bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular mechanism of depolarization-dependent inactivation in W366F mutant of Kv1.2
Authors: Kondo H. X. , Yoshida N. , Shirota M. , Kinoshita K. 
Published: May 2018

ABSTRACTVoltage-gated potassium channels play crucial roles in regulating membrane potential. They are activated by membrane depolarization, allowing the selective permeation of potassium ions across the plasma membrane, and enter a nonconducting state after lasting depolarization of membrane potential, a process known as inactivation. Inactivation in voltage-activated potassium channels occurs through two distinct mechanisms, N-type inactivation and C-type inactivation. C-type inactivation is caused by conformational changes in the extracellular mouth of the channel, while N-type inactivation is elicited by changes in the cytoplasmic mouth of the protein. The W434F-mutated Shaker channel is known as a nonconducting mutant and is in a C-type inactivation state at a depolarizing membrane potential. To clarify the structural properties of C-type inactivated protein, we performed molecular dynamics simulations of the wild-type and W366F (corresponding to W434F in Shaker) mutant of the Kv1.2-2.1 chimera channel. The W366F mutant was in a nearly nonconducting state with a depolarizing voltage and recovered from inactivation with a reverse voltage. Our simulations and 3D-RISM analysis suggested that structural changes in the selective filter upon membrane depolarization trap potassium ions around the entrance of the selectivity filter and prevent ion permeation. This pore restriction is involved in the molecular mechanism of C-type inactivation.
Voltage-sensitive dye delivery through the blood brain barrier using adenosine receptor agonist Regadenoson
Authors: Pak Rebecca W. , Kang Jeeun , Valentine Heather , Loew Leslie M. , Thorek Daniel L.J. , Boctor Emad M. , Wong Dean F. , Kang Jin U. 
Published: May 2018

AbstractOptical imaging of brain activity has mostly employed genetically manipulated mice, which cannot be translated to clinical human usage. Observation of brain activity directly is challenging due to difficulty in delivering dyes and other agents through the blood brain barrier (BBB). Using fluorescence imaging, we have demonstrated the feasibility of delivering the near-infrared voltage-sensitive dye (VSD) IR-780 perchlorate to the brain tissue through pharmacological techniques, via an adenosine agonist (Regadenoson). Comparison of VSD fluorescence of mouse brains without and with Regadenoson showed significantly increased residence time of the fluorescence signal in the latter case, indicative of VSD diffusion into the brain tissue. Dose and timing of Regadenoson were varied to optimize BBB permeability for VSD delivery.
Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation
Authors: Srivastava Anuj , Sarsani Vishal Kumar , Fiddes Ian , Sheehan Susan M. , Seger Rita L. , Barter Mary E. , Neptune-Bear Selena , Lindqvist Charlotte , Korstanje Ron 
Published: May 2018

AbstractThe prevalence of chronic kidney disease (CKD) is rising worldwide and 10-15% of the global population currently suffers from CKD and its complications. Given the increasing prevalence of CKD there is an urgent need to find novel treatment options. The American black bear (Ursus americanus) copes with months of lowered kidney function and metabolism during hibernation without the devastating effects on metabolism and other consequences observed in humans. In a biomimetic approach to better understand kidney adaptations and physiology in hibernating black bears, we established a high-quality genome assembly. Subsequent RNA-Seq analysis of kidneys comparing gene expression profiles in black bears entering (late fall) and emerging (early spring) from hibernation identified 169 protein-coding genes that were differentially expressed. Of these, 101 genes were downregulated and 68 genes were upregulated after hibernation. Fold changes ranged from 1.8-fold downregulation (RTN4RL2) to 2.4-fold upregulation (CISH). Most notable was the upregulation of cytokine suppression genes (SOCS2, CISH, and SERPINC1) and the lack of increased expression of cytokines and genes involved in inflammation. The identification of these differences in gene expression in the black bear kidney may provide new insights in the prevention and treatment of CKD.
Trans-ethnic polygenic analysis supports genetic overlaps of lumbar disc degeneration with height, body mass index, and bone mineral density
Authors: Zhou Xueya , Cheung Ching-Lung , Karasugi Tatsuki , Karppinen Jaro , Samartzis Dino , Hsu Yi-Hsiang , Mak Timothy Shin-Heng , Song You-Qiang , Chiba Kazuhiro , Kawaguchi Yoshiharu , Li Yan , Chan Danny , Cheung Kenneth Man-Chee , Ikegawa Shiro , Cheah Kathryn Song-Eng , Sham Pak Chung 
Published: May 2018

AbstractLumbar disc degeneration (LDD) is age-related break-down in the fibrocartilaginous joints between lumbar vertebrae. It is a major cause of low back pain and is conventionally assessed by magnetic resonance imaging (MRI). Like most other complex traits, LDD is likely polygenic and influenced by both genetic and environmental factors. However, genome-wide association studies (GWASs) of LDD have uncovered few susceptibility loci due to the limited sample size. Previous epidemiology studies of LDD also reported multiple heritable risk factors, including height, body mass index (BMI), bone mineral density (BMD), lipid levels, etc. Genetics can help elucidate causality between traits and suggest loci with pleiotropic effects. One such approach is polygenic score (PGS) which summarizes the effect of multiple variants by the summation of alleles weighted by estimated effects from GWAS. To investigate genetic overlaps of LDD and related heritable risk factors, we calculated the PGS of height, BMI, BMD and lipid levels in a Chinese population-based cohort with spine MRI examination and a Japanese case-control cohort of lumbar disc herniation (LDH) requiring surgery. Because most large-scale GWASs were done in European populations, PGS of corresponding traits were created using weights from European GWASs. We calibrated their prediction performance in independent Chinese samples, then tested associations with MRI-derived LDD scores and LDH affection status. The PGS of height, BMI, BMD and lipid levels were strongly associated with respective phenotypes in Chinese, although phenotype variances explained were lower than in Europeans which would reduce the power to detect genetic overlaps. Despite of this, the PGS of BMI and lumbar spine BMD were significantly associated with LDD scores; and the PGS of height was associated with the increased the liability of LDH. Furthermore, linkage disequilibrium score regression suggested that, osteoarthritis, another degenerative disorder that shares common features with LDD, also showed genetic correlations with height, BMI and BMD. The findings suggest a common key contribution of biomechanical stress to the pathogenesis of LDD and will direct the future search for pleiotropic genes.
MiRNA expression profiles of serum exosomes derived from individuals with latent and active tuberculosis
Authors: Lyu Lingna , Wang Jinghui , Jia Hongyan , Pan Liping , Li Zihui , Du Fengjiao , Du Boping , Sun Qi , Zhang Zongde 
Published: May 2018

ABSTRACTTuberculosis (TB) has become a leading cause of death worldwide, which is largely attributed to the difficulties in diagnosis and treatment of TB patients. Exosomes carrying RNA, particularly miRNA, have been indicated their functional and diagnostic potential in diseases, including tuberculosis (TB). In the present study, we performed RNA-seq based analysis on exosomal miRNA profiles for clinical specimens of healthy controls (HC), active tuberculosis (TB) and latent tuberculosis infection (LTBI). We identified many distinct up-regulated and down-regulated differentially expressed miRNA and further screened top 20 in each compared groups which might provide a potential panel for differentiation of HC, LTBI, and TB. We classified all the differentially expressed miRNAs into six expression patterns and identified three persistently up-regulated miRNA (hsa-miR-140-3p, hsa-miR-3184-5p and hsa-miR-423-3p) as potential markers during TB progression. Combined with our previously detected exsomal mRNA, we screened the genes overlapped with predicted mRNA targets of differentially expressed miRNA and analyzed their involvement in Biological Process, indicating a decreased signaling transduction and increased cell death in LTBI and TB. Our results indicate the selective packaging of RNA cargoes into exosomes under different stages of Mycobacterium tuberculosis infection and facilitate further study of TB pathogenesis and development.IMPORTANCEThe main reason for failure to eliminate TB is lack of understanding molecular mechanism of TB pathogenesis and difficulties in TB diagnosis and treatment. Exosomes provide a promising research tool because they are released from various cells containing valuable biochemical information related to diseases. We reveale distinct miRNA expression profile of the exosomes, which indicates selective packaging of RNA cargoes into exosomes under different stages of Mycobacterium tuberculosis infection. Further, we also provide evidence of related miRNA candidates potentially involving in TB progression and facilitating discovery of TB biomarkers.
The Effects of Vancomycin on the Viability and Osteogenic Potential of Bone-derived Mesenchymal Stem Cells
Authors: Booysen Elzaan , Sadie-Van Gijsen Hanél , Deane Shelly M. , Ferris William , Dicks Leon M.T. 
Published: May 2018

ABSTRACTPeriprosthetic joint infections (PJI), caused by methicillin-resistant Staphylococcus aureus (MRSA), is the major cause of total hip arthroplasty (THA) failures. Traditionally, MRSA is treated with vancomycin, administrated intravenously or applied directly onto infected tissue. The effect of direct (as opposed to systemic) vancomycin treatment on bone formation and remodelling is largely unknown. The minimal inhibitory concentration (MIC) of vancomycin was determined by adding 200 μl of different concentrations (1 – 20 μg/ml) to actively growing cultures of S. aureus Xen 31 (methicillin-resistant) and S. aureus Xen 36 (methicillin-sensitive), respectively, and recording changes in optical density over 24 h. Bone marrow-derived and proximal femur-derived mesenchymal stem cells (bmMSCs and pfMSCs) from rat femora were exposed to 1 x MIC (5 μg/ml) and 4 x MIC (20 μg/ml) of vancomycin for 7 days. Cell viability was determined by staining with crystal violet and MTT (3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide), respectively, and osteogenic differentiation by staining with Alizarin Red S. Vancomycin had no effect on the viability of bmMSCs and pfMSCs, even at high levels (20 μg/ml). The osteogenic differentiation of pfMSCs was partially inhibited, while osteogenesis in bmMSCs was not severely affected. The direct application of vancomycin to infected bone tissue, even at excessive levels, may preserve the viability of resident MSC populations. Short-term demineralization may thus be reversed after cessation of vancomycin treatment, improving the outcome of THA surgery.
Hookworm-derived small molecule extracts suppress pathology in a mouse model of colitis and inhibit secretion of key inflammatory cytokines in primary human leukocytes
Authors: Wangchuk Phurpa , Constantinoiu Constantin , Kouremenos Konstantinos A. , Becker Luke , Jones Linda , Shepherd Catherine , Buitrago Geraldine , Giacomin Paul , Daly Norelle , McConville Malcolm J. , Ryan Rachael Y. M. , Miles John J. , Loukas Alex 
Published: May 2018

ABSTRACTIatrogenic hookworm therapy shows promise for treating disorders that result from a dysregulated immune system, including inflammatory bowel disease (IBD). Here we use a metabolomics approach to characterize the non-protein small molecule complement of hookworms. Gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analyses of somatic tissue extracts revealed the presence of 52 polar metabolites and 22 non-polar components including short chain fatty acids (SCFA). Several of these small metabolites, notably the SCFA, have been shown to have anti-inflammatory properties in various diseases, including IBD. Using a murine model of colitis and human peripheral blood mononuclear cells, we demonstrate that somatic tissue extracts of the hookwormAncylostoma caninumcontain small molecules with anti-inflammatory activities. Of the five extracts tested, two of them significantly protected mice against T cell-mediated immunopathology and weight loss in a chemically-induced colitis model. Moreover, one of the anti-colitic extracts suppressedex vivoproduction of inflammatory cytokines from primary human leukocytes. While the origin of the SCFA (parasite or host microbiota-derived) present in the hookworm somatic tissue extracts cannot be ascertained from this study, it is possible thatA. caninummay be actively promoting an anti-inflammatory host microbiome by facilitating immune crosstalk through SCFA production.
On the Development of Sesamoid Bones
Authors: Eyal Shai , Rubin Sarah , Krief Sharon , Levin Lihi , Zelzer Elazar 
Published: May 2018

ABSTRACTSesamoid bones are a special group of small auxiliary bones that form in proximity to joints and contribute to their stability and function. Sesamoid bones display high degree of variability in size, location, penetrance and anatomical connection to the main skeleton across vertebrate species. Therefore, providing a comprehensive developmental model or classification system for sesamoid bones is challenging. Here, we examine the developmental mechanisms of three anatomically different sesamoid bones, namely patella, lateral fabella and digit sesamoids. Through a comprehensive comparative analysis at the cellular, molecular and mechanical levels, we demonstrate that all three types of sesamoid bones originated fromSox9+/Scx+progenitors under the regulation of TGFβ and independent of mechanical stimuli from muscles. We show that BMP4 was necessary specifically for differentiation of patella but not of lateral fabella or digit sesamoids, whereas BMP2 regulated the growth of all examined sesamoids. Next, we show that whereas patella and digit sesamoids initially formed in juxtaposition to long bones, the lateral fabella formed independently at a distance. Finally, we provide evidence suggesting that while patella detached from the femur by formation of a synovial joint, digit sesamoids detached from the phalanx by a fibrocartilage joint. Collectively, these findings highlight both common and divergent molecular and mechanical features of sesamoid bone development, thereby advancing our understanding of their evolutionary plasticity.
CRISPR screen reveals that EHEC’s T3SS and Shiga toxin rely on shared host factors for infection
Authors: Pacheco Alline R. , Lazarus Jacob E. , Sit Brandon , Schmieder Stefanie , Lencer Wayne I. , Blondel Carlos J. , Doench John G. , Davis Brigid M. , Waldor Matthew K. 
Published: May 2018

AbstractEnterohemorrhagicEscherichia coli(EHEC) has two critical virulence factors – a type III secretion system (T3SS) and Shiga toxins (Stx) – that are required for the pathogen to colonize the intestine and cause diarrheal disease. Here, we carried out a genome-wide CRISPR/Cas9 loss-of-function screen to identify host loci that facilitate EHEC infection of intestinal epithelial cells. Many of the guide RNAs identified targeted loci known to be associated with sphingolipid biosynthesis, particularly for production of globotriaosylceramide (Gb3), the Stx receptor. Two loci (TM9SF2 and LAPTM4A) with largely unknown functions were also targeted. Mutations in these loci not only rescued cells from Stx-mediated cell death, but also prevented cytotoxicity associated with the EHEC T3SS. These mutations interfered with early events associated with T3SS and Stx pathogenicity, markedly reducing entry of T3SS effectors into host cells and binding of Stx. The convergence of Stx and T3SS onto overlapping host targets provides guidance for design of new host-directed therapeutic agents to counter EHEC infection.ImportanceEnterohemorrhagicEscherichia coli(EHEC) has two critical virulence factors – a type III secretion system (T3SS) and Shiga toxins (Stx) – that are required for colonizing the intestine and causing diarrheal disease. We screened a genome-wide collection of CRISPR mutants derived from intestinal epithelial cells and identified mutants with enhanced survival following EHEC infection. Many had mutations that disrupted synthesis of a subset of lipids (sphingolipids) that includes the Stx receptor globotriaosylceramide (Gb3), and hence protect against Stx intoxication. Unexpectedly, we found that sphingolipids also mediate early events associated with T3SS pathogenicity. Since antibiotics are contraindicated for the treatment of EHEC, therapeutics targeting sphingolipid biosynthesis are a promising alternative, as they could provide protection against both of the pathogen’s key virulence factors.
Knowledge, attitudes and awareness of the human papillomavirus among health professionals in New Zealand
Authors: Sherman Susan M. , Bartholomew Karen , Denison Hayley J. , Patel Hersha , Moss Esther L. , Douwes Jeroen , Bromhead Collette 
Published: May 2018

AbstractBackgroundHuman papillomavirus (HPV) is a common sexually transmitted infection that is implicated in 99.7% of cervical cancers and several other cancers that affect both men and women. Despite the role that HPV plays in an estimated 5% of all cancers and the evolving role of HPV vaccination and testing in protecting the public against these cancers, preliminary research in New Zealand health care professionals suggest knowledge about HPV may not be sufficient.MethodsA total of 230 practice nurses, smear takers and other clinical and laboratory staff who attended a range of training events completed a cross-sectional survey between April 2016 and July 2017. The survey explored four broad areas: demographics and level of experience, HPV knowledge (general HPV knowledge, HPV triage and test of cure (TOC) knowledge and HPV vaccine knowledge), attitudes towards the HPV vaccine and self-perceived adequacy of HPV knowledge.ResultsThe mean score on the general HPV knowledge questions was 13.2 out of 15, with only 25.2% of respondents scoring 100%. In response to an additional question, 14.0% thought (or were unsure) that HPV causes HIV/AIDS. The mean score on the HPV Triage and TOC knowledge questions was 7.4 out of 10, with only 9.1% scoring 100%. The mean score on the HPV vaccine knowledge questions was 6.0 out of 7 and 44.3% scored 100%. Only 62.6% of respondents agreed or strongly agreed that they were adequately informed about HPV, although 71.8% agreed or strongly agreed that they could confidently answer HPV-related questions asked by patients. Multivariate analyses revealed that knowledge in each domain predicted confidence in responding to patient questions. Furthermore, the number of years since training predicted both HPV knowledge and Triage and TOC knowledge.DiscussionAlthough overall level of knowledge was adequate, there were significant gaps in knowledge, particularly about the role of HPV testing in the New Zealand National Cervical Screening Programme. More education is required to ensure that misinformation and stigma do not inadvertently result from interactions between health practitioners and the public.
Variability of core microbiota in newly diagnosed treatment-naïve paediatric Inflammatory Bowel Disease patients
Authors: de Meij T.G.J. , de Groot E.F.J. , Peeters C.F.W. , de Boer N.K.H , Kneepkens C.M.F. , Eck A. , Benninga M.A. , Savelkoul P.H.M. , van Bodegraven A.A. , Budding A.E 
Published: May 2018

AbstractBACKGROUND & AIMSIntestinal microbiota is considered to play a crucial role in the aetiology of inflammatory bowel disease (IBD). We aimed to describe faecal microbiota composition and dynamics in a large cohort of children with de novo (naïve) IBD, in comparison to healthy paediatric controls (HC).METHODSIn this prospective study, performed at two tertiary centres, faecal samples from newly diagnosed, treatment-naïve paediatric IBD patients were collected prior to bowel cleansing for colonoscopy (t0) and 1, 3 and 6 weeks and 3 months after initiation of therapy. The microbial profiles of Crohn’s disease (CD) and Ulcerative colitis (UC) patients were compared with HC and linked to therapeutic response. Microbiota composition was analysed by IS-pro technology.RESULTSMicrobial profiles of 104 new IBD-patients (63 CD, 41 UC, median age 14.0 years) were compared to 61 HC (median 7.8 years). IBD was mainly characterised by decreased abundance of Alistipes finegoldi and Alistipes putredinis, which characterize a healthy state microbial core. The classifier including these core species as predictors achieved an AUC of the ROC curve of .87. Core bacteria tended to regain abundance during treatment, but did not reach healthy levels.CONCLUSIONFaecal microbiota profiles of children with de novo CD and UC can be discriminated from HC with high accuracy, mainly driven by a decreased abundance of species shaping the microbial core in the healthy state. Paediatric IBD can therefore be characterized by decreased abundance of certain bacterial species reflecting the healthy state rather than by the introduction of pathogens.
Misfolded proteins share a common capacity in disrupting LLPS organizing membrane-less organelles
Authors: Kang Jian , Lim Liangzhong , Song Jianxing 
Published: May 2018

AbstractProfilin-1 mutants cause ALS by gain of toxicity but the underlying mechanism remains unknown. Here we showed that three PFN1 mutants have differential capacity in disrupting dynamics of FUS liquid droplets underlying the formation of stress granules (SGs). Subsequently we extensively characterized conformations, dynamics and hydrodynamic properties of C71G-PFN1, FUS droplets and their interaction by NMR spectroscopy. C71G-PFN1 co-exists between the folded (55.2%) and unfolded (44.8%) states undergoing exchanges at 11.7 Hz, while its unfolded state non-specifically interacts with FUS droplets. Results together lead to a model for dynamic droplets to recruit misfolded proteins, which functions seemingly at great cost: simple accumulation of misfolded proteins within liquid droplets is sufficient to reduce their dynamics. Further aggregation of misfolded proteins within droplets might irreversibly disrupt/destroy structures and dynamics of droplets, as increasingly observed on SGs, an emerging target for various neurodegenerative diseases. Therefore, our study implies that other misfolded proteins might also share the capacity in disrupting LLPS.