bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of Early Response Genes Prevents Changes in Global Joint Metabolomic Profiles in Mouse Post-Traumatic Osteoarthritis
Authors: Haudenschild Dominik R. , Carlson Alyssa K. , Zignego Donald L. , Yik Jasper H.N. , Hilmer Jonathan K. , June Ronald K. 
Published: July 2018

Osteoarthritis (OA) is the most common degenerative joint disease, and joint injury increases the risk of OA by 10-fold. Although the injury event itself damages joint tissues, a substantial amount of secondary damage is mediated by the cellular responses to the injury. Cellular responses include the production and activation of proteases (MMPs, ADAMTSs, Cathepsins), the production of inflammatory cytokines, and we hypothesize, changes to the joint metabolome. The trajectory of cellular responses is driven by the transcriptional activation of early response genes, which requires Cdk9-dependent RNA Polymerase II phosphorylation. Flavopiridol is a potent and selective inhibitor of Cdk9 kinase activity, which prevents the transcriptional activation of early response genes. To model post-traumatic osteoarthritis, we subjected mice to non-invasive ACL-rupture joint injury. Following injury, mice were treated with flavopiridol to inhibit Cdk9-dependent transcriptional activation, or vehicle control. Global joint metabolomics were analyzed 1 hour after injury. We found that injury induced metabolomic changes, including increases in Vitamin D3 metabolism and others. Importantly, we found that inhibition of primary response gene activation at the time of injury largely prevented the global changes in the metabolomics profiles. Cluster analysis of joint metabolomes identified groups of injury-induced and drug-responsive metabolites, which may offer novel targets for cell-mediated secondary joint damage. Metabolomic profiling provides an instantaneous snapshot of biochemical activity representing cellular responses, and these data demonstrate the potential for inhibition of early response genes to alter the trajectory of cell-mediated degenerative changes following joint injury.Significance StatementJoint injury is an excellent predictor of future osteoarthritis. It is increasingly apparent that the acute cellular responses to injury contribute to the initiation and pathogenesis of OA. Although changes to the joint transcriptome have been extensively studied in the context of joint injury, little is known about changes to small-molecule metabolites. Here we use a non-invasive ACL rupture model of joint injury in mice to identify injury-induced changes to the global metabolomic profiles. In one experimental group we prevented the activation of primary response gene transcription using the Cdk9 inhibitor flavopiridol. Through this comparison, we identified two sets of metabolites that change acutely after joint injury: those that require transcription of primary response genes, and those that do not.
Chromulinavorax destructans, a pathogenic TM6 bacterium with an unusual replication strategy targeting protist mitochondrion
Authors: Deeg Christoph M. , Zimmer Matthias M. , George Emma , Husnik Filip , Keeling Patrick J. , Suttle Curtis A. 
Published: July 2018

AbstractMost of the diversity of microbial life is not available in culture, and as such we lack even a fundamental understanding of the biological diversity of several branches on the tree of life. One branch that is highly underrepresented is the candidate phylum TM6, also known as the Dependentiae. Their biology is known only from reduced genomes recovered from metagenomes around the world and two isolates infecting amoebae, all suggest that they live highly host-associated lifestyles as parasites or symbionts.Chromulinavorax destructansis an isolate from the TM6/Dependentiae that infects and lyses the abundant heterotrophic flagellate,Spumella elongata. Chromulinavorax destructansis characterized by a high degree of reduction and specialization for infection, so much so it was discovered in a screen for giant viruses. Its 1.2 Mb genome shows no metabolic potential andC. destructansinstead relies on extensive transporter system to import nutrients, and even energy in the form of ATP from the host. Accordingly, it replicates in a viral-like fashion, while extensively reorganizing and expanding the host mitochondrion. 44% of proteins contain signal sequences for secretion, which includes many proteins of unknown function as well as 98 copies of ankyrin-repeat domain proteins, known effectors of host modulation, suggesting the presence of an extensive host-manipulation apparatus.
Where do animals covered by the US Animal Welfare Act live? Analysis of USDA licensed and registered entities
Authors: Bennett Allyson J. , Schoenbeck Erin G. 
Published: August 2018

AbstractNonhuman animals are housed in captivity for a range of purposes in the US and other countries. The regulation, oversight, and public transparency of decisions related to the care and use of those animals varies by species and activity. The goals of this paper are 1) to provide a concise and accessible summary of the number and types of facilities either registered or licensed by the USDA and overseen by the federal agency; and 2) to provide concise comparisons of the relative proportion of different types of use of nonhuman animals that fall under the AWA (Animal Welfare Act). Analysis of the publicly-available list of USDA certificate holders produced descriptive data for each state and the US overall. Licensed exhibitors (N=2,640; 33% of total) and breeders (N=2,701; 34% of total) comprise two-thirds of the 8,002 USDA certificate holders. Registered research facilities (N=1,110) account for 14% of the total USDA certificates. The final 19% consists of licensed dealers (N=763; 9%) and registered carriers or interim handlers (N=788; 10%). The number and distribution of types of certificates varies across states. The largest number of exhibitors and dealers are in Florida, while the largest number of breeders are in Missouri. California has the largest number of research registered facilities. Finally, a comparison of the estimated number of animals in the US that are pets, used in agriculture, exhibition, and research suggests that animals in research are between 0.07-2.3% of the total. The comparison also highlights areas in which public information about captive animals in the US is uneven or missing altogether. Together, the current report provides a concise view of basic information and data relevant to public consideration and policy decisions about animals housed in the set of captive settings to which the AWA applies.
Identifying Genes in Published Pathway Figure Images
Authors: Riutta Anders , Hanspers Kristina , Pico Alexander R. 
Published: July 2018

BACKGROUNDPathway figures are commonly found in the biomedical literature providing intuitive models of complex processes in a visually concise format. The contents of a pathway figure often reflect the key findings and relevant context of an article. Unfortunately, the vast majority of pathway figures are drawn as one-off static images despite freely available pathway tools and resources, thus rendering their contents inaccessible to search, data mining and downstream analysis.APPROACHLeveraging advances in optical character recognition and domain expertise in pathway modeling, we devised an approach to identify genes in published pathway figures. The approach was optimized against a set of figure images obtained from PubMed Central and tested against a set of 400 curated pathways with known content from WikiPathways (F-measure 95.2%).RESULTSApplied to 3982 published pathway figures spanning a four year period, our approach identified 29,189 gene symbols representing 4159 unique gene identifiers. The gene content unlocked from just this small sample of published figures includes novel and diverse pathway associations unmatched by any pathway database. Our approach over doubled the number of genes associated with the articles containing these figures as compared to combined annotations available from PubMed and PubTator. Encouraged by these initial results, we plan to scale the approach to make the molecular contents of the continuing stream of published pathway figures more accessible.
High efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells
Authors: Johnston Andrew D. , Simões-Pires Claudia A. , Suzuki Masako , Greally John M. 
Published: July 2018

ABSTRACTWhile lymphoblastoid cell lines (LCLs) represent a valuable resource for population genetic studies, they are usually regarded as difficult for CRISPR-mediated genomic editing. It would be valuable to be able to take the results of their functional variant studies and test them in the same LCLs. We describe a protocol using a single-stranded donor oligonucleotide (ssODN) strategy for ‘scarless’ editing in LCLs. The protocol involves optimized transfection, flow cytometric sorting of transfected cells to single cells in multi-well plates and growth in conditioned, serum-rich medium, followed by characterization of the clones. Amplicon sequencing reveals the relative proportions of alleles with different editing events, with sequencing of DNA from clones showing the frequencies of events in individual cells. We find 12/60 (20%) of clones selected in this manner to have the desired ssODN-mediated recombination event. Long-range PCR of DNA at the edited locus and of RT-PCR products for the gene traversing the edited locus reveals 3/6 characterized clones (50%) to have large structural mutations of the region that are missed by sequencing just the edited site. The protocol does not require the use of lentiviruses or stable transfection, and makes LCLs a realistic cell type for consideration for CRISPR-mediated genomic targeting.
Two Novel α-L-Arabinofuranosidases from Bifidobacterium longum subsp. longum belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade Arabinan
Authors: Komeno Masahiro , Hayamizu Honoka , Fujita Kiyotaka , Ashida Hisashi 
Published: July 2018

ABSTRACTArabinose-containing poly-or oligosaccharides are suitable carbohydrate sources for Bifidobacterium longum subsp. longum, though their degradation pathways are poorly understood. In this study, we found that the gene expression levels of bllj 1852 and bllj 1853 from B. longum subsp. longum JCM 1217 were enhanced in the presence of arabinan. Both genes encode previously uncharacterized glycoside hydrolase (GH) family 43 enzymes. Subsequently, we cloned those genes and characterized the recombinant enzymes expressed in Escherichia coli. Both enzymes exhibited α-L-arabinofuranosidase activity toward synthetic p-nitrophenyl glycoside, but the specificities for L-arabinofuranosyl linkages were different. BLLJ_1852 catalyzed the hydrolysis of α1,2- and α1,3-L-arabinofuranosyl linkages found in the side chains of arabinan and arabinoxylan. BLLJ_1852 released L-arabinose 100 times faster from arabinan than from arabinoxylan but did not act on arabinogalactan. BLLJ_1853 catalyzed the hydrolysis of α1,5-L-arabinofuranosyl linkages found on the arabinan backbone. BLLJ_1853 released L-arabinose from arabinan but not from arabinoxylan or arabinogalactan. Both enzyme activities were largely suppressed with EDTA treatment, suggesting that they require divalent metal ions. BLLJ_1852 was moderately activated in the presence of all divalent cations tested, whereas BLLJ_1853 activity was inhibited by Cu2+. The GH43 domains of BLLJ_1852 and BLLJ_1853 are classified into GH43 subfamilies 27 and 22, respectively, but hardly share similarity with other biochemically characterized members in the corresponding subfamilies.IMPORTANCEWe identified two novel α-L-arabinofuranosidases from B. longum subsp. longum JCM 1217 that act on different linkages in arabinan. These enzymes may be required for efficient degradation and assimilation of arabinan in the probiotic bifidobacteria. The genes encoding these enzymes are located side-by-side in a gene cluster involved in metabolic pathways for plant-derived polysaccharides, which may confer adaptability in adult intestines.
Discovery of a bacterial peptide as a modulator of GLP-1 and metabolic disease
Authors: Tomaro-Duchesneau Catherine , LeValley Stephanie L. , Röth Daniel , Sun Liang , Horrigan Frank T. , Kalkum Markus , Hyser Joseph M. , Britton Robert A. 
Published: July 2018

AbstractEarly work in germ-free rodents highlighted the gut microbiota’s importance in metabolic disease, including Type II Diabetes Mellitus (T2DM) and obesity. Glucagon-like peptide-1 (GLP-1) is an incretin secreted by enteroendocrine L-cells lining the gastrointestinal epithelium. GLP-1 has important functions including promoting insulin secretion, insulin sensitivity, and β-cell mass, while inhibiting gastric emptying and appetite. We set out to elucidate how the microbiota can modulate GLP-1 secretion, with the goal to identify microbial strains with GLP-1 stimulatory activity as a metabolic disease therapeutic. Over 1500 human-derived strains were isolated from fecal, breast milk, and colon and intestinal biopsy samples from healthy individuals. In vitro screening for GLP-1 modulation was performed by incubating bacterial cell-free supernatants with NCI H716 human L-cells. Approximately 45 strains capable of increasing GLP-1 levels, measured by ELISA, were discovered. Interestingly, all positive strains were identified as Staphylococcus epidermidis by 16S rRNA sequencing. Non-GLP-1 stimulatory S. epidermidis strains were also identified. Mass spectrometry analysis identified a 3 kDa peptide, termed GLP-1 stimulating peptide (GspA), present in GLP-1 positive but absent in GLP-1 neutral S. epidermidis. Studies in human L-cells and intestinal enteroids demonstrated that GspA alone is sufficient to enhance GLP-1 secretion. When administered in high-fat-fed mice, GspA-producing S. epidermidis significantly reduced markers associated with obesity and T2DM, including adiposity and hyperinsulinemia. Further characterization of GspA suggests a GLP-1 stimulatory action via calcium signaling. The presented results identify a novel host-microbe interaction which may ultimately lead to the development of a microbial peptide-based therapeutic for obesity and T2DM.ImportanceThe human gastrointestinal microbiota has been shown to modulate metabolic disease, including Type II Diabetes Mellitus and obesity, through mechanisms involving gut hormone secretion. We initiated this study to identify bacterial strains that can stimulate one of these hormones, glucagon-like peptide-1. We first identified that some strains of Staphylococcus epidermidis have such stimulatory activity. We then found that these strains could be used in a mouse model of high-fat feeding to reduce markers associated with metabolic disease, including adiposity and elevated insulin levels. We also identified the peptide from S. epidermidis that stimulates glucagon-like peptide-1 and propose a mode of action through calcium signaling. This newly identified microbial-derived peptide and host-microbe interaction provide a promising therapeutic approach against Type II Diabetes Mellitus and obesity.
A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios
Authors: Ishikawa Sohta A. , Zhukova Anna , Iwasaki Wataru , Gascuel Olivier 
Published: July 2018

AbstractThe reconstruction of ancestral scenarios is widely used to study the evolution of characters along a phylogenetic tree. In the likelihood framework one commonly uses the marginal posterior probabilities of the character states, and the joint reconstruction of the most likely scenario. Both approaches are somewhat unsatisfactory. Marginal reconstructions provide users with state probabilities, but these are difficult to interpret and visualize, while joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts and the Brier criterion to associate each node in the tree to a set of likely states. A unique state is predicted in the tree regions with low uncertainty, while several states are predicted in the uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated to the same states and use graph visualization tools. The method is implemented in the PastML program and web server.The results on simulated data consistently show the accuracy and robustness of the approach. The method is applied to large tree comprising 3,619 sequences from HIV-1M subtype C sampled worldwide, which is processed in a few minutes. Results are very convincing: we retrieve and visualize the main transmission routes of HIV-1C; we demonstrate that drug resistance mutations mostly emerge independently under treatment pressure, but some resistance clusters are found, corresponding to transmissions among untreated patients.
microRNA regulation of persistent stress-enhanced memory
Authors: Sillivan Stephanie E. , Jamieson Sarah , de Nijs Laurence , Jones Meghan , Snijders Clara , Klengel Torsten , Joseph Nadine F. , Krauskopf Julian , Kleinjans Jos , Vinkers Christiaan H. , Boks Marco P.M. , Geuze Elbert , Vermetten Eric , Ressler Kerry J. , Rutten Bart P.F. , Rumbaugh Gavin , Miller Courtney A. 
Published: July 2018

AbstractDisruption of persistent, stress-associated memories is relevant for treating posttraumatic stress disorder (PTSD) and related syndromes, which develop in a subset of individuals following a traumatic event. Using a stress-enhanced fear learning protocol that results in differential susceptibility in inbred mice, we integrated small-RNA sequencing with quantitative proteomics on basolateral amygdala tissue collected one month after training. We identified persistently changed microRNAs, including mir-135b-5p, and predicted target proteins associated with PTSD-like heightened fear expression. Functional manipulations of mir-135b-5p bidirectionally modulated stress-associated memory. mir-135b-5p is expressed in human amygdala and its passenger strand was elevated in serum from a well-characterized military PTSD cohort. miR-135b-5p is a therapeutic target for dampening persistent, stress-enhanced memory and its passenger strand a potential biomarker for responsivity to a mir-135-based therapeutic.One Sentence Summarymir-135 can be manipulated to weaken persistent, stress-associated memory and serve as a biomarker of PTSD.
MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma
Authors: Zeineldin Maged , Federico Sara , Chen Xiang , Fan Yiping , Xu Beisi , Stewart Elizabeth , Zhou Xin , Jeon Jongrye , Griffiths Lyra , Easton John , Mulder Heather , Yergeau Donald , Liu Yanling , Wu Jianrong , Ryn Collin Van , Naranjo Arlene , Hogarty Michael D. , Kamiński Marcin M. , Valentine Marc , Pruett-Miller Shondra M. , Pappo Alberto , Zhang Jinghui , Clay Michael R. , Bahrami Armita , Lee Seungjae , Shelat Anang , George Rani E. , Mardis Elaine R. , Wilson Richard K. , Downing James R. , Dyer Michael A. ,   for the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project
Published: July 2018

SUMMARYAggressive cancers often have activating mutations in growth-controlling oncogenes and inactivating mutations in tumor-suppressor genes. In neuroblastoma, amplification of the MYCN oncogene and inactivation of the ATRX tumor-suppressor gene correlate with high-risk disease and poor prognosis. Here we show that ATRX mutations and MYCN amplification are mutually exclusive across all ages and stages in neuroblastoma. Using human cell lines and mouse models, we found that elevated MYCN expression and ATRX mutations are incompatible. Elevated MYCN levels promote metabolic reprogramming, mitochondrial dysfunction, reactive-oxygen species generation, and DNA-replicative stress. The combination of replicative stress caused by defects in the ATRX–histone chaperone complex and that induced by MYCN-mediated metabolic reprogramming leads to synthetic lethality. Therefore, ATRX and MYCN represent an unusual example, where inactivation of a tumor-suppressor gene and activation of an oncogene are incompatible. This synthetic lethality may eventually be exploited to improve outcomes for patients with high-risk neuroblastoma.
A unifying model to predict multiple object orienting behaviors in tethered flies
Authors: Poehlmann Andreas , Soselisa Sayan J. , Fenk Lisa M. , Straw Andrew D. 
Published: July 2018

AbstractIndividual visual processing circuits forDrosophilalocomotor control have been studied in detail, but contributions of specific pathways to multiple behaviors remain unclear. To address how both flexible and stereotyped visual object response behaviors potentially share neural circuit components, we investigated models of asymmetric motion responses. Such models have predicted that object fixation without explicit neural encoding of position is possible. Here we investigated what neural circuits and behaviors are consistent with such models. In behavioral experiments on tethered flying flies, we found close correspondence between T4/T5-neuron dependent turning responses to objects and model output for high frequency perturbations. Furthermore, we found that the model predicts key results from several published accounts of stereotyped object tracking. The concurrence of experiment and theory suggests a neural substrate and algorithmic basis for stereotyped object tracking and informs future studies of flexible visual behaviors and their neural bases.
Urinary protein changes in the early phase of smoking-induced Chronic Obstructive Pulmonary Disease in a rat model
Authors: Huang He , Wang Ting , Gao Youhe 
Published: July 2018

AbstractChronic obstructive pulmonary disease (COPD) is a group of severe respiratory diseases. Identifying COPD through early urinary biomarkers by proteomics technology may help to reduce the mortality rate of the disease, improve the quality of life of patients and reduce the burden on society. Urine samples from a COPD rat model induced by smoking were taken at week 2, week 4 and week 8. By LC-MS/MS, 15 differential proteins with human orthologs were identified. After smoking for 2 weeks when there were no significant pathological changes, 8 differential proteins were identified: 2 proteins had been reported to be markers of COPD, while 4 proteins were associated with COPD. After smoking for 4 weeks, which is when slight pathological changes were observed, 7 differential proteins were identified: 3 of them were reported to be associated with COPD, while 1 protein had been reported to be a marker of COPD. After smoking for 8 weeks, there were significant pathological changes: 5 differential proteins were identified, 3 of which were reported to be associated with COPD. The results of this study suggest that differential urinary proteins may provide important clues for the early diagnosis of COPD.