predictors of humoral immune responses to common pathogens and vaccines
Authors: Scepanovic Petar , Alanio Cécile , Hammer Christian , Hodel Flavia , Bergstedt Jacob , Patin Etienne , Thorball Christian W. , Chaturvedi Nimisha , Charbit Bruno , Abel Laurent , Quintana-Murci Lluis , Duffy Darragh , Albert Matthew L. , Fellay Jacques ,   The Milieu Intérieur Consortium
Published: January 2018

AbstractIntroductionHumoral immune responses to infectious agents or vaccination vary substantially among individuals, and many of the factors responsible for this variability remain to be defined. Current evidence suggests that human genetic variation influences (i) serum immunoglobulin levels, (ii) seroconversion rates, and (iii) intensity of antigen-specific immune responses. Here, we evaluate the impact of intrinsic (age and sex), environmental and genetic factors on the variability of humoral response to common pathogens and vaccines.MethodsWe characterized the serological response to 15 antigens from common human pathogens or vaccines, in an age‐ and sex-stratified cohort of 1,000 healthy individuals (Milieu Intérieur cohort). Using clinical-grade serological assays, we measured total IgA, IgE, IgG and IgM levels, as well as qualitative (serostatus) and quantitative IgG responses to cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1 & 2, varicella zoster virus, Helicobacter pylori, Toxoplasma gondii, influenza A virus, measles, mumps, rubella, and hepatitis B virus. Following genome-wide genotyping of single nucleotide polymorphisms and imputation, we examined associations between ~5 million genetic variants and antibody responses using single marker and gene burden tests.Results and discussionWe identified age and sex as important determinants of humoral response, with older individuals and women having higher rates of seropositivity for most antigens. Genome-wide association studies revealed significant associations between variants in the human leucocyte antigen (HLA) class II region on chromosome 6 and anti-EBV and anti-rubella IgG levels. We used HLA imputation to fine map these associations to amino acid variants in the peptide-binding groove of HLA-DRβ1 and HLA-DPβ1, respectively. We also observed significant associations for total IgA levels with two loci on chromosome 2 and with specific KIR-HLA combinations.ConclusionsUsing extensive serological testing and genome-wide association analyses in a well-characterized cohort of healthy individuals, we demonstrate that age, sex and specific human genetic variants contribute to inter-individual variability in humoral response. By highlighting genes and pathways implicated in the normal antibody response to frequently encountered antigens, these findings provide a basis to better understand disease pathogenesis.
Exposure of zebra mussels to extracorporeal shock waves demonstrates formation of new mineralized tissue inside and outside the focus zone
Authors: Sternecker Katharina , Geist Juergen , Beggel Sebastian , Dietz-Laursonn Kristin , de la Fuente Matias , Frank Hans-Georg , Furia John P. , Milz Stefan , Schmitz Christoph 
Published: January 2018

AbstractA substantial body of evidence supports the use of extracorporeal shock wave therapy (ESWT) for fracture nonunions in human medicine. However, the success rate (i.e., radiographic union at six months after ESWT) is only approximately 75%. Detailed knowledge regarding the underlying mechanisms that induce bio-calcification after ESWT is limited. The aim of the present study was to analyze the biological response within mineralized tissue of a new invertebrate model organism, the zebra mussel Dreissena polymorpha, after exposure with extracorporeal shock waves (ESWs). Mussels were exposed to ESWs with positive energy density of 0.4 mJ/mm2 or were sham exposed. Detection of newly calcified tissue was performed by concomitantly exposing the mussels to fluorescent markers. Two weeks later, the fluorescence signal intensity of the valves was measured. Mussels exposed to ESWs showed a statistically significantly higher mean fluorescence signal intensity within the shell zone than mussels that were sham exposed. Additional acoustic measurements revealed that the increased mean fluorescence signal intensity within the shell of those mussels that were exposed to ESWs was independent of the size and position of the focal point of the ESWs. These data demonstrate that induction of bio-calcification after ESWT may not be restricted to the region of direct energy transfer of ESWs into calcified tissue. The results of the present study are of relevance for better understanding of the molecular and cellular mechanisms that induce formation of new mineralized tissue after ESWT. Specifically, bio-calcification following ESWT may extend beyond the direct area of treatment.Summary statementThe use of zebra mussels in research on extracorporeal shock wave (ESW) therapy for fracture nonunions allows new insights into the complex process of induction of biomineralization by ESWs.
Optimizing CRISPR/Cas9 System to Precisely Model Plasminogen Activator Inhibitor-1 Point Mutations in Mice
Authors: Liu Yang , Saunders Thomas L. , Sisson Thomas , Blackburn Robert , Ginsberg David S. , Day Duane 
Published: January 2018

AbstractCRISPR/Cas9 has become a powerful genome editing tool in recent years. CRISPR/Cas9 can be utilized to not only efficiently generate knock out models in various organisms, but also to precisely model human disease or variants to study gene function and develop therapies. However, the latter remains challenging because of low knock-in (KI) efficiency. In this study, precise gene editing modeling plasminogen activator inhibitor-1 (PAI-1) ‐tissue plasminogen activator (tPA) binding deficiency and PAI-1-vitronectin binding deficiency were generated respectively in mice. Optimization of single guide RNAs (sgRNA) and repair templates, and utilization of restriction fragment length polymorphism (RFLP) to detect KI events are described. Injection of sgRNA/Cas9/single-stranded oligodeoxynucleotide (ssODN) into mouse zygotes resulted in homozygous changes of two silent mutations and changed Arg369>Ala, which abolishes PAI-1 inhibitory activity against tPA. Targeting Arg124 and Gln146 simultaneously involved in vitronectin binding proved to be challenging. However, we successfully generated these relatively distant mutations (23 amino acids apart) seamlessly. Generation of the Arg124 mutation alone was achieved with over 60% efficiency along with the integration of a restriction site, compared to the relatively low double mutation frequency. In summary, our data indicates that the distance between desired mutations and CRISPR-induced double-stranded break (DSB) site is the most critical factor for achieving high efficiency in precise gene modification.
To jump or not to jump: The Bereitschaftspotential required to jump into 192-meter abyss
Authors: Nann M. , Cohen L.G. , Deecke L. , Soekadar S.R. 
Published: January 2018

AbstractSelf-initiated voluntary acts, such as pressing a button, are preceded by a negative electrical brain potential, the Bereitschaftspotential (BP), that can be recorded over the human scalp using electroencephalography (EEG). Up to now, the BP required to initiate voluntary acts has only been recorded under well-controlled laboratory conditions.It is thus not known if this form of brain activity also underlies motor initiation in possible life-threatening decision making, such as jumping into a 192-meter abyss, an act requiring extraordinary willpower. Here, we report BP before self-initiated 192-meter extreme bungee jumping across two semi-professional cliff divers (both male, mean age 19.3 years). We found that the spatiotemporal dynamics of the BP is comparable to that recorded under laboratory conditions. These results, possible through recent advancements in wireless and portable EEG technology, document for the first time pre-movement brain activity preceding possible life-threatening decision making.
Genomic dissection of Systemic Lupus Erythematosus: Distinct Susceptibility, Activity and Severity Signatures
Authors: Panousis Nikolaos I. , Bertsias George , Ongen Halit , Gergianaki Irini , Tektonidou Maria , Trachana Maria , Romano-Palumbo Luciana , Bielser Deborah , Howald Cedric , Pamfil Cristina , Fanouriakis Antonis , Kosmara Despoina , Repa Argyro , Sidiropoulos Prodromos , Dermitzakis Emmanouil T. , Boumpas Dimitrios T. 
Published: January 2018

AbstractRecent genetic and genomics approaches have yielded novel insights in the pathogenesis of Systemic Lupus Erythematosus (SLE) but the diagnosis, monitoring and treatment still remain largely empirical1,2. We reasoned that molecular characterization of SLE by whole blood transcriptomics may facilitate early diagnosis and personalized therapy. To this end, we analyzed genotypes and RNA-seq in 142 patients and 58 matched healthy individuals to define the global transcriptional signature of SLE. By controlling for the estimated proportions of circulating immune cell types, we show that the Interferon (IFN) and p53 pathways are robustly expressed. We also report cell-specific, disease-dependent regulation of gene expression and define a core/susceptibility and a flare/activity disease expression signature, with oxidative phosphorylation, ribosome regulation and cell cycle pathways being enriched in lupus flares. Using these data, we define a novel index of disease activity/severity by combining the validated Systemic Lupus Erythematosus Disease Activity Index (SLEDAI)1with a new variable derived from principal component analysis (PCA) of RNA-seq data. We also delineate unique signatures across disease endo-phenotypes whereby active nephritis exhibits the most extensive changes in transcriptome, including prominent drugable signatures such as granulocyte and plasmablast/plasma cell activation. The substantial differences in gene expression between SLE and healthy individuals enables the classification of disease versus healthy status with median sensitivity and specificity of 83% and 100%, respectively. We explored the genetic regulation of blood transcriptome in SLE and found 3142cis-expression quantitative trait loci (eQTLs). By integration of SLE genome-wide association study (GWAS) signals and eQTLs from 44 tissues from the Genotype-Tissue Expression (GTEx) consortium, we demonstrate that the genetic causality of SLE arises from multiple tissues with the top causal tissue being the liver, followed by brain basal ganglia, adrenal gland and whole blood. Collectively, our study defines distinct susceptibility and activity/severity signatures in SLE that may facilitate diagnosis, monitoring, and personalized therapy.
Effects of inhibitors on Hsp90’s conformational dynamics, cochaperone and client interactions
Authors: Schmid Sonja , Götz Markus , Hugel Thorsten 
Published: January 2018

AbstractThe molecular chaperone and heat-shock protein Hsp90 has become a central target in anti-cancer therapy. Nevertheless, the effect of Hsp90 inhibition is still not understood at the molecular level, preventing a truly rational drug design. Here we report on the effect of the most prominent drug candidates, namely radicicol, geldanamycin, derivatives of purine and novobiocin, on Hsp90’s characteristic conformational dynamics and the binding of three interaction partners. Unexpectedly, the global opening and closing transitions are hardly affected by Hsp90 inhibitors. Instead, the conformational equilibrium, as well as the associated kinetic rate constants remain almost untouched. Moreover, we find no significant changes in the binding of the cochaperones Aha1 and p23 nor of the model substrate Δ131Δ. This holds true for both, competitive and allosteric inhibitors. Therefore, direct inhibition mechanisms, affecting only one molecular interaction, are unlikely. Based on our results, we speculate that the inhibitory action observed in vivo is caused by a combination of subtle effects, which can be used in the search for novel Hsp90 inhibition mechanisms.
Using multivariate time series methods to estimate location and climate change effects on temperature readings employed in electricity demand simulation
Authors: Bowden Ross S. , Clarke Brenton R. 
Published: January 2018

SummaryLong‐term historical daily temperatures are used in electricity forecasting to simulate the probability distribution of future demand but can be affected by changes in recording site and climate. This paper presents a method of adjusting for the effect of these changes on daily maximum and minimum temperatures. The adjustment technique accommodates the autocorrelated and bivariate nature of the temperature data which has not previously been taken into account. The data are from Perth, Western Australia, the main electricity demand centre for the South‐West of Western Australia. The statistical modelling involves a multivariate extension of the univariate time series ‘interleaving method’, which allows fully efficient simultaneous estimation of the parameters of replicated Vector Autoregressive Moving Average processes. Temperatures at the most recent weather recording location in Perth are shown to be significantly lower compared to previous sites. There is also evidence of long‐term heating due to climate change especially for minimum temperatures.
The impact of bisphenol S on bovine granulosa and theca cells
Authors: Campen KA , Lavallee M , Combelles CMH 
Published: January 2018

ContentsBisphenol S (BPS) is an endocrine‐disrupting chemical with multiple potential mechanisms of action, including as an oestrogen receptor agonist. BPS is increasingly used in plastics and thermal receipts as a substitute for bisphenol A, which has been phased out due to concerns about human health implications. The ability of BPS to alter female reproductive function in mammals has not been widely studied, despite the importance of normal hormone signalling for female reproduction. The aim of this study was to investigate how BPS (in a wide range of doses, including very low doses) affects granulosa cell and theca cell steroid hormone production and cell viability in the bovine. Granulosa cell oestradiol production was stimulated when cells were exposed to 100 μM BPS under basal conditions, but there was no effect of BPS when cells were stimulated with follicle‐stimulating hormone (FSH). Additionally, there was no effect of BPS on granulosa cell progesterone production or cell viability under basal or FSH‐stimulated conditions. BPS did not affect theca cell androstenedione or progesterone production, or theca cell viability under basal or luteinizing hormone‐stimulated conditions. This study suggests for the first time that BPS may alter oestradiol production by bovine granulosa cells, albeit at a concentration that is unlikely to be physiologically relevant. Further studies are needed to determine the effects of BPS on the bovine oocyte and on other functions of follicular cells.
Effect of local scrotal heating on the expression of tight junction‐associated molecule Occludin in boar testes
Authors: Zhang Z , Fan X , Xi H , Ji R , Shen H , Shi A , He J 
Published: January 2018

ContentsThe aim of this study was to determine whether local scrotal heating (42°C, for 1 hr) had an effect on the expression of tight junction (TJ)‐associated molecule Occludin in boar testes. Adult boars (Landrace, n = 6) were used and randomly divided into two groups (n = 3 each). Three boars were given local scrotal exposure to 42°C for approximately 1 h with a home‐made electric blanket of controlled temperature as local scrotal heating group, the other three boars received no heat treatment and were left at standard room temperature as control group. After 6 hr, all boars were castrated and the testes were harvested. qRT‐PCR, Western blotting and immunohistochemistry were used to explore the expression and localization of Occludin. qRT‐PCR and Western blotting showed that the protein and mRNA levels of Occludin significantly decreased in local scrotal heating group as compared to the control. Furthermore, immunoreactivity staining of Occludin was localized at the sites of the blood–testis barrier (BTB) and formed an almost consecutive and strong immunoreactivity strand in the control, while Occludin was limited to Sertoli cells (SCs) and no obvious immunoreactivity strand was present in local scrotal heating group. These data indicated that local scrotal heating decreased the expression of TJ‐associated molecule Occludin, which may be involved in heat‐induced spermatogenesis damage.