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https://www.readbyqxmd.com/read/28340408/ongoing-evolution-of-pseudomonas-aeruginosa-pao1-sublines-complicates-studies-of-dna-damage-repair-and-tolerance
#1
Julia Sidorenko, Tatjana Jatsenko, Maia Kivisaar
Sublines of the major P. aeruginosa reference strain PAO1 are derivatives of the original PAO1 isolate, which are maintained in laboratories worldwide. These sublines display substantial genomic and phenotypic variation due to ongoing microevolution. Here, we examined four sublines, MPAO1, PAO1-L, PAO1-DSM and PAO1-UT, originated from different laboratories, and six DNA polymerase-deficient mutants from the P. aeruginosa MPAO1 transposon library for their employment in elucidation of DNA damage repair and tolerance mechanisms in P...
March 16, 2017: Mutation Research
https://www.readbyqxmd.com/read/28340400/pharmacoinformatics-exploration-of-polyphenol-oxidases-leading-to-novel-inhibitors-by-virtual-screening-and-molecular-dynamic-simulation-study
#2
Mubashir Hassan, Qamar Abbas, Zaman Ashraf, Ahmed A Moustafa, Sung-Yum Seo
Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis...
March 15, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28340358/lysosomal-rupture-induced-by-structurally-distinct-chitosans-either-promotes-a-type-1-ifn-response-or-activates-the-inflammasome-in-macrophages
#3
David Fong, Pascal Grégoire-Gélinas, Alexandre P Cheng, Tal Mezheritsky, Marc Lavertu, Sachiko Sato, Caroline D Hoemann
Chitosan is a family of glucosamine and N-acetyl glucosamine polysaccharides with poorly understood immune modulating properties. Here, functional U937 macrophage responses were analyzed in response to a novel library of twenty chitosans with controlled degree of deacetylation (DDA, 60-98%), molecular weight (1 to >100 kDa), and acetylation pattern (block vs. random). Specific chitosan preparations (10 or 190 kDa 80% block DDA and 3, 5, or 10 kDa 98% DDA) either induced macrophages to release CXCL10 and IL-1ra at 5-50 μg/mL, or activated the inflammasome to release IL-1β and PGE2 at 50-150 μg/mL...
March 15, 2017: Biomaterials
https://www.readbyqxmd.com/read/28340301/ten-years-of-barcoding-at-the-african-centre-for-dna-barcoding
#4
Simeon Bezeng Bezeng, T Jonathan Davies, Barnabas H Daru, Ronny Mukala Kabongo, Olivier Maurin, Kowiyou Yessoufou, Herman van der Bank, Michelle Van der Bank
The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that the two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants...
March 24, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28340066/diagnostic-test-accuracy-of-ultrasound-for-synovitis-in-rheumatoid-arthritis-systematic-review-and-meta-analysis
#5
Kaoru Takase-Minegishi, Nobuyuki Horita, Kouji Kobayashi, Ryusuke Yoshimi, Yohei Kirino, Shigeru Ohno, Takeshi Kaneko, Hideaki Nakajima, Richard J Wakefield, Paul Emery
Objective.: To evaluate diagnostic test accuracy of US compared with MRI for the detection of synovitis in RA patients. Methods.: A systematic literature search was performed in the PubMed, EMBASE, Cochrane Library and Web of Science Core Collection databases. Studies evaluating the diagnostic test accuracy of US for synovitis detected by MRI as the reference standard for wrist, MCP, PIP and knee joints were included. To assess the overall accuracy, we calculated the diagnostic odds ratio using a DerSimonian-Laird random effects model and the area under the curve (AUC) for the hierarchical summary receiver operating characteristics using Holling's proportional hazards models...
March 3, 2017: Rheumatology
https://www.readbyqxmd.com/read/28340005/inappropriate-shocks-in-single-chamber-and-subcutaneous-implantable-cardioverter-defibrillators-a-systematic-review-and-meta-analysis
#6
Angelo Auricchio, J Harrison Hudnall, Edward J Schloss, Laurence D Sterns, Takashi Kurita, Albert Meijer, Dedra H Fagan, Tyson Rogers
Aims: Single-chamber (VR-ICD) and subcutaneous (S-ICD) implantable cardioverter-defibrillators are effective to protect patients against sudden death but expose them to higher risk of inappropriate shock (IS). We sought to quantify the annual rate and influencing factors of ISs in VR- and S-ICDs from the literature. Methods and results: PubMed, Embase, and Cochrane Library were searched for full text articles with IS rates. Poisson distribution estimated proportion of patients with ISs; rates were annualized based on follow-up duration...
March 10, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/28339835/the-association-between-proton-pump-inhibitor-use-and-the-risk-of-adverse-kidney-outcomes-a-systematic-review-and-meta-analysis
#7
Surapon Nochaiwong, Chidchanok Ruengorn, Ratanaporn Awiphan, Kiatkriangkrai Koyratkoson, Chayutthaphong Chaisai, Kajohnsak Noppakun, Wilaiwan Chongruksut, Kednapa Thavorn
Background: Existing epidemiological studies illustrate that proton pump inhibitors (PPIs) may be related to adverse kidney outcomes. To date, no comprehensive meta-analysis has been conducted to evaluate and quantify this association. Methods: We performed a systematic review and meta-analysis of studies to assess the association between PPI use and the risk of adverse kidney outcomes. We searched MEDLINE, Embase, SCOPUS, Web of Science, CINAHL, Cochrane Library and grey literature with no language restrictions (through 31 October 2016)...
February 23, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/28339493/timely-meta-analysis-on-the-efficacy-of-adoptive-immunotherapy-for-hepatocellular-carcinoma-patients-after-curative-therapy
#8
Han-Yue Mo, Ying-Yang Liao, Xue-Mei You, Alessandro Cucchetti, Bao-Hong Yuan, Ru-Hong Li, Jian-Hong Zhong, Le-Qun Li
AIMS: The role of adoptive immunotherapy (AIT) for patients with hepatocellular carcinoma (HCC) who have received curative therapy is still not well illustrated. This timely meta-analysis aims to update the current evidence on efficacy and safety of AIT for patients with HCC who have received curative therapy. METHODS: We searched PubMed, EMBASE, Scopus and the Cochrane Library Through January 2017 for relevant studies. Mortality and tumor recurrence were compared between patients with or without adjuvant AIT...
2017: PloS One
https://www.readbyqxmd.com/read/28339199/structure-based-discovery-of-new-antagonist-and-biased-agonist-chemotypes-for-the-kappa-opioid-receptor
#9
Zhong Zheng, Xi-Ping Huang, Thomas J Mangano, Rodger Zou, Xin Chen, Saheem Zaidi, Bryan L Roth, Raymond C Stevens, Vsevolod Katritch
The ongoing epidemics of opioid overdose raises an urgent need for effective anti-addiction therapies and addiction-free painkillers. The κ-opioid receptor (KOR) has emerged as a promising target for both indications, raising demand for new chemotypes of KOR antagonists, as well as G-protein-biased agonists. We employed the crystal structure of the KOR-JDTic complex and ligand-optimized structural templates to perform virtual screening of available compound libraries for new KOR ligands. The prospective virtual screening campaign yielded a high 32% hit rate, identifying novel fragment-like and lead-like chemotypes of KOR ligands...
March 24, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28335477/association-between-circulating-vitamin-d-level-and-urolithiasis-a-systematic-review-and-meta-analysis
#10
REVIEW
Henglong Hu, Jiaqiao Zhang, Yuchao Lu, Zongbiao Zhang, Baolong Qin, Hongbin Gao, Yufeng Wang, Jianning Zhu, Qing Wang, Yunpeng Zhu, Yang Xun, Shaogang Wang
Many studies compared the serum/plasma 1,25 dihydroxyvitamin D₃ (1,25(OH)₂D) and 25 hydroxyvitamin D₃ (25(OH)D) between people with and without nephrolithiasis, and their results were conflicting. After systematically searching PubMed, Web of Science, The Cochrane Library, CNKI, and the Wanfang Database, we conducted a meta-analysis. Thirty-two observational studies involving 23,228 participants were included. Meta-analysis of these studies showed that of stone formers (SFs), calcium SFs had significantly higher concentrations of 1,25(OH)₂D (weighted mean difference (WMD), 10...
March 18, 2017: Nutrients
https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#11
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335400/online-classification-of-contaminants-based-on-multi-classification-support-vector-machine-using-conventional-water-quality-sensors
#12
Pingjie Huang, Yu Jin, Dibo Hou, Jie Yu, Dezhan Tu, Yitong Cao, Guangxin Zhang
Water quality early warning system is mainly used to detect deliberate or accidental water pollution events in water distribution systems. Identifying the types of pollutants is necessary after detecting the presence of pollutants to provide warning information about pollutant characteristics and emergency solutions. Thus, a real-time contaminant classification methodology, which uses the multi-classification support vector machine (SVM), is proposed in this study to obtain the probability for contaminants belonging to a category...
March 13, 2017: Sensors
https://www.readbyqxmd.com/read/28335389/characteristics%C3%A2-and%C3%A2-lethality%C3%A2-of%C3%A2-a%C3%A2-novel%C3%A2-recombinant%C3%A2-dermonecrotic%C3%A2-venom%C3%A2-phospholipase%C3%A2-d%C3%A2-from%C3%A2-hemiscorpius%C3%A2-lepturus
#13
Elham Torabi, Mahdi Behdani, Mohammad Hosseininejad Chafi, Reza Moazzami, Jean-Marc Sabatier, Vahid Khalaj, Delavar Shahbazzadeh, Kamran Pooshang Bagheri
Hemoscorpius lepturus is the most medically important scorpion in Iran. The clinical signs of H. lepturus envenomation are remarkably similar to those reported for brown spiders, including dermonecrosis, hematuria, renal failure and even death. The lethality and toxicity of brown spiders' venom have been attributed to its phospholipase D activity. This study aims to identify a phospholipase D with possible lethality and dermonecrotic activity in H. lepturus venom. In this study, a cDNA library of the venom glands was generated by Illumina RNA sequencing...
March 13, 2017: Toxins
https://www.readbyqxmd.com/read/28335031/ethics-of-health-policy-and-systems-research-a-scoping-review-of-the-literature
#14
Bridget Pratt, Amy Paul, Adnan A Hyder, Joseph Ali
Health policy and systems research (HPSR) is increasingly funded and undertaken as part of health system strengthening efforts worldwide. HPSR ethics is also a relatively new and emerging field, with numerous normative and descriptive questions that have largely not been considered. Normative questions include what ethical principles and values should guide HPSR. Descriptive questions include what ethical concerns arise when conducting HPSR. A small but growing body of scholarly work characterizes the various ethics issues inherent in HPSR...
March 15, 2017: Health Policy and Planning
https://www.readbyqxmd.com/read/28335006/a-platform-for-functional-assessment-of-large-variant-libraries-in-mammalian-cells
#15
Kenneth A Matreyek, Jason J Stephany, Douglas M Fowler
Sequencing-based, massively parallel genetic assays have revolutionized our ability to quantify the relationship between many genotypes and a phenotype of interest. Unfortunately, variant library expression platforms in mammalian cells are far from ideal, hindering the study of human gene variants in their physiologically relevant cellular contexts. Here, we describe a platform for phenotyping variant libraries in transfectable mammalian cell lines in two steps. First, a landing pad cell line with a genomically integrated, Tet-inducible cassette containing a Bxb1 recombination site is created...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334977/sclip-an-integrated-platform-to-study-rna-protein-interactomes-in-biomedical-research-identification-of-cstf2tau-in-alternative-processing-of-small-nuclear-rnas
#16
Yulia Kargapolova, Michal Levin, Karl Lackner, Sven Danckwardt
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334848/systematic-review-of-surveillance-by-social-media-platforms-for-illicit-drug-use
#17
Donna M Kazemi, Brian Borsari, Maureen J Levine, Beau Dooley
Background: The use of social media (SM) as a surveillance tool of global illicit drug use is limited. To address this limitation, a systematic review of literature focused on the ability of SM to better recognize illicit drug use trends was addressed. Methods: A search was conducted in databases: PubMed, CINAHL via Ebsco, PsychINFO via Ebsco, Medline via Ebsco, ERIC, Cochrane Library, Science Direct, ABI/INFORM Complete and Communication and Mass Media Complete...
March 14, 2017: Journal of Public Health
https://www.readbyqxmd.com/read/28334828/flexible-crispr-library-construction-using-parallel-oligonucleotide-retrieval
#18
Abigail Read, Shaojian Gao, Eric Batchelor, Ji Luo
CRISPR/Cas9-based gene knockout libraries have emerged as a powerful tool for functional screens. We present here a set of pre-designed human and mouse sgRNA sequences that are optimized for both high on-target potency and low off-target effect. To maximize the chance of target gene inactivation, sgRNAs were curated to target both 5΄ constitutive exons and exons that encode conserved protein domains. We describe here a robust and cost-effective method to construct multiple small sized CRISPR library from a single oligo pool generated by array synthesis using parallel oligonucleotide retrieval...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#19
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334798/risk-factors-for-postoperative-delirium-in-patients-undergoing-major-head-and-neck-cancer-surgery-a-meta-analysis
#20
Yun Zhu, Gangpu Wang, Shengwen Liu, Shanghui Zhou, Ying Lian, Chenping Zhang, Wenjun Yang
Objective: Postoperative delirium is common after extensive surgery. This study aimed to collate and synthesize published literature on risk factors for delirium in patients with head and neck cancer surgery. Methods: Three databases were searched (MEDLINE, Embase, and Cochrane Library) between January 1987 and July 2016. The Newcastle Ottawa Scale (NOS) was adopted to evaluate the study quality. Pooled odds ratios or mean differences for individual risk factors were estimated using the Mantel-Haenszel and inverse-variance methods...
February 24, 2017: Japanese Journal of Clinical Oncology
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