bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic analysis of the mesophilic Thermotogae genusMesotogareveals phylogeographic structure and genomic determinants of its distinct metabolism
Authors: Nesbø Camilla L. , Charchuk Rhianna , Pollo Stephen M. J. , Budwill Karen , Kublanov Ilya V. , Haverkamp Thomas H.A. , Foght Julia 
Published: May 2018

SummaryThe genusMesotoga, the only described mesophilicThermotogaelineage, is common in mesothermic anaerobic hydrocarbon-rich environments. Besides mesophily,Mesotogadisplays lineage-specific phenotypes, such as no or little H2production and dependence on sulfur-compound reduction, which may influence its ecological role. We used comparative genomics of 18Mesotogastrains (pairwise 16S rRNA identity > 99%) and a transcriptome ofM. primato investigate how life at moderate temperatures affects phylogeography and to interrogate the genomic features of its lineage-specific metabolism. We propose thatMesotogaaccomplish H2oxidation and thiosulfate reduction using a sulfide dehydrogenase and a hydrogenase-complex and that a pyruvate:ferredoxin oxidoreductase acquired fromClostridiais responsible for oxidizing acetate. Phylogenetic analysis revealed three distinctMesotogalineages (89.6-99.9% average nucleotide identity [ANI] within lineages, 79.3-87.6% ANI between lineages) having different geographic distribution patterns and high levels of intra-lineage recombination but little geneflow between lineages. Including data from metagenomes, phylogeographic patterns suggest that geographical separation historically has been more important forMesotogathan hyperthermophilicThermotogaand we hypothesize that distribution ofMesotogais constrained by their anaerobic lifestyle. Our data also suggest that recent anthropogenic activities and environments (e.g., wastewater treatment, oil exploration) have expandedMesotogahabitats and dispersal capabilities.Originality-Significance StatementThis study comprises one of the first whole-genome-based phylogeographic analyses of anaerobic mesophiles, and our data suggest that such microbes are more restricted by geography than are thermophiles (and mesophilic aerobes). This is likely to be a general trait for similar anaerobic organisms – and therefore broadly relevant to and testable in other environments. Moreover,Mesotogabacteria are part of the largely understudied subsurface ecosystem that has relatively recently been recognized as a new and important biosphere. Understanding the forces responsible for the distribution of organisms in the subsurface, as well as the identification of genes responsible forMesotoga’s distinct metabolism, will contribute to the understanding of these communities.
A genetically encoded fluorescent sensor for in vivo imaging of GABA
Authors: Marvin Jonathan S. , Shimoda Yoshiteru , Malgoire Vincent , Leite Marco , Kawashima Takashi , Jensen Thomas P. , Knott Erika L. , Novak Ondrej , Podgorski Kaspar , Leidenheimer Nancy J. , Rusakov Dmitri A. , Ahrens Misha B. , Kullmann Dimitri M. , Looger Loren L. 
Published: May 2018

AbstractCurrent techniques for monitoring GABA, the primary inhibitory neurotransmitter in vertebrates, cannot follow ephemeral transients in intact neural circuits. We applied the design principles used to create iGluSnFR, a fluorescent reporter of synaptic glutamate, to develop a GABA sensor using a protein derived from a previously unsequenced Pseudomonas fluorescens strain. Structure-guided mutagenesis and library screening led to a usable iGABASnFR (ΔF/Fmax ~ 2.5, Kd ~ 9 μM, good specificity, adequate kinetics). iGABASnFR is genetically encoded, detects single action potential-evoked GABA release events in culture, and produces readily detectable fluorescence increases in vivo in mice and zebrafish. iGABASnFR enabled tracking of: (1) mitochondrial GABA content and its modulation by an anticonvulsant; (2) swimming-evoked GABAergic transmission in zebrafish cerebellum; (3) GABA release events during inter-ictal spikes and seizures in awake mice; and (4) GABAergic tone decreases during isoflurane anesthesia. iGABASnFR will permit high spatiotemporal resolution of GABA signaling in intact preparations.
Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis
Authors: Vera-Wolf Patricia , Cárdenas Juan P. , Morton Amanda M. , Norambuena Tomás , Torres Rafael , Leon Luis E. , Bik Elisabeth M. , Ugalde Juan A. , Almonacid Daniel E. , Richman Jessica , Apte Zachary S 
Published: May 2018

AbstractMicrobial community analysis can be biased by multiple technical factors, such as storage conditions, DNA extraction, or amplification conditions. In a high-throughput laboratory that relies on samples obtained from thousands of different subjects, knowledge of the extent of subject-introduced sampling and storage variation on the outcome of the inferred microbiome, as well as the effect of laboratory-introduced variation caused by reagent batches, equipment, or operator on the consistency of these processes within the laboratory is paramount. Here, we analyzed the effect of sampling from different parts of the same stool specimen or on different consecutive days, as well as short-term storage of samples at different temperatures on microbiome profiles obtained by 16S rRNA gene amplification. Each of these factors had relatively little effect on the microbial composition. In addition, replicate amplification of 44 stool samples showed reproducible results. Finally, 363 independent replicate extractions and amplifications of a single human homogenized stool (HS) specimen showed reproducible results (average Lin’s correlation = 0.95), with little variation introduced by HS batch, operator, extraction equipment, or DNA sequencer. In all cases, variations between replicates were significantly smaller than those between individual samples; subject identity always was the largest determinant. We propose that homogenized stool specimens could be used as quality control to routinely monitor the laboratory process and to validate new methods.
Analysis of differentially methylated regions in primates and non-primates provides support for the evolutionary hypothesis of schizophrenia
Authors: Banerjee Niladri , Polushina Tatiana , Bettella Francesco , Steen Vidar M. , Andreassen Ole A. , Hellard Stephanie Le 
Published: May 2018

AbstractIntroductionThe persistence of schizophrenia in human populations separated by geography and time led to the evolutionary hypothesis that proposes schizophrenia as a by-product of the higher cognitive abilities of modern humans. To explore this hypothesis, we used here an evolutionary epigenetics approach building on differentially methylated regions (DMRs) of the genome.MethodsWe implemented a polygenic enrichment testing pipeline using the summary statistics of genome-wide association studies (GWAS) of schizophrenia and 12 other phenotypes. We investigated the enrichment of association of these traits across genomic regions with variable methylation between modern humans and great apes (orangutans, chimpanzees and gorillas; primate DMRs) and between modern humans and recently extinct hominids (Neanderthals and Denisovans; non-primate DMRs).ResultsRegions that are hypo-methylated in humans compared to great apes show enrichment of association with schizophrenia only if the major histocompatibility complex (MHC) region is included. With the MHC region removed from the analysis, only a modest enrichment for SNPs of low effect persists. The INRICH pipeline confirms this finding after rigorous permutation and bootstrapping procedures.ConclusionThe analyses of regions with differential methylation changes in humans and great apes do not provide compelling evidence of enrichment of association with schizophrenia, in contrast to our previous findings on more recent methylation differences between modern humans, Neanderthals and Denisovans. Our results further support the evolutionary hypothesis of schizophrenia and indicate that the origin of some of the genetic susceptibility factors of schizophrenia may lie in recent human evolution.
A potential role for GrgA in regulation of σ28-dependent transcription in the obligate intracellular bacterial pathogen Chlamydia trachomatis
Authors: Desai Malhar , Wurihan Wurihan , Di Rong , Fondell Joseph D. , Nickels Bryce E. , Bao Xiaofeng , Fan Huizhou 
Published: May 2018

ABSTRACTThe sexually transmitted obligate intracellular bacterial pathogen Chlamydia trachomatis has a unique developmental cycle consisting of two contrasting cellular forms. Whereas the primary Chlamydia sigma factor, σ66, is involved in the expression of the majority of chlamydial genes throughout the developmental cycle, expression of several late genes requires the alternative sigma factor σ28. In prior work we identified GrgA as a Chlamydia-specific transcription factor that activates σ66-dependent transcription by binding DNA and interacting with a non-conserved region (NCR) of σ66. Here, we extend these findings by showing GrgA can also activate σ28-dependent transcription through direct interaction with σ28. We measure the binding affinity of GrgA for both σ66and σ28, and we identify regions of GrgA important for σ28-dependent transcription. Similar to results obtained with σ66, we find that GrgA’s interaction with σ28 involves a NCR located upstream of conserved region 2 of σ28. Our findings suggest GrgA is an important regulator of both σ66- and σ28-dependent transcription in C. trachomatis and further highlight NCRs of bacterial RNA polymerase as targets for regulatory factors unique to particular organisms.
Kaposi’s sarcoma-associated herpesvirus ORF68 is a DNA binding protein required for viral genome cleavage and packaging
Authors: Gardner Matthew R , Glaunsinger Britt A 
Published: May 2018

AbstractHerpesviral DNA packaging into nascent capsids requires multiple conserved viral proteins that coordinate genome encapsidation. Here, we investigated the role of the ORF68 protein of Kaposi’s sarcoma-associated herpesvirus (KSHV), a protein required for viral DNA encapsidation whose function remains largely unresolved across the herpesviridae. We found that KSHV ORF68 is expressed with early kinetics and localizes predominantly to viral replication compartments, although it is dispensable for viral DNA replication and gene expression. However, in agreement with its proposed role in viral DNA packaging, KSHV-infected cells lacking ORF68 failed to cleave viral DNA concatemers, accumulated exclusively immature B-capsids, and released no infectious progeny virions. ORF68 has no predicted domains aside from a series of putative zinc finger motifs. However,in vitrobiochemical analyses of purified ORF68 protein revealed that it robustly binds DNA and is associated with nuclease activity. These activities provide new insights into the role of KSHV ORF68 in viral genome encapsidation.ImportanceKaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi’s sarcoma and several B-cell cancers, causing significant morbidity and mortality in immunocompromised individuals. A critical step in the production of infectious viral progeny is the packaging of the newly replicated viral DNA genome into the capsid, which involves coordination between at least seven herpesviral proteins. While the majority of these packaging factors have been well studied in related herpesviruses, the role of the KSHV ORF68 protein and its homologs remains unresolved. Here, using a KSHV mutant lacking ORF68, we confirm its requirement for viral DNA processing and packaging in infected cells. Furthermore, we show that the purified ORF68 protein directly binds DNA and is associated with a metal-dependent cleavage activity on double stranded DNAin vitro. These activities suggest a novel role for ORF68 in herpesviral genome processing and encapsidation.
Effective soil extraction method for cultivating previously uncultured soil bacteria
Authors: Manh Nguyen Tuan , Seo Chan , Ji Moongi , Paik Man-Jeong , Myung Seung-Woon , Kim Jaisoo 
Published: May 2018

ABSTRACTHere, a new medium named as intensive soil extract medium (ISEM) based on new soil extract (NSE) using 80% ethanol was used to efficiently isolate previously uncultured bacteria and new taxonomic candidates, which accounted for 49% and 55% of the total isolates examined (n=258), respectively. The new isolates were affiliating with seven phyla such asProteobacteria, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, andBacteroidetes. The result of chemical analysis showed that NSE included more diverse components of low-molecular-weight organic substances than two conventional soil extracts using distilled water. Cultivation of previously uncultured bacteria is expected to extend knowledge through the discovery of new phenotypic, physiological and functional properties, and even roles of unknown genes.IMPORTANCEEither metagenomics or single-cell sequencing can detect unknown genes from uncultured microbial strains in environments and may find their significant potential metabolites and roles. However, such gene/genome-based techniques still have a critical problem making impossible for further applications through cultivation. To solve this problem, various approaches for cultivation of uncultured bacteria have been developed, but they still have lack of skill to grow them on solid media for isolation and subculture.
Validation of novelMycobacterium tuberculosisisoniazid resistance mutations not detectable by common molecular tests
Authors: Kandler Justin L. , Mercante Alexandra D. , Dalton Tracy L. , Ezewudo Matthew N. , Cowan Lauren S. , Burns Scott P. , Metchock Beverly ,   Global PETTS Investigatorsc, Cegielski Peter , Posey James E. 
Published: May 2018

AbstractResistance to the first-line anti-tuberculosis (TB) drug, isoniazid (INH), is widespread, and the mechanism of resistance is unknown in approximately 15% of INH-resistant (INH-R) strains. To improve molecular detection of INH-R TB, we used whole genome sequencing (WGS) to analyze 52 phenotypically INH-RMycobacterium tuberculosiscomplex (MTBC) clinical isolates that lacked the commonkatGS315T orinhApromoter mutations. Approximately 94% (49/52) of strains had mutations at known INH-associated loci that were likely to confer INH resistance. All such mutations would be detectable by sequencing more DNA adjacent to existing target regions. Use of WGS minimized the chances of missing infrequent INH resistance mutations outside commonly targeted hotspots. We used recombineering to generate 12 observed clinicalkatGmutations in the pansusceptible H37Rv reference strain and determined their impact on INH resistance. Our functional genetic experiments have confirmed the role of seven suspected INH resistance mutations and discovered five novel INH resistance mutations. All recombineeredkatGmutations conferred resistance to INH at a minimum inhibitory concentration of ≥0.25 μg/mL and should be added to the list of INH resistance determinants targeted by molecular diagnostic assays. We conclude that WGS is a superior method for detection of INH-R MTBC compared to current targeted molecular testing methods and could provide earlier diagnosis of drug-resistant TB.
Clinical scoring is the most sensitive biomarker detecting developing sepsis in newborn mice
Authors: Fehlhaber Beate , Rübensam Kathrin , Heinemann Anna S. , Pfeifer Sandra , von Köckritz-Blickwede Maren , Viemann Dorothee 
Published: May 2018

AbstractNewborn individuals are highly susceptible to infectious diseases. For better insights into age-specific host-pathogen interactions infection models are increasingly employed in neonatal mice. However, for newborn mice no measures are available to objectify the clinical disease state, particularly not in a longitudinal manner, to meet legal animal welfare requirements. We developed a scoring system for newborn mice that relies on observational and examination-based parameters and validated it by applying aStaphylococcus aureus-induced infection model in two different mouse strains.The scoring results strongly correlated with the death kinetics independent of which mouse strain was used. A score above 7 predicted fatality. While the score values increased already at early sepsis stages the large majority of plasma cytokine levels remained comparable to those in uninfected control neonates. The levels of interleukin (Il)-6, chemokine C-C motif ligand 5, Il-1α and tumor necrosis factor α were not increased before 24 hours after infection and correlated only at this late stage of sepsis with the scored disease state.We propose the first clinical scoring system that serves as important research tool to evaluate the clinical course of sepsis in newborn mice. It detects health impairments of newborn pups in a highly sensitive and longitudinal manner, providing information about the disease severity as well as prognosis.
Lethality of leptospirosis depends on sex: male hamsters succumb to infection with lower doses of pathogenic Leptospira
Authors: Gomes Charles K. , Guedes Mariana , Potula Hari-Hara , Dellagostin Odir A. , Gomes-Solecki Maria 
Published: May 2018

ABSTRACTLeptospirosis is a widespread zoonotic disease caused by pathogenic spirochetes of the genus Leptospira which affect both humans and animals. A somewhat contradictory published body of evidence suggests that sex impacts severity outcomes of human Leptospirosis. In this study, we used an acute animal model of disease to analyze how male and female hamsters infected side-by-side with low but increasing doses of L. interrogans under the same exposure conditions develop Leptospirosis. We found that female hamsters were considerably more resistant to Leptospirosis given that 87.5% survived infection; male hamsters did not gain weight and 93.7% succumbed to infection with the same infectious doses. Analysis of bacterial burden in kidney of male hamsters showed that infection with the lowest dose (103) resulted in a 4Log increase of L. interrogans, whereas females infected with the same dose had a reduction of ~1Log, after 28 days of infection. Non-surviving hamsters had signs of compromised renal function (higher levels of creatinine in blood), as well as increased levels of anti-inflammatory IL-10 and innate response pro-inflammatory CCL3, CxCL10 and TNF-α in kidney, as well as ColA1 which is a marker of kidney fibrosis. In endemic areas, humans are more often exposed to the lower infection doses which were lethal to males, than the higher doses which were lethal to males and females. It is possible that the frequency of lower infectious doses in nature and increased biological susceptibility both contribute for aggravated outcomes of leptospirosis in males.
The Repertoire of Mutational Signatures in Human Cancer
Authors: Alexandrov Ludmil B , Kim Jaegil , Haradhvala Nicholas J , Huang Mi Ni , Ng Alvin WT , Wu Yang , Boot Arnoud , Covington Kyle R , Gordenin Dmitry A , Bergstrom Erik N , Islam S M Ashiqul , Lopez-Bigas Nuria , Klimczak Leszek J , McPherson John R , Morganella Sandro , Sabarinathan Radhakrishnan , Wheeler David A , Mustonen Ville ,   the PCAWG Mutational Signatures Working Group, Getz Gad , Rozen Steven G , Stratton Michael R 
Published: May 2018

ABSTRACTSomatic mutations in cancer genomes are caused by multiple mutational processes each of which generates a characteristic mutational signature. Using 84,729,690 somatic mutations from 4,645 whole cancer genome and 19,184 exome sequences encompassing most cancer types we characterised 49 single base substitution, 11 doublet base substitution, four clustered base substitution, and 17 small insertion and deletion mutational signatures. The substantial dataset size compared to previous analyses enabled discovery of new signatures, separation of overlapping signatures and decomposition of signatures into components that may represent associated, but distinct, DNA damage, repair and/or replication mechanisms. Estimation of the contribution of each signature to the mutational catalogues of individual cancer genomes revealed associations with exogenous and endogenous exposures and defective DNA maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes contributing to the development of human cancer including a comprehensive reference set of mutational signatures in human cancer.
LAESI mass spectrometry imaging as a tool to differentiate the root metabolome of native and range-expanding plant species
Authors: Kulkarni Purva , Wilschut Rutger A. , Verhoeven Koen J.F. , van der Putten Wim H. , Garbeva Paolina 
Published: May 2018

ABSTRACTOur understanding of chemical diversity in biological samples has greatly improved through recent advances in mass spectrometry (MS). MS-based-imaging (MSI) techniques have further enhanced this by providing spatial information on the distribution of metabolites and their relative abundance.This study aims to employ laser-assisted electrospray ionization (LAESI) MSI as a tool to profile and compare the root metabolome of two pairs of native and range expanding plant species.It has been proposed that successful range-expanding plant species, like introduced exotic invaders, have a novel, or a more diverse secondary chemistry. Although some tests have been made using aboveground plant materials, tests using root materials are rare. We tested the hypothesis that range-expanding plants possess more diverse root chemistries than native plant species.To examine the root chemistry of the selected plant species, LAESI-MSI was performed in positive ion mode and data was acquired in a mass range of m/z 50-1200 with a spatial resolution of 100 µm. The acquired data was analyzed using in-house scripts, and differences in the spatial profiles were studied for discriminatory mass features.
The results revealed clear differences in the metabolite profiles amongst and within both pairs of congeneric plant species, in the form of distinct metabolic fingerprints. The use of ambient conditions and the fact that no sample preparation was required, established LAESI-MSI as an ideal technique for untargeted metabolomics and for direct correlation of the acquired data to the underlying metabolomic complexity present in intact plant samples.
1H MR Spectroscopy of the Motor Cortex Immediately following Transcranial Direct Current Stimulation at 7 Tesla
Authors: Ryan Kayla , Wawrzyn Krzysztof , Gati Joseph , Chronik Blaine A. , Wong Dickson , Duggal Neil , Bartha Robert 
Published: May 2018

AbstractTranscranial direct current stimulation (tDCS) is a form of non-invasive brain stimulation that may modulate cortical excitability, metabolite concentration, and human behaviour. The supplementary motor area (SMA) has been largely ignored as a potential target for tDCS neurorehabilitation but is an important region in motor compensation after brain injury with strong efferent connections to the primary motor cortex (M1). The objective of this work was to measure tissue metabolite changes in the human motor cortex immediately following tDCS. We hypothesized that bihemispheric tDCS would change levels of metabolites involved in neuromodulation including N-acetylaspartate, glutamate, and creatine. In this single-blind, randomized, cross-over study, fifteen healthy adults aged 21-60 participated in two 7T MRI sessions, to identify changes in metabolite concentrations by magnetic resonance spectroscopy. Immediately after 20 minutes of tDCS, there were no significant changes in metabolite levels or metabolite ratios comparing tDCS to sham. However there was a trend toward increased NAA/tCr concentration (p=0.08) in M1 under the stimulating cathode. There was a strong, positive correlation between the change in the absolute concentration of NAA and the change in the absolute concentration of tCr (p<0.001) suggesting an effect of tDCS. Both NAA and creatine are important markers of neurometabolism. Our findings provide novel insight into the modulation of neural metabolites in the motor cortex immediately following application of bihemispheric tDCS.