bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic inhibition ofPCSK9, atherogenic lipoprotein concentrations, and calcific aortic valve stenosis
Authors: Perrot Nicolas , Moschetta Donato , Boekholdt S. Matthijs , Valerio Vincenza , Martinsson Andreas , Capoulade Romain , Mass Elvira , Clavel Marie-Annick , Wareham Nicholas J. , Dina Christian , Chen Hao Yu , Engert James C. , Thanassoulis George , Mathieu Patrick , Bossé Yohan , Pibarot Philippe , Smith J. Gustav , Camera Marina , Thériault Sébastien , Poggio Paolo , Arsenault Benoit J. 
Published: March 2019

AbstractBackgroundProprotein convertase subtilisin/kexin type 9 (PCSK9) inhibition reduces plasma concentrations of low-density lipoprotein cholesterol (LDL-C), apolipoprotein B (apoB) and lipoprotein(a) [Lp(a)]. Atherogenic lipoprotein levels have been linked with calcific aortic valve stenosis (CAVS). Our objectives were to determine the association between variants inPCSK9and lipoprotein-lipid levels, coronary artery disease (CAD) and CAVS, and to evaluate if PCSK9 could be implicated in aortic valve interstitial cells (VICs) calcification.MethodsWe built a genetic risk score weight for LDL-C levels (wGRS) using 10 independentPCSK9single nucleotide polymorphisms and determined its association with lipoprotein-lipid levels in 9692 participants of the EPIC-Norfolk study. We investigated the association between the wGRS and CAD and CAVS in the UK Biobank, as well as the association between thePCSK9R46L variant and CAVS in a meta-analysis of published prospective, population-based studies (Copenhagen studies, 1463 cases/101,620 controls) and unpublished studies (UK Biobank, 1350 cases/349,043 controls, Malmö Diet and Cancer study, 682 cases/5963 controls and EPIC-Norfolk study, 508 cases/20,421 controls). We evaluated PCSK9 expression and localization in explanted aortic valves by capillary Western blot and immunohistochemistry in patients with and without CAVS. Von Kossa staining was used to visualize aortic leaflet calcium deposits. PCSK9 expression under oxidative stress conditions in VICs was assessed.ResultsThe wGRS was significantly associated with lower LDL-C and apoB (p<0.001), but not with Lp(a). In the UK Biobank, the association ofPCSK9variants with CAD were positively correlated with their effects on apoB levels. CAVS was less prevalent in carriers of thePCSK9R46L variant [odds ratio=0.71 (95% confidence interval, 0.57-0.88), p<0.001]. PCSK9 expression was elevated in the aortic valves of patients with aortic sclerosis and CAVS compared to controls. In calcified leaflets, PCSK9 co-localized with calcium deposits. PCSK9 expression was induced by oxidative stress in VICs.ConclusionGenetic inhibition ofPCSK9is associated with lifelong reductions in the levels of non-Lp(a) apoB-containing lipoproteins as well as lower odds of CAD and CAVS. PCSK9 is abundant in fibrotic and calcified aortic leaflets. Oxidative stress increases PCSK9 expression in VICs. These results provide a rationale for performing randomized clinical trials of PCSK9 inhibition in CAVS.
Translation enhancement by a Dictyostelium gene sequence in Escherichia coli
Authors: Kondo Tomo , Yumura Shigehiko 
Published: March 2019

AbstractMethods for heterologous protein production in Escherichia coli have revolutionized biotechnology and the bioindustry. It is ultimately important to increase the amount of protein product from bacteria. To this end, a variety of tools, such as effective promoters, have been developed. Here, we present a versatile molecular tool based on a phenomenon termed “translation enhancement by a Dictyostelium gene sequence” (“TED”) in E. coli. We found that protein expression was increased when a gene sequence of Dictyostelium discoideum was placed upstream of the Shine-Dalgarno sequence located between the promoter and the initiation codon of a target gene. The most effective sequence among the genes examined was mlcR, which encodes the myosin regulatory light chain, a subunit of myosin II. Serial deletion analysis revealed that at least 10 bases of the 3’ end of the mlcR gene enhanced the production of green fluorescent protein in cells. We applied this tool to a T7 expression system and found that the expression level of the proteins tested was increased when compared with the conventional method. Thus, current protein production systems can be improved by combination with TED.
Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard
Authors: Kanger Kärt , Guilford Nigel G.H. , Lee HyunWoo , Nesbø Camilla L. , Truu Jaak , Edwards Elizabeth A. 
Published: March 2019

ABSTRACTAntimicrobial resistance is a globally recognized public health risk. High incidence of antibiotic resistant bacteria and antibiotic resistance genes (ARGs) in solid organic waste necessitates the development of effective treatment strategies. The objective of this study was to assess ARG diversity and abundance as well as the relationship between resistome and microbial community structure during anaerobic co-digestion (AD) of food waste, paper and cardboard. A lab-scale solid-state AD system consisting of six sequentially fed leach beds (each with a solids retention time of 42 days) and an upflow anaerobic sludge blanket (UASB) reactor was operated under mesophilic conditions continuously for 88 weeks to successfully treat municipal organic waste and produce biogas. A total of ten samples from digester feed and digestion products were collected for microbial community analysis including SSU rRNA gene sequencing, total community metagenome sequencing and quantitative PCR. Taxonomic analyses revealed that AD changed the taxonomic profile of the microbial community: digester feed was dominated by bacterial and eukaryotic taxa while anaerobic digestate possessed a large proportion of archaea mainly belonging to the methanogenic genusMethanosaeta. ARGs were identified in all samples with significantly higher richness and relative abundance per 16S rRNA gene in digester feed compared to digestion products. Multidrug resistance was the most abundant ARG type. AD was not able to completely remove ARGs as shown by ARGs detected in digestion products. Using metagenomic assembly and binning we detected potential bacterial hosts of ARGs in digester feed, that includedErwinia, Bifidobacteriaceae, Lactococcus lactisandLactobacillus.IMPORTANCESolid organic waste is a significant source of antibiotic resistance genes (ARGs) (1) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here we studied the antibiotic resistome and microbial community structure within an anaerobic digester treating a mixture of food waste, paper and cardboard. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. We identified the host organisms of some of the ARGs including potentially pathogenic as well as non-pathogenic bacteria, and we detected mobile genetic elements required for horizontal gene transfer. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.
A single dose of dietary nitrate increases maximal muscle speed and power in healthy older men and women
Authors: Coggan Andrew R. , Hoffman Richard L. , Gray Derrick A. , Moorthi Ranjani N. , Thomas Deepak P. , Leibowitz Joshua L. , Thies Dakkota , Peterson Linda R. 
Published: March 2019

AbstractBackgroundAging results in reductions in maximal muscular strength, speed, and power, which often lead to functional limitations highly predictive of disability, institutionalization, and mortality in the elderly. This may be partially due to reduced nitric oxide (NO) bioavailability. We therefore hypothesized that dietary nitrate (NO3−), a source of NO via the NO3− → nitrite (NO2−) → NO enterosalivary pathway, could increase muscle contractile function in older subjects.MethodsTwelve healthy older (age 71±1 y) subjects were studied using a randomized, doubleblind, placebo-controlled, crossover design. After fasting overnight, subjects were tested 2 h after ingesting beetroot juice containing or devoid of 13.4±0.5 mmol NO3−. Plasma NO3− and NO2− and breath NO were measured periodically, and muscle function was determined using isokinetic dynamometry.ResultsNO3− ingestion increased (P<0.001) plasma NO3−, plasma NO2−, and breath NO by 1050%, 140%, and 110%, respectively. Maximal velocity of knee extension increased (P<0.01) by 1.1±0.3 rad/s, or by 10.9±3.5%. Maximal knee extensor power increased (P<0.05) by 0.14±0.06 W/kg, or by 4.4±2.3%.ConclusionsAcute dietary NO3− intake improves muscle contractility in older individuals. These findings have important implications for this population, in whom diminished muscle function can lead to functional limitations, dependence, and even premature death.
Scans of the MYC mRNA reveal multiple stable secondary structures—including a 3′ UTR motif, conserved across vertebrates, that can affect gene expression
Authors: O’Leary Collin A. , Andrews Ryan J. , Tompkins Van S. , Chen Jonathan L. , Childs-Disney Jessica L. , Disney Matthew D. , Moss Walter N. 
Published: March 2019

AbstractThe MYC gene encodes a human transcription factor and proto-oncogene that is dysregulated in over half of all known cancers. To better understand potential post-transcriptional regulatory features affecting MYC expression, we analyzed secondary structure in the MYC mRNA using a program that is optimized for finding small locally-folded motifs with a high propensity for function. This was accomplished by calculating folding metrics across the MYC sequence using a sliding analysis window and generating unique consensus base pairing models weighted by their lower-than-random predicted folding energy. A series of 30 motifs were identified, primarily in the 5’ and 3’ untranslated regions, which show evidence of structural conservation and compensating mutations across vertebrate MYC homologs. This analysis was able to recapitulate known elements found within an internal ribosomal entry site, as well as discover a novel element in the 3’ UTR that is unusually stable and conserved. This novel motif was shown to affect MYC expression: likely via modulation of miRNA target accessibility. In addition to providing basic insights into mechanisms that regulate MYC expression, this study provides numerous, potentially druggable RNA targets for the MYC gene, which is considered “undruggable” at the protein level.
The DNA-binding protein HTa fromThermoplasma acidophilumis an archaeal histone analog
Authors: Hocher Antoine , Rojec Maria , Swadling Jacob B. , Esin Alexander , Warnecke Tobias 
Published: March 2019

AbstractHistones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are phylogenetically widespread, often highly abundant, but not universal: several archaeal lineages have lost histone genes from their coding repertoire. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we use micrococcal nuclease digestion followed by high-throughput sequencing (MNase-Seq) to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeonThermoplasma acidophilum. We confirm and extend prior results showing thatT. acidophilumharbours a HU family protein, HTa, that is highly expressed and protects a sizeable fraction of the genome from MNase digestion. Charting HTa-based chromatin architecture across the growth cycle and comparing it to that of three histone-encoding archaea (Methanothermus fervidus, Thermococcus kodakarensisandHaloferax volcanii), we then present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around a conspicuous dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.
A nematode-specific gene underlies bleomycin-response variation inCaenorhabditis elegans
Authors: Brady Shannon C. , Zdraljevic Stefan , Bisaga Karol W. , Tanny Robyn E. , Cook Daniel E. , Lee Daehan , Wang Ye , Andersen Erik C. 
Published: March 2019

ABSTRACTBleomycin is a powerful chemotherapeutic drug used to treat a variety of cancers. However, individual patients vary in their responses to bleomycin. The identification of genetic differences that underlie this response variation could improve treatment outcomes by tailoring bleomycin dosages to each patient. We used the model organismCaenorhabditis elegansto identify genetic determinants of bleomycin-response differences by performing linkage mapping on recombinants derived from a cross between the laboratory strain (N2) and a wild strain (CB4856). This approach identified a small genomic region on chromosome V that underlies bleomycin-response variation. Using near-isogenic lines and strains with CRISPR-Cas9 mediated deletions and allele replacements, we discovered that a novel nematode-specific gene (scb-1) is required for bleomycin resistance. Although the mechanism by which this gene causes variation in bleomycin responses is unknown, we suggest that a rare variant present in the CB4856 strain might cause differences in the potential stress-response function ofscb-1between the N2 and CB4856 strains, thereby leading to differences in bleomycin resistance.
Sphingomyelin is critical in organizing phosphoinositide dynamics during phagocytic uptake of Mycobacterium tuberculosis
Authors: Niekamp Patrick , Guzman Gaelen , Leier Hans , Rashidfarrokhi Ali , Richina Veronica , Holthius Joost , Tafesse Fikadu G. 
Published: March 2019

AbstractTuberculosis, the pathological result of infection by Mycobacterium tuberculosis (M.tb), represents a massive and persistent global health burden with vast overrepresentation in regions with poor access to healthcare. This pathogen survives intracellularly within lung macrophages, and has been shown to extensively reprogram the host lipid compartment to the effect of enhanced survival and immune evasion. Sphingolipids are a class of lipid with extensive functions in a wide variety of cellular contexts, including apoptosis, autophagy, stress response, and inflammation. There remains a significant knowledge gap surrounding the lipid-mediated interactions between M.tb and its host. Our investigation aims to explore the mechanisms through which M.tb harnesses host-derived sphingolipids to gain entry to the host and to survive intracellularly. To this end, we use chemical and genetic perturbations of the sphingolipid de novo synthesis pathway and fluorescence microscopy to show that sphingolipids are required for efficient phagocytosis of M.tb. We furthermore show that the dynamics of phosphoinositides at the phagosomal synapse are perturbed upon blockade of sphingolipid synthesis. Finally, we demonstrate that perturbing the homeostasis of a specific sphingolipid (sphingomyelin) through both enrichment and depletion at the cell surface reduces M.tb uptake. This work represents a first step in building comprehensive knowledge of the mechanisms of host-pathogen interactions in M.tb, and demonstrates a cohort of methodologies that may be applied to a variety of pathogenic contexts.
New transcriptional circuit evolved by coding sequence changes in a master regulator followed by cis-regulatory changes in its target genes
Authors: Britton Candace S. , Sorrells Trevor R. , Johnson Alexander D. 
Published: March 2019

AbstractWhile changes in both the coding-sequence of transcriptional regulators and in the cis-regulatory sequences recognized by them have been implicated in the evolution of transcriptional circuits, little is known of how they evolve in concert. We describe an evolutionary pathway in fungi where a new transcriptional circuit (a-specific gene repression by Matα2) evolved by coding changes in an ancient master regulator, followed millions of years later by cis-regulatory sequence changes in the genes of its future regulon. We discerned this order of events by analyzing a group of species in which the coding changes in the regulator are present, but the cis-regulatory changes in the target genes are not. In this group we show that the coding changes became necessary for the regulator’s deeply conserved function and were therefore preserved. We propose that the changes first arose without altering the overall function of the regulator (although changing the details of its mechanism) and were later co-opted to “jump start” the formation of the new circuit.
Consequences of recombination for the evolution of the mating type locus inChlamydomonas reinhardtii
Authors: Hasan Ahmed R. , Duggal Jaspreet K. , Ness Rob W. 
Published: March 2019

SummaryRationaleRecombination suppression in sex chromosomes and mating type loci can lead to degeneration due to reduced selection efficacy and Muller’s ratchet effects. However, genetic exchange in the form of non-crossover gene conversions may still take place within crossover-suppressed regions. Recent work has found evidence that gene conversion may explain the low levels of allelic differentiation in the dimorphic mating type locus (MT) of the isogamous algaChlamydomonas reinhardtii. However, no one has tested whether gene conversion is sufficient to avoid the degeneration of functional sequence withinMT.MethodsHere, we calculate levels of linkage disequilibrium (LD) acrossMTas a proxy for recombination rate and investigate its relationship to patterns of population genetic variation and the efficacy of selection in the region.ResultsWe find that levels of LD predict selection efficacy acrossMT, and that purifying selection is stronger in shared genes thanMT-limited genes to the point of being equivalent to that of autosomal genes.ConclusionsWe argue that isogamous systems without secondary sexual characteristics exhibit reduced selective pressure to differentiate sex chromosomes, and that recombination via gene conversion plays an important role in both reducing differentiation and preventing degeneration of crossover suppressed mating type loci.
Short-term depression and long-term plasticity together tune sensitive range of synaptic plasticity
Authors: Deperrois Nicolas , Graupner Michael 
Published: March 2019

AbstractSynaptic efficacy is subjected to activity-dependent changes on short- and long time scales. While short-term changes decay over minutes, long-term modifications last from hours up to a lifetime and are thought to constitute the basis of learning and memory. Both plasticity mechanisms have been studied extensively but how their interaction shapes synaptic dynamics is little known. To investigate how both short- and long-term plasticity together control the induction of synaptic depression and potentiation, we used numerical simulations and mathematical analysis of a calcium-based model, where pre- and postsynaptic activity induces calcium transients driving synaptic long-term plasticity. We found that the model implementing known synaptic short-term dynamics in the calcium transients can be successfully fitted to long-term plasticity data obtained in visual- and somatosensory cortex. Interestingly, the impact of spike-timing and firing rate changes on plasticity occurs in the prevalent firing rate range, which is different in both cortical areas considered here. Our findings suggest that short- and long-term plasticity are together tuned to adapt plasticity to area-specific activity statistics such as firing rates.Author summarySynaptic long-term plasticity, the long-lasting change in efficacy of connections between neurons, is believed to underlie learning and memory. Synapses furthermore change their efficacy reversibly in an activity-dependent manner on the subsecond time scale, referred to as short-term plasticity. It is not known how both synaptic plasticity mechanisms – long- and short-term – interact during activity epochs. To address this question, we used a biologically-inspired plasticity model in which calcium drives changes in synaptic efficacy. We applied the model to plasticity data from visual- and somatosensory cortex and found that synaptic changes occur in very different firing rate ranges, which correspond to the prevalent firing rates in both structures. Our results suggest that short- and long-term plasticity act in a well concerted fashion.
Molecular Phenotyping of Oxidative Stress in Diabetes Mellitus with Point-of-care NMR system
Authors: Peng Weng Kung , Chen Lan , Boehm Bernhard O , Han Jongyoon , Loh Tze Ping 
Published: March 2019

AbstractDiabetes mellitus is one of the fastest growing health burdens globally. Oxidative stress which has been implicated to the pathogenesis of diabetes complication (e.g., cardiovascular event) were, however, poorly understood. We report a novel approach to rapidly manipulate the redox chemistry (in a single drop) of blood using point-of-care NMR system. We exploit the fact that oxidative stress changes the subtle molecular motion of water-proton in the blood, and thus inducing a measurable shift in magnetic resonance relaxation properties. This technique is label-free and the whole assays finish in a few minutes. Various redox states of the hemoglobin were mapped out using our newly proposed two-dimensional map, known as T1-T2magnetic state diagram. We demonstrated the clinical utilities of this technique to rapidly sub-stratify diabetes subjects based on their oxidative status (in conjunction to the traditional glycemic level), to improve the patient risk stratification and thus the overall outcome of clinical diabetes care and management. (155 words)Key Points for SummariesA novel approach to rapidly manipulate the redox chemistry (in a single drop) of blood using point-of-care NMR system.Assessment of the oxidative status, in conjunction to their glycemic level allows sub-stratification of diabetes subjects which was demonstrated clinically.Visual Abstract