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https://www.readbyqxmd.com/read/28335589/global-functional-analysis-of-butanol-sensitive-escherichia-coli-and-its-evolved-butanol-tolerant-strain
#1
Haeyoung Jeong, Seung-Won Lee, Sun Hong Kim, Eun-Youn Kim, Sinyeon Kim, Sung Ho Yoon
Butanol is a promising alternative to ethanol and is desirable for use in transportation fuels and additives to gasoline and diesel fuels. Microbial production of butanol is challenging primarily due to its toxicity and low titer of production. Herein, we compared the transcriptome and phenome of wild-type Escherichia coli and its butanol-tolerant evolved strain to understand the global cellular physiology and metabolism responsible for butanol tolerance. When the ancestral butanol-sensitive E. coli was exposed to butanol, gene activities involved in respiratory mechanisms and oxidative stress were highly perturbed...
March 24, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28335481/genetic-variants-contributing-to-colistin-cytotoxicity-identification-of-tgif1-and-hoxd10-using-a-population-genomics-approach
#2
Michael T Eadon, Ronald J Hause, Amy L Stark, Ying-Hua Cheng, Heather E Wheeler, Kimberly S Burgess, Eric A Benson, Patrick N Cunningham, Robert L Bacallao, Pierre C Dagher, Todd C Skaar, M Eileen Dolan
Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines...
March 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335009/open-chromatin-profiling-of-human-postmortem-brain-infers-functional-roles-for-non-coding-schizophrenia-loci
#3
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T Dudley, Manuel Mattheisen, Nikolaos K Robakis, Vahram Haroutunian, Panos Roussos
Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS)...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334957/quechers-based-method-for-pesticides-analysis-in-adipose-tissue-associated-with-rat-ovaries
#4
Nathalie Zamariola, Pedro Toledo Netto, Carla Adriene da Silva Franchi, João Lauro Viana de Camargo, Mary Rosa Rodrigues de Marchi
The concomitant exposure to low doses of various pesticides is one of the most relevant issues in human toxicology today. An experimental toxicology study was developed to evaluate the effects of this type of exposure on the reproductive capacity of females of three species of rats that were exposed to mixtures of dicofol, dieldrin, endosulfan and permethrin at low doses (LOAEL and NOAEL). In this context, we have developed a method for determining pesticides in adipose tissue (0.5 g, 49% lipid) associated with the ovaries, based on the QuEChERS (quick, easy, cheap, effective, rugged and safe) strategy...
March 14, 2017: Journal of Analytical Toxicology
https://www.readbyqxmd.com/read/28334916/mocap-large-scale-inference-of-transcription-factor-binding-sites-from-chromatin-accessibility
#5
Xi Chen, Bowen Yu, Nicholas Carriero, Claudio Silva, Richard Bonneau
Differential binding of transcription factors (TFs) at cis-regulatory loci drives the differentiation and function of diverse cellular lineages. Understanding the regulatory interactions that underlie cell fate decisions requires characterizing TF binding sites (TFBS) across multiple cell types and conditions. Techniques, e.g. ChIP-Seq can reveal genome-wide patterns of TF binding, but typically requires laborious and costly experiments for each TF-cell-type (TFCT) condition of interest. Chromosomal accessibility assays can connect accessible chromatin in one cell type to many TFs through sequence motif mapping...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334860/genetic-regulation-of-gene-expression-in-the-epileptic-human-hippocampus
#6
Nasir Mirza, Richard Appleton, Sasha Burn, Daniel du Plessis, Roderick Duncan, Jibril Osman Farah, Bjarke Feenstra, Anders Hviid, Vivek Josan, Rajiv Mohanraj, Arif Shukralla, Graeme J Sills, Anthony G Marson, Munir Pirmohamed
Epilepsy is a serious and common neurological disorder. Expression quantitative loci (eQTL) analysis is a vital aid for the identification and interpretation of disease-risk loci. Many eQTLs operate in a tissue- and condition-specific manner. We have performed the first genome-wide cis-eQTL analysis of human hippocampal tissue to include not only normal (n = 22) but also epileptic (n = 22) samples. We demonstrate that disease-associated variants from an epilepsy GWAS meta-analysis and a febrile seizures (FS) GWAS are significantly more enriched with epilepsy-eQTLs than with normal hippocampal eQTLs from two larger independent published studies...
March 3, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334807/allele-specific-quantitative-proteomics-unravels-molecular-mechanisms-modulated-by-cis-regulatory-pparg-locus-variation
#7
Heekyoung Lee, Kun Qian, Christine von Toerne, Lena Hoerburger, Melina Claussnitzer, Christoph Hoffmann, Viktoria Glunk, Simone Wahl, Michaela Breier, Franziska Eck, Leili Jafari, Sophie Molnos, Harald Grallert, Ingrid Dahlman, Peter Arner, Cornelia Brunner, Hans Hauner, Stefanie M Hauck, Helmut Laumen
Genome-wide association studies identified numerous disease risk loci. Delineating molecular mechanisms influenced by cis-regulatory variants is essential to understand gene regulation and ultimately disease pathophysiology. Combining bioinformatics and public domain chromatin information with quantitative proteomics supports prediction of cis-regulatory variants and enabled identification of allele-dependent binding of both, transcription factors and coregulators at the type 2 diabetes associated PPARG locus...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334728/does-emergency-presentation-of-cancer-represent-poor-performance-in-primary-care-insights-from-a-novel-analysis-of-linked-primary-and-secondary-care-data
#8
Peter Murchie, Sarah M Smith, Michael S Yule, Rosalind Adam, Melanie E Turner, Amanda J Lee, Shona Fielding
BACKGROUND: People diagnosed with cancer following emergency presentation have poorer short-term survival. To what extent this signifies a missed opportunity for earlier diagnosis in primary care remains unclear as little detailed data exist on the patient/general practitioner interaction beforehand. METHODS: Analysis of primary care and regional data for 1802 cancer patients from Northeast Scotland. Adjusted odds ratios (OR) and 95% confidence intervals (CIs) for patient and GP practice predictors of emergency presentation...
March 23, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28334724/incidence-of-multiple-sclerosis-in-puerto-rico-2014-a-population-based-study
#9
Angel Chinea, Carlos F Ríos-Bedoya, Cristina Rubi, Ivonne Vicente, Eduardo R Estades, Yatzka G Hernandez-Silvestrini
BACKGROUND: Multiple sclerosis (MS) affects millions of people worldwide. The estimates for MS incidence are difficult to obtain but are important for understanding MS etiology, developing prevention strategies, and service planning. This study is aimed at estimating the 2014 incidence of MS in Puerto Rico (PR). METHODS: The PR MS Foundation's registry was used as the data source. Neurologists, specialty pharmacies, MRI centers, health insurance companies, and the PR Department of Health identified MS cases missed by the registry...
March 24, 2017: Neuroepidemiology
https://www.readbyqxmd.com/read/28334469/stereoisomerism-of-bis-sigma-zincane-complexes-evidence-for-an-intramolecular-pathway
#10
Mark Richard Crimmin, Olga Ekkert, Andrew White
The first bis(sigma-zincane) complexes, heterotrimetallic species [M(CO)4(2-HZnBDI)2], have been prepared (BDI = 2-{2,6-i-Pr2C6H3NCMe}2CH). For M = Cr a single stereoisomer is observed in solution and the solid-state. For M = Mo and W, cis and trans isomers where found to reversibly interconvert at 297 K. Despite the huge steric demands of the ligand on zinc, in all cases the cis isomer was found to be the most thermodynamically stable. The activation parameters for the isomerization when M = Mo are H‡ = 20...
March 23, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28334268/an-algorithmic-perspective-of-de-novo-cis-regulatory-motif-finding-based-on-chip-seq-data
#11
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
Transcription factors are proteins that bind to specific DNA sequences and play important roles in controlling the expression levels of their target genes. Hence, prediction of transcription factor binding sites (TFBSs) provides a solid foundation for inferring gene regulatory mechanisms and building regulatory networks for a genome. Chromatin immunoprecipitation sequencing (ChIP-seq) technology can generate large-scale experimental data for such protein-DNA interactions, providing an unprecedented opportunity to identify TFBSs (a...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334180/sugar-diet-affects-odor-reception-but-variation-in-sugar-concentration-plays-minimal-role-in-the-response-of-the-parasitoid-microplitis-croceipes-hymenoptera-braconidae-to-host-related-plant-volatiles
#12
Matthew Burrows, Tolulope Morawo, Henry Fadamiro
Parasitoids utilize various sugar resources in nature, and rely on odor cues from plants to locate their food and hosts. However, lack of sugar in the diet may negatively impact odor reception in parasitoids, thus affecting foraging efficiency. We used Microplitis croceipes (Cresson) (Hymenoptera: Braconidae), a larval endoparasitoid of Heliothis virescens (F.) (Lepidoptera: Noctuidae), as a model species to test the hypothesis that variation in sugar diet of parasitoids affects their olfactory response to host-related odors...
March 3, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28333969/the-associations-of-personality-traits-and-parental-education-with-smoking-behaviour-among-adolescents
#13
Aina M Yáñez, Alfonso Leiva, Andreu Estela, Iva Čukić
We examined whether personality traits and parental education are associated with smoking initiation in a sample of Spanish secondary school students. Participants, taken from the ITACA study (842 adolescents aged 14-15 years), completed a questionnaire assessing personality traits of the Five Factor Model, smoking behaviours and parental education. Multinomial logistic regression models controlling for age and sex were used to determine the independent associations and interactions of personality traits and parental education with risk of ever trying smoking, as well as with being a regular smoker in adolescence...
2017: PloS One
https://www.readbyqxmd.com/read/28333947/surgical-interventions-to-treat-humerus-shaft-fractures-a-network-meta-analysis-of-randomized-controlled-trials
#14
Jia-Guo Zhao, Jia Wang, Xiao-Hui Meng, Xian-Tie Zeng, Shi-Lian Kan
BACKGROUND: There are three main surgical techniques to treat humeral shaft fractures: open reduction and plate fixation (ORPF), intramedullary nail (IMN) fixation, and minimally invasive percutaneous osteosynthesis (MIPO). We performed a network meta-analysis to compare three surgical procedures, including ORPF, IMN fixation, and MIPO, to provide the optimum treatment for humerus shaft fractures. METHODS: MEDLINE, EMBASE, Cochrane Bone, Joint and Muscle Trauma Group Specialised Register, and Cochrane library were researched for reports published up to May 2016...
2017: PloS One
https://www.readbyqxmd.com/read/28333928/network-perturbation-by-recurrent-regulatory-variants-in-cancer
#15
Kiwon Jang, Kwoneel Kim, Ara Cho, Insuk Lee, Jung Kyoon Choi
Cancer driving genes have been identified as recurrently affected by variants that alter protein-coding sequences. However, a majority of cancer variants arise in noncoding regions, and some of them are thought to play a critical role through transcriptional perturbation. Here we identified putative transcriptional driver genes based on combinatorial variant recurrence in cis-regulatory regions. The identified genes showed high connectivity in the cancer type-specific transcription regulatory network, with high outdegree and many downstream genes, highlighting their causative role during tumorigenesis...
March 23, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28333449/epigenetic-modulation-of-endophytic-eupenicillium-sp-lg41-by-a-histone-deacetylase-inhibitor-for-production-of-decalin-containing-compounds
#16
Gang Li, Souvik Kusari, Christopher Golz, Hartmut Laatsch, Carsten Strohmann, Michael Spiteller
An endophytic fungus, Eupenicillium sp. LG41, isolated from the Chinese medicinal plant Xanthium sibiricum, was subjected to epigenetic modulation using an NAD(+)-dependent histone deacetylase (HDAC) inhibitor, nicotinamide. Epigenetic stimulation of the endophyte led to enhanced production of two new decalin-containing compounds, eupenicinicols C and D (3 and 4), along with two biosynthetically related known compounds, eujavanicol A (1) and eupenicinicol A (2). The structures and stereochemistry of the new compounds were elucidated by extensive spectroscopic analysis using LC-HRMS, NMR, optical rotation, and ECD calculations, as well as single-crystal X-ray diffraction...
March 23, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28333365/clozapine-combined-with-different-antipsychotic-drugs-for-treatment-resistant-schizophrenia
#17
REVIEW
Sarah Barber, Uwaila Olotu, Martina Corsi, Andrea Cipriani
BACKGROUND: Between 40% and 70% of people with treatment-resistant schizophrenia do not respond to clozapine, despite adequate blood levels. For these people, a number of treatment strategies have emerged, including the prescription of a second anti-psychotic drug in combination with clozapine. OBJECTIVES: To determine the clinical effects of various clozapine combination strategies with antipsychotic drugs in people with treatment-resistant schizophrenia both in terms of efficacy and tolerability...
March 23, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28333256/analgesia-use-during-pregnancy-and-risk-of-cryptorchidism-a-systematic-review-and-meta-analysis
#18
Jason Gurney, Lorenzo Richiardi, Katherine A McGlynn, Virginia Signal, Diana Sarfati
STUDY QUESTION: Are boys who are born to mothers who use analgesics during pregnancy at increased risk of cryptorchidism compared to those born to mothers who do not take analgesia? SUMMARY ANSWER: In this systematic review and meta-analysis of 10 published studies, we observed only weak evidence of an association between analgesia use during pregnancy and risk of cryptorchidism in the son. WHAT IS KNOWN ALREADY: Concentrations of analgesia relevant to human exposure have been implicated as causing endocrine disturbances in the developing foetal testis...
March 8, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28333240/structure-of-the-transcriptional-regulatory-network-correlates-with-regulatory-divergence-in-drosophila
#19
Bing Yang, Patricia J Wittkopp
Transcriptional control of gene expression is regulated by biochemical interactions between cis-regulatory DNA sequences and trans-acting factors that form complex regulatory networks. Genetic changes affecting both cis- and trans-acting sequences in these networks have been shown to alter patterns of gene expression as well as higher-order organismal phenotypes. Here, we investigate how the structure of these regulatory networks relates to patterns of polymorphism and divergence in gene expression. To do this, we compared a transcriptional regulatory network inferred for Drosophila melanogaster to differences in gene regulation observed between two strains of D...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333207/endometrial-thickness-in-women-undergoing-iui-with-ovarian-stimulation-how-thick-is-too-thin-a-systematic-review-and-meta-analysis
#20
N S Weiss, M N van Vliet, J Limpens, P G A Hompes, C B Lambalk, M H Mochtar, F van der Veen, B W J Mol, M van Wely
STUDY QUESTION: Is pre-ovulatory endometrial thickness (EMT) in women with unexplained subfertility undergoing IUI with ovarian stimulation (OS) associated with pregnancy chances? SUMMARY ANSWER: We found no evidence for an association between EMT and pregnancy chances. WHAT IS KNOWN ALREADY: It has been suggested that OS with clomiphene citrate (CC) results in a lower EMT than with gonadotrophins or aromatase inhibitors, but the clinical consequences in terms of pregnancy are unclear...
February 23, 2017: Human Reproduction
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