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https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#1
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28820871/genetic-predisposition-to-fetal-alcohol-syndrome-association-with-congenital-disorders-of-n-glycosylation
#2
María E de la Morena-Barrio, María J Ballesta-Martínez, Raquel López-Gálvez, Ana I Antón, Vanessa López-González, Laia Martínez-Ribot, José Padilla, Antonia Miñano, Oscar García-Algar, Miguel Del Campo, Javier Corral, Encarna Guillén-Navarro, Vicente Vicente
BACKGROUND: Fetal alcohol syndrome (FAS) is caused by maternal alcohol consumption during pregnancy, although additional factors must be involved, as development and severity are not directly related to alcohol intake. The abnormal glycosylation caused by alcohol might play a role in FAS according to the clinical similarities shared with congenital disorders of glycosylation (CDG). Thus, mutations underlying CDG, affecting genes involved in glycosylation, could also be involved in FAS...
August 18, 2017: Pediatric Research
https://www.readbyqxmd.com/read/28820869/necrotizing-enterocolitis-and-high-intestinal-iron-uptake-due-to-genetic-variants
#3
Wolfgang Göpel, Josephine Drese, Tanja K Rausch, Nele Twisselmann, Bettina Bohnhorst, Andreas Müller, Axel Franz, Andreas Ziegler, Christoph Härtel, Egbert Herting
BACKGROUND: Intestinal iron is a nutritional compound, which is essential for enteric microbiota. We evaluated the hypothesis that polymorphisms which are known modifiers of intestinal iron uptake in adults are associated with necrotizing enterocolitis (NEC) in preterm infants. METHODS: Preterm infants (birth weight below 1,500 grams) were studied. Single nucleotide polymorphisms with known effects on serum iron levels (rs1800562, rs1799945, rs855791) were determined by polymerase chain reaction...
August 18, 2017: Pediatric Research
https://www.readbyqxmd.com/read/28820624/retinopathy-and-optic-atrophy-expanding-the-phenotypic-spectrum-of-pathogenic-variants-in-the-aars2-gene
#4
Jason H Peragallo, Stephanie Keller, Marjo S van der Knaap, Bruno P Soares, Suma P Shankar
BACKGROUND: Optic atrophy may be the sequela of optic nerve injury due to any insult, including isolated and syndromic genetic diseases. Alanyl-tRNA synthetase 2 (AARS2) pathogenic variants have been reported to cause leukodystrophy with ovarian failure, and cardiomyopathy (#615889) as well as combined oxidative phosphorylation deficiency-8 (#614096). We report a young child who presented with decreased vision due to optic atrophy and was found to harbor missense variants in the AARS2 gene expanding the phenotypic expression of the AARS2 gene...
August 18, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28820457/role-of-cyp2c9-cyp2c19-and-ephx-polymorphism-in-the-pharmacokinetic-of-phenytoin-a-study-on-uruguayan-caucasian-subjects
#5
Natalia Guevara, Cecilia Maldonado, Manuel Uría, Raquel González, Manuel Ibarra, Silvana Alvariza, Antonella Carozzi, Carlos Azambuja, Pietro Fagiolino, Marta Vázquez
Phenytoin (PHT) oxidative route leads to its main metabolite p-hydroxyphenytoin (p-HPPH), by means of CYP2C9 and CYP2C19. Formation of p-HPPH proceeds via a reactive arene-oxide intermediate. This intermediate can also be converted into PHT dihydrodiol by microsomal epoxide hydrolase (EPHX). The three enzymes are polymorphically expressed and the genetic variants are responsible for changes in the enzyme activity. In order to evaluate the effect that these polymorphisms have on PHT metabolism, PHT and p-HPPH plasma concentrations were measured and the genotype for the three enzymes was assessed in 50 Uruguayan epileptic patients...
August 18, 2017: Pharmaceuticals
https://www.readbyqxmd.com/read/28820339/emergence-of-visceral-leishmaniasis-in-sri-lanka-a-newly-established-health-threat
#6
H V Y D Siriwardana, P Karunanayake, L Goonerathne, N D Karunaweera
BACKGROUND: Sri Lanka is a new focus of human cutaneous leishmaniasis caused by a genetic variant of usually visceralizing parasite Leishmania donovani. Over 3000 cases have been reported to our institution alone, during the past two decades. Recent emergence of visceral leishmaniasis is of concern. METHODS: Patients suspected of having visceral leishmaniasis (n = 120) fulfilling at least two of six criteria (fever > 2 weeks, weight loss, tiredness affecting daily functions, splenomegaly, hepatomegaly and anemia) were studied using clinic-epidemiological, immunological and haematological parameters...
August 18, 2017: Pathogens and Global Health
https://www.readbyqxmd.com/read/28820331/polo-like-kinase-1-plk1-dependent-phosphorylation-of-methylenetetrahydrofolate-reductase-mthfr-regulates-replication-via-histone-methylation
#7
Xueyan Li, Shanshan Nai, Yuehe Ding, Qizhi Geng, Bingtao Zhu, Kai Yu, Wei-Guo Zhu, Meng-Qiu Dong, Xiao-Dong Su, Xingzhi Xu, Jing Li
Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme regulating the folate cycle and its genetic variations have been associated with various human diseases. Previously we identified that MTHFR is phosphorylated by cyclin-dependent kinase 1 (CDK1) at T34 and MTHFR underlies heterochromatin maintenance marked by H3K9me3 levels. Herein we demonstrate that pT34 creates a binding motif that docks MTHFR to the polo-binding domain (PBD) of polo-like kinase 1 (PLK1), a fundamental kinase that orchestrates many cell cycle events...
August 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28820204/droplet-microfluidics-for-synthetic-biology
#8
REVIEW
Philip C Gach, Kosuke Iwai, Peter W Kim, Nathan J Hillson, Anup K Singh
Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility...
August 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28820077/genetic-variants-of-pear1-are-associated-with-platelet-function-and-antiplatelet-drug-efficacy-a-systematic-review-and-meta-analysis
#9
Qian Xiang, Shuang Zhou, Joshua P Lewis, Alan R Shuldiner, Guanhua Ren, Yimin Cui
BACKGROUND: Platelet endothelial aggregation receptor 1 (PEAR1) may affect platelet-platelet contact and aggregation. The aim of this study was to assess the association between PEAR1 polymorphisms and risks of platelet aggregation. METHODS: We searched the PubMed, EmBase, and Cochrane Library electronic databases for articles published through November 30th. 2016. Meta-analysis was performed to examine the relationship between PEAR1 and platelet aggregation and sensitivity analysis by removing individual study from meta-analysis...
August 17, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28819944/contribution-of-inherited-thrombophilia-to-recurrent-miscarriage-in-the-polish-population
#10
Hubert Wolski, Magdalena Barlik, Krzysztof Drews, Andrzej Klejewski, Grażyna Kurzawińska, Marcin Ożarowski, Zdzisław Łowicki, Agnieszka Seremak-Mrozikiewicz
INTRODUCTION: The aim of the study was to evaluate the contribution of genetic variants determining inherited thrombophilia to recurrent miscarriage (RM) in the Polish population. The following polymorphisms were analyzed: 1691G>A, 1328T>C of coagulation factor V, 20210G>A of coagulation factor II, R353Q (11496G>A) of coagulation factor VII, 667C>T, 1298A>C, 1793G>A of MTHFR. MATERIAL AND METHODS: A total of 359 women with ≥ 2 subsequent recurrent miscarriages (303 < 13 weeks of gestation (w...
2017: Ginekologia Polska
https://www.readbyqxmd.com/read/28819827/interaction-between-selp-genetic-polymorphisms-with-inflammatory-cytokine-interleukin-6-il-6-gene-variants-on-cardiovascular-disease-in-chinese-han-population
#11
Lu Kou, Ning Yang, Bo Dong, Yang Li, Jingyu Yang, Qin Qin
The aim of the study is to investigate the impact of SELP and IL-6 genetic single-nucleotide polymorphisms (SNPs) and its gene-gene interaction on cardiovascular disease (CVD) risk based on Chinese population. A total of 1082 subjects (519 males, 563 females), with a mean age of 53.9 ± 13.1 years, were selected, including 540 CVD patients and 542 normal control participants. Logistic regression model was used to examine the association between six SNPs and CVD risk. Odds ratio (OR) and 95% confident interval (95% CI) were calculated...
August 18, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28819774/whole-exome-sequencing-of-wild-derived-inbred-strains-of-mice-improves-power-to-link-phenotype-and-genotype
#12
Peter L Chang, Emily Kopania, Sara Keeble, Brice A J Sarver, Erica Larson, Annie Orth, Khalid Belkhir, Pierre Boursot, François Bonhomme, Jeffrey M Good, Matthew D Dean
The house mouse is a powerful model to dissect the genetic basis of phenotypic variation, and serves as a model to study human diseases. Despite a wealth of discoveries, most classical laboratory strains have captured only a small fraction of genetic variation known to segregate in their wild progenitors, and existing strains are often related to each other in complex ways. Inbred strains of mice independently derived from natural populations have the potential to increase power in genetic studies with the addition of novel genetic variation...
August 17, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28819537/-nod2-gene-mutation-in-moroccan-patients-with-crohn-s-disease-prevalence-genotypic-study-and-correlation-of-nod2-gene-mutation-with-the-phenotype-of-crohn-s-disease
#13
Mouna Tamzaourte, Ikram Errabih, Hayat Krami, Fadlouallah Maha, Lahmiri Maria, Nadia Benzzoubeir, Laaziza Ouazzani, Ahmed Sefiani, Houria Ouazzani
The aim of this study was to determine the prevalence of NOD2/CARD15 gene mutations in a group of Moroccan patients with Crohn's disease and to study its correlation with genotype-phenotypic expression. We conducted a cross-sectional case-control study over a period of 16 months. 101 patients with Crohn's disease were enrolled between January 2012 and April 2013 as well as a control group of 107 patients. We performed a genetic analysis to identify 3 NOD2 gene variants: p.Arg702Trp, p.Gly908Arg and p.Leu1007fsins...
2017: Pan African Medical Journal
https://www.readbyqxmd.com/read/28819444/association-of-hla-drb1-hla-dqb1-polymorphisms-with-hpv-16-e6-variants-among-young-cervical-cancer-patients-in-china
#14
Yan Hu, Jin-Ze Wu, Hua Zhu, Sheng-Hui Zhang, Yan-Ying Zhu, Yi-Yao Wu, Ci-Xia Shuai
Potential correlation of human papillomavirus (HPV) 16 E6 variants and human leukocyte antigen (HLA) class II polymorphisms has been suggested in patients with cervical cancer, so far little information is available about the possible interaction between E6 variants and HLA class II variability during the obviously accelerated progression to cervical cancer in young women. In this study, we aimed to explore the association between the HPV16 E6 variants and HLA-DRB1, DQB1 alleles in a Chinese young cervical cancer population...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819253/majority-of-human-traits-do-not-show-evidence-for-sex-specific-genetic-and-environmental-effects
#15
Sven Stringer, Tinca Polderman, Danielle Posthuma
Sex differences in the etiology of human trait variation are a major topic of interest in the social and medical sciences given its far-reaching implications. For example, in genetic research, the presence of sex-specific effects would require sex-stratified analysis, and in clinical practice sex-specific treatments would be warranted. Here, we present a study of 2,335,920 twin pairs, in which we tested sex differences in genetic and environmental contributions to variation in 2,608 reported human traits, clustered in 50 trait categories...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819221/functional-validation-of-gpihbp1-and-identification-of-a-functional-mutation-in-gpihbp1-for-milk-fat-traits-in-dairy-cattle
#16
Jie Yang, Xuan Liu, Dan Wang, Chao Ning, Haifei Wang, Qin Zhang, Li Jiang
In a previous genome-wide association study (GWAS) on milk production traits in a Chinese Holstein population, we revealed that GPIHBP1 is a novel promising candidate gene for milk fat content traits. In this study, we performed over-expression and RNAi experiments on GPIHBP1 in bovine primary mammary epithelial cells. The results showed that the expression of several important milk fat-related genes (LPL, CD36, VLDLR, ACACA and FASN) increased or decreased when the expression of GPIHBP1 was up- or down-regulated...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819144/predicting-hair-cortisol-levels-with-hair-pigmentation-genes-a-possible-hair-pigmentation-bias
#17
Alexander Neumann, Gerard Noppe, Fan Liu, Manfred Kayser, Frank C Verhulst, Vincent W V Jaddoe, Elisabeth F C van Rossum, Henning Tiemeier
Cortisol concentrations in hair are used to create hormone profiles spanning months. This method allows assessment of chronic cortisol exposure, but might be biased by hair pigmentation: dark hair was previously related to higher concentrations. It is unclear whether this association arises from local effects, such as increased hormone extractability, or whether the association represents systemic differences arising from population stratification. We tested the hypothesis that hair pigmentation gene variants are associated with varying cortisol levels independent of genetic ancestry...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819071/genetic-and-non-genetic-factors-associated-with-protein-abundance-of-flavin-containing-monooxygenase-3-in-human-liver
#18
Meijuan Xu, Deepak Kumar Bhatt, Catherine K Yeung, Katrina G Claw, Amarjit S Chaudhry, Andrea Gaedigk, Robin E Pearce, Ulrich Broeckel, Roger Gaedigk, Debbie Nickerson, Erin Schuetz, Allan E Rettie, Steven Leeder, Kenneth E Thummel, Bhagwat Prasad
Hepatic flavin-containing monooxygenase 3 (FMO3) metabolizes a broad array of nucleophilic heteroatom (e.g., N or S)-containing xenobiotics (e.g., amphetamine, sulindac, benzydamine, ranitidine, tamoxifen, nicotine, and ethioniamide), as well as endogenous compounds (e.g., catecholamine and trimethylamine). To predict the effect of genetic and non-genetic factors on the hepatic metabolism of FMO3 substrates, we quantified FMO3 protein abundance in human liver microsomes (HLM; n=445) by LC-MS/MS proteomics. Genotyping/gene-resequencing, mRNA expression, and functional activity (with benzydamine as a probe substrate) of FMO3 were also performed...
August 17, 2017: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/28819016/a-syndromic-extreme-insulin-resistance-caused-by-biallelic-poc1a-mutations-in-exon-10
#19
Elisa Giorgio, Elisa Rubino, Alessandro Bruselles, Simone Pizzi, Innocenzo Rainero, Sergio Duca, Fabio Sirchia, Barbara Pasini, Marco Tartaglia, Alfredo Brusco
POC1A encodes a protein with a role in centriole assembly and stability, and in ciliogenesis. Biallelic loss of function mutations affecting POC1A cause SOFT syndrome, an ultra-rare condition characterized by short stature, onychodysplasia, facial dysmorphism and hypotrichosis. Using exome sequencing, we identified a homozygous frameshift mutation (c.1047_1048dupC; p.G337Rfs*25) in a patient presenting with short stature, facial hirsutism, alopecia, dyslipidemia and extreme insulin resistance. The truncating variant affected exon 10, which is retained in only two of the three POC1A mature RNAs, due to alternative processing of the transcript...
August 17, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28818866/systematic-identification-of-determinants-for-single-strand-annealing-mediated-deletion-formation-in-saccharomyces-cerevisiae
#20
Maia Segura-Wang, Megumi Onishi-Seebacher, Adrian M Stütz, Balca R Mardin, Jan O Korbel
To ensure genomic integrity, living organisms have evolved diverse molecular processes for sensing and repairing damaged DNA. If improperly repaired, DNA damage can give rise to different types of mutations, an important class of which are the genomic structural variants (SVs). In spite of their importance for phenotypic variation and genome evolution, potential contributors to SV formation in Saccharomyces cerevisiae (budding yeast), a highly tractable model organism, are not fully recognized. Here we developed and applied a genome-wide assay to identify yeast gene knock-out mutants associated with de novo deletion formation, in particular single strand annealing (SSA) -mediated deletion formation in a systematic manner...
August 17, 2017: G3: Genes—Genomes—Genetics
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