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https://www.readbyqxmd.com/read/28103259/characterization-and-genetic-variation-of-vibrio-cholerae-isolated-from-clinical-and-environmental-sources-in-thailand
#1
Achiraya Siriphap, Pimlapas Leekitcharoenphon, Rolf S Kaas, Chonchanok Theethakaew, Frank M Aarestrup, Orasa Sutheinkul, Rene S Hendriksen
Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/28101531/osteopontin-is-a-blood-biomarker-for-microglial-activation-and-brain-injury-in-experimental-hypoxic-ischemic-encephalopathy
#2
Yikun Li, Eric B Dammer, Xiaohui Zhang-Brotzge, Scott Chen, Duc M Duong, Nicholas T Seyfried, Chia-Yi Kuan, Yu-Yo Sun
Clinical management of neonatal hypoxic-ischemic encephalopathy (HIE) suffers from the lack of reliable surrogate marker tests. Proteomic analysis may identify such biomarkers in blood, but there has been no proof-of-principle evidence to support this approach. Here we performed in-gel trypsin digestion of plasma proteins from four groups of 10-d-old mice [untouched and 24 h after low-dose lipopolysaccharide (LPS) exposure, hypoxia-ischemia (HI), or LPS/HI injury; n = 3 in each group) followed by liquid chromatography-tandem mass spectrometry and bioinformatics analysis to search for HI- and LPS/HI-associated brain injury biomarkers...
January 2017: ENeuro
https://www.readbyqxmd.com/read/28099904/tianfoshen-oral-liquid-a-cfda-approved-clinical-traditional-chinese-medicine-normalizes-major-cellular-pathways-disordered-during-colorectal-carcinogenesis
#3
Siliang Wang, Hengbin Wang, Yin Lu
Colorectal cancer remains the third leading cause of cancer death worldwide, suggesting exploration of novel therapeutic avenues may be useful. In this study, therefore, we determined whether Tianfoshen oral liquid, a Chinese traditional medicine that has been used to treat non-small cell lung cancer, would be therapeutically beneficial for colorectal cancer patients. Our data show that Tianfoshen oral liquid effectively inhibits growth of colorectal cancer cells both in vitro and in vivo. We further employed a comprehensive strategy that included chemoinformatics, bioinformatics and network biology methods to unravel novel insights into the active compounds of Tianfoshen oral liquid and to identify the common therapeutic targets and processes for colorectal cancer treatment...
January 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28099887/comparative-proteomics-of-paired-vocal-fold-and-oral-mucosa-fibroblasts
#4
Michael Karbiener, Barbara Darnhofer, Marie-Therese Frisch, Beate Rinner, Ruth Birner-Gruenberger, Markus Gugatschka
: Injuries of the vocal folds frequently heal with scar formation, which can have lifelong detrimental impact on voice quality. Current treatments to prevent or resolve scars of the vocal fold mucosa are highly unsatisfactory. In contrast, the adjacent oral mucosa is mostly resistant to scarring. These differences in healing tendency might relate to distinct properties of the fibroblasts populating oral and vocal fold mucosae. We thus established the in vitro cultivation of paired, near-primary vocal fold fibroblasts (VFF) and oral mucosa fibroblasts (OMF) to perform a basic cellular characterization and comparative cellular proteomics...
January 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28099515/polymorphisms-and-mutational-covariation-associated-with-death-in-a-prospective-cohort-of-hiv-aids-patients-receiving-long-term-art-in-china
#5
Pengtao Liu, Yi Feng, Jianjun Wu, Suian Tian, Bin Su, Zhe Wang, Lingjie Liao, Hui Xing, Yinghui You, Yiming Shao, Yuhua Ruan
BACKGROUND: HIV drug resistance is associated with faster clinical progression of AIDS. However, the effect of significant polymorphisms and mutational covariation on mortality among HIV/AIDS patients receiving long-term antiretroviral therapy (ART), have rarely been studied. METHODS: In this prospective cohort study from December 2003 to December 2014, we present a new computational modelling approach based on bioinformatics-based models and several statistical methods to elucidate the molecular mechanisms involved in the acquisition of polymorphisms and mutations on death in HIV/AIDS patients receiving long-term ART in China...
2017: PloS One
https://www.readbyqxmd.com/read/28098823/integrative-mirna-gene-expression-analysis-enables-refinement-of-associated-biology-and-prediction-of-response-to-cetuximab-in-head-and-neck-squamous-cell-cancer
#6
Loris De Cecco, Marco Giannoccaro, Edoardo Marchesi, Paolo Bossi, Federica Favales, Laura D Locati, Lisa Licitra, Silvana Pilotti, Silvana Canevari
This paper documents the process by which we, through gene and miRNA expression profiling of the same samples of head and neck squamous cell carcinomas (HNSCC) and an integrative miRNA-mRNA expression analysis, were able to identify candidate biomarkers of progression-free survival (PFS) in patients treated with cetuximab-based approaches. Through sparse partial least square-discriminant analysis (sPLS-DA) and supervised analysis, 36 miRNAs were identified in two components that clearly separated long- and short-PFS patients...
January 14, 2017: Genes
https://www.readbyqxmd.com/read/28097472/proceedings-of-the-third-international-molecular-pathological-epidemiology-mpe-meeting
#7
REVIEW
Peter T Campbell, Timothy R Rebbeck, Reiko Nishihara, Andrew H Beck, Colin B Begg, Alexei A Bogdanov, Yin Cao, Helen G Coleman, Gordon J Freeman, Yujing J Heng, Curtis Huttenhower, Rafael A Irizarry, N Sertac Kip, Franziska Michor, Daniel Nevo, Ulrike Peters, Amanda I Phipps, Elizabeth M Poole, Zhi Rong Qian, John Quackenbush, Harlan Robins, Peter K Rogan, Martha L Slattery, Stephanie A Smith-Warner, Mingyang Song, Tyler J VanderWeele, Daniel Xia, Emily C Zabor, Xuehong Zhang, Molin Wang, Shuji Ogino
Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods, and resources from epidemiology, pathology, biostatistics, bioinformatics, and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases...
January 17, 2017: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/28096648/identification-of-genetic-and-epigenetic-variants-associated-with-breast-cancer-prognosis-by-integrative-bioinformatics-analysis
#8
Arunima Shilpi, Yingtao Bi, Segun Jung, Samir K Patra, Ramana V Davuluri
INTRODUCTION: Breast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for the identification of these variances is complicated by the interplay between inherited genetic and epigenetic aberrations. Therefore, this study provides an extrapolate outlook to the sinister partnership between DNA methylation and single-nucleotide polymorphisms (SNPs) in relevance to the identification of prognostic markers in breast cancer...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28095864/microrna-141-enhances-anoikis-resistance-in-metastatic-progression-of-ovarian-cancer-through-targeting-klf12-sp1-survivin-axis
#9
Celia S L Mak, Mingo M H Yung, Lynn M N Hui, Leanne L Leung, Rui Liang, Kangmei Chen, Stephanie S Liu, Yiming Qin, Thomas H Y Leung, Kai-Fai Lee, Karen K L Chan, Hextan Y S Ngan, David W Chan
BACKGROUND: Cancer metastasis is determined by the formation of the metastatic niche and the ability of cancer cells to adapt to microenvironmental stresses. Anoikis resistance is a fundamental feature of metastatic cancer cell survival during metastatic cancer progression. However, the mechanisms underlying anoikis resistance in ovarian cancer are still unclear. METHODS: Expressions of miRNA-141 and its downstream targets were evaluated by qPCR, Western blotting, Immunohistochemical (IHC) and in situ hybridization (ISH) assays...
January 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28093680/the-international-diffuse-intrinsic-pontine-glioma-registry-an-infrastructure-to-accelerate-collaborative-research-for-an-orphan-disease
#10
Joshua Baugh, Ute Bartels, James Leach, Blaise Jones, Brooklyn Chaney, Katherine E Warren, Jenavieve Kirkendall, Renee Doughman, Cynthia Hawkins, Lili Miles, Christine Fuller, Tim Hassall, Eric Bouffet, Adam Lane, Darren Hargrave, Jacques Grill, Lindsey M Hoffman, Chris Jones, Alex Towbin, Sharon A Savage, Michelle Monje, Xiao-Nan Li, David S Ziegler, Sophie Veldhuijzen van Zanten, Christof M Kramm, Dannis G van Vuurden, Maryam Fouladi
Diffuse intrinsic pontine glioma (DIPG), a rare, often fatal childhood brain tumor, remains a major therapeutic challenge. In 2012, investigators, funded by the DIPG Collaborative (a philanthropic partnership among 29 private foundations), launched the International DIPG Registry (IDIPGR) to advance understanding of DIPG. Comprised of comprehensive deidentified but linked clinical, imaging, histopathological, and genomic repositories, the IDIPGR uses standardized case report forms for uniform data collection; serial imaging and histopathology are centrally reviewed by IDIPGR neuro-radiologists and neuro-pathologists, respectively...
January 16, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28093075/gavin-gene-aware-variant-interpretation-for-medical-sequencing
#11
K Joeri van der Velde, Eddy N de Boer, Cleo C van Diemen, Birgit Sikkema-Raddatz, Kristin M Abbott, Alain Knopperts, Lude Franke, Rolf H Sijmons, Tom J de Koning, Cisca Wijmenga, Richard J Sinke, Morris A Swertz
We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele frequencies from the ExAC database, likely variant impact using SnpEff, and estimated deleteriousness based on CADD scores for >3000 genes. In a benchmark on 18 clinical gene sets, we achieve a sensitivity of 91.4% and a specificity of 76.9%. This accuracy is unmatched by 12 other tools. We provide GAVIN as an online MOLGENIS service to annotate VCF files and as an open source executable for use in bioinformatic pipelines...
January 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28092471/genomics-pipelines-and-data-integration-challenges-and-opportunities-in-the-research-setting
#12
Jeremy Davis-Turak, Sean M Courtney, E Starr Hazard, W Bailey Glen, Willian da Silveira, Timothy Wesselman, Larry P Harbin, Bethany J Wolf, Dongjun Chung, Gary Hardiman
The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28091987/expression-and-prognostic-value-of-micrornas-in-lower-grade-glioma-depends-on-idh1-2-status
#13
Wen Cheng, Xiufang Ren, Chuanbao Zhang, Sheng Han, Anhua Wu
Histological and genomic characteristics are widely used in glioma management and research. This study investigated their relationship to the expression and prognostic value of microRNAs (miRNAs) in lower-grade glioma (LGG). A total of 447 LGG samples with available clinical and genomic information from The Cancer Genome Atlas database were reviewed. Samples with isocitrate dehydrogenase (IDH) 1/2 mutations (n = 366) were randomly divided into training and validation sets to establish and confirm a four-miRNA-based risk classifier...
January 16, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28090096/a-bioinformatics-practicum-to-develop-student-understanding-of-immunological-rejection-of-protein-drugs
#14
Lauren A O'Donnell, Wilson S Meng, Benjamin J Andrick, Alexa M Borello
Objectives. To design and implement a bioinformatics exercise that applies immunological principles to predicting rejection of protein drugs based upon patient genotype. Design. Doctor of pharmacy (PharmD) students used the Immune Epitope Database, a freely available bioinformatics tool. Over a 2-week laboratory, students interrogated whether a protein drug would be predicted to induce an immune response based upon patient genotype. Results were presented at the last laboratory session, and students completed reports discussing their findings...
November 25, 2016: American Journal of Pharmaceutical Education
https://www.readbyqxmd.com/read/28089718/cathelicidin-antimicrobial-peptide-from-alligator-mississippiensis-has-antibacterial-activity-against-multi-drug-resistant-acinetobacter-baumanii-and-klebsiella-pneumoniae
#15
Stephanie M Barksdale, Evelyn J Hrifko, Monique L van Hoek
Alligator mississippiensis (American alligator), a member of order Crocodilia, lives in bacteria-laden environments but is not often known to succumb to bacterial infections. Their serum has been shown to have antibacterial activity beyond that of human serum, and it is believed that this activity is partially due to cationic antimicrobial peptides (CAMPs). CAMPs are produced by many organisms as part of the innate immune system. CAMPs are attractive possible therapies against multi-drug resistant bacteria, such as those found in biofilm-infected war wounds, because they seldom cause genetic resistance in bacteria and are effective against antibiotic resistant bacteria...
January 12, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28088792/impact-of-nudt15-polymorphisms-on-thiopurines-induced-myelotoxicity-and-thiopurines-tolerance-dose
#16
Dandan Yin, Xuyang Xia, Junlong Zhang, Shouyue Zhang, Fei Liao, Ge Zhang, Yan Zhang, Qianqian Hou, Xue Yang, Hong Wang, Zhigui Ma, Heyao Wang, Yiping Zhu, Wei Zhang, Yuelan Wang, Bo Liu, Lanlan Wang, Heng Xu, Yang Shu
Thiopurines are widely used as anticancer and immunosuppressive agents. However, life-threatening myelotoxicity has been noticed and largely explained by genetic variations, including NUDT15 polymorphisms (e.g., rs116855232). In this study, we conduct a meta-analysis to investigate the impact of rs116855232 on thiopurines-induced myelotoxicity susceptibility (1752 patients from 7 independent cohorts), as well as on thiopurines intolerance dose (2745 patients from 13 cohorts). Variant allele of rs116855232 contributes 7...
January 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28072411/the-early-growth-response-protein-1-mir-30a-5p-neurogenic-differentiation-factor-1-axis-as-a-novel-biomarker-for-schizophrenia-diagnosis-and-treatment-monitoring
#17
S Liu, F Zhang, Y Y Shugart, L Yang, X Li, Z Liu, N Sun, C Yang, X Guo, J Shi, L Wang, L Cheng, K Zhang, T Yang, Y Xu
To date, diagnosis of schizophrenia is still based on clinical interviews and careful observations, which is subjective and variable, and can lead to misdiagnosis and/or delay in diagnosis. As early intervention in schizophrenia is important in improving outcomes, objective tests that can be used for schizophrenia diagnosis or treatment monitoring are thus in great need. MicroRNAs (miRNAs) negatively regulate target gene expression and their biogenesis is tightly controlled by various factors including transcription factors (TFs)...
January 10, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28069547/overexpression-of-mir-92a-promotes-the-tumor-growth-of-osteosarcoma-by-suppressing-f-box-and-wd-repeat-containing-protein-7
#18
Xuesheng Jiang, Xiongfeng Li, Fengfeng Wu, Hongliang Gao, Guorong Wang, Hua Zheng, Huajun Wang, Jianyou Li, Chao Chen
MicroRNAs (miRNAs) have been reported to be critical players in osteosarcoma (OS). Among numerous cancer-related miRNAs, the expression level of miR-92a and its potential role in OS has not been investigated. Here, We showed that overexpression of miR-92a was identified in OS specimens and cells compared to normal bone tissues. The high level of miR-92a was correlated with high T classification and advanced clinical stages of OS patients. Notably, miR-92a highly expressing OS patients showed a notably reduced survival rate...
January 6, 2017: Gene
https://www.readbyqxmd.com/read/28059593/clinical-relevance-of-epigenetics-in-the-onset-and-management-of-type-2-diabetes-mellitus
#19
Linda Sommese, Alberto Zullo, Francesco Paolo Mancini, Rossella Fabbricini, Andrea Soricelli, Claudio Napoli
Epigenetics is involved in the altered expression of gene networks that underlie insulin resistance and insufficiency. Major genes controlling β-cell differentiation and function, such as PAX4, PDX1, and GLP1 receptor, are epigenetically controlled. Epigenetics can cause insulin resistance through immunomediated pro-inflammatory actions related to several factors, such as NF-kB, osteopontin, and Toll-like receptors. Hereafter, we provide a critical and comprehensive summary on this topic with a particular emphasis on translational and clinical aspects...
January 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28059585/initiation-of-aberrant-dna-methylation-patterns-and-heterogeneity-in-precancerous-lesions-of-human-hepatocellular-cancer
#20
Ryan A Hlady, Dan Zhou, William Puszyk, Lewis R Roberts, Chen Liu, Keith D Robertson
While intratumor heterogeneity contributes to disease progression, metastasis, and resistance to chemotherapy, it also provides a route to understanding the evolution and drivers of disease. Defects in epigenetic landscapes are intimately linked to pathogenesis of a variety of human diseases, with epigenetic deregulation promoting tumorigenesis. Understanding epigenetic heterogeneity is crucial in hepatocellular carcinoma (HCC), where epigenetic alterations are frequent, early, and pathogenic events. We determined genome-wide DNA methylation and copy number variation leveraging the Infinium 450 K in a series of regenerative nodules from within single patient livers...
January 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
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