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https://www.readbyqxmd.com/read/29161757/impact-of-cyp3a5-genomic-variances-on-clinical-outcomes-among-african-american-kidney-transplant-recipients
#1
Tomefa E Asempa, Lorita M Rebellato, Suzanne Hudson, Kimberly Briley, Angela Q Maldonado
Little is known about the impact of CYP3A5 polymorphisms on transplantation outcomes among African-American (AA) kidney transplant recipients. To assess this issue, clinical outcomes were compared between AA CYP3A5*1 expressers versus non-expressers. This retrospective cohort study analyzed AA kidney transplant recipients. Biopsy-proven acute rejection (BPAR), delayed graft function (DGF), glomerular filtration rate (GFR), infections and tacrolimus dosing requirements were examined in 106 immunologically high-risk AA kidney transplant patients over a 2 year follow-up period...
November 21, 2017: Clinical Transplantation
https://www.readbyqxmd.com/read/29161464/increased-efficiency-of-targeted-mutagenesis-by-crispr-cas9-in-plants-using-heat-stress
#2
Chantal Le Blanc, Fei Zhang, Josefina Mendez, Yamile Lozano, Krishna Chatpar, Vivian Irish, Yannick Jacob
The CRISPR/Cas9 system has greatly improved our ability to engineer targeted mutations in eukaryotic genomes. While CRISPR/Cas9 appears to work universally, the efficiency of targeted mutagenesis and the adverse generation of off-target mutations vary greatly between different organisms. In this study, we report that Arabidopsis plants subjected to heat stress at 37°C show much higher frequencies of CRISPR-induced mutations compared to plants grown continuously at the standard temperature (22°C). Using quantitative assays relying on GFP reporter genes, we found that targeted mutagenesis by CRISPR/Cas9 in Arabidopsis is increased by ~5-fold in somatic tissues and up to 100-fold in the germline upon heat treatment...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29161442/origin-and-evolution-of-the-bartonella-gene-transfer-agent
#3
Daniel Tamarit, Minna-Maria Neuvonen, Philipp Engel, Lionel Guy, Siv G E Andersson
Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces that drive the emergence of GTAs are still poorly understood. Two GTAs have been identified in the Alphaproteobacteria: the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range that includes vector-borne intracellular bacteria of the genus Bartonella...
November 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29161414/structural-diversity-of-the-nucleosome
#4
Masako Koyama, Hitoshi Kurumizaka
In eukaryotes, genomic DNA is compacted in chromatin, which generally suppresses transcription, replication, repair, and recombination. The fundamental unit of chromatin is the nucleosome, whose structure was first determined at atomic resolution in 1997. However, recent findings have revealed that the nucleosome is not a structurally homogenous entity. Nucleosomes containing histone variants often have subtle but clear differences in their structural and functional characteristics, as compared to the canonical nucleosome...
November 17, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29161307/repeat-polymorphisms-in-the-homo-sapiens-heme-oxygenase-1-gene-in-diabetic-and-idiopathic-gastroparesis
#5
Simon J Gibbons, Madhusudan Grover, Kyoung Moo Choi, Akhilesh Wadhwa, Adeel Zubair, Laura A Wilson, Yanhong Wu, Thomas L Abell, William L Hasler, Kenneth L Koch, Richard W McCallum, Linda A B Nguyen, Henry P Parkman, Irene Sarosiek, William J Snape, James Tonascia, Frank A Hamilton, Pankaj J Pasricha, Gianrico Farrugia
BACKGROUND: Idiopathic and diabetic gastroparesis in Homo sapiens cause significant morbidity. Etiology or risk factors have not been clearly identified. Failure to sustain elevated heme oxygenase-1 (HO1) expression is associated with delayed gastric emptying in diabetic mice and polymorphisms in the HO1 gene (HMOX1, NCBI Gene ID:3162) are associated with worse outcomes in other diseases. AIM: Our hypothesis was that longer polyGT alleles are more common in the HMOX1 genes of individuals with gastroparesis than in controls without upper gastrointestinal motility disorders...
2017: PloS One
https://www.readbyqxmd.com/read/29161273/enrichment-of-colorectal-cancer-associations-in-functional-regions-insight-for-using-epigenomics-data-in-the-analysis-of-whole-genome-sequence-imputed-gwas-data
#6
Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stéphane Bézieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister, Christian Fuchsberger, Mark A Jenkins, Suzanne M Leal, Mathieu Lemire, Polly A Newcomb, Steven Gallinger, John D Potter, Robert E Schoen, Martha L Slattery, Joshua D Smith, Loic Le Marchand, Emily White, Brent W Zanke, Goncalo R Abeçasis, Christopher S Carlson, Ulrike Peters, Deborah A Nickerson, Anshul Kundaje, Li Hsu
BACKGROUND: The evaluation of less frequent genetic variants and their effect on complex disease pose new challenges for genomic research. To investigate whether epigenetic data can be used to inform aggregate rare-variant association methods (RVAM), we assessed whether variants more significantly associated with colorectal cancer (CRC) were preferentially located in non-coding regulatory regions, and whether enrichment was specific to colorectal tissues. METHODS: Active regulatory elements (ARE) were mapped using data from 127 tissues and cell-types from NIH Roadmap Epigenomics and Encyclopedia of DNA Elements (ENCODE) projects...
2017: PloS One
https://www.readbyqxmd.com/read/29160898/variation-in-range-size-and-dispersal-capabilities-of-microbial-taxa
#7
Mallory J Choudoir, Albert Barberán, Holly L Menninger, Rob R Dunn, Noah Fierer
Geographic range size can span orders of magnitude for plant and animal species, with the study of why range sizes vary having preoccupied biogeographers for decades. In contrast, there have been few comparable studies of how range size varies across microbial taxa and what traits may be associated with this variation. We determined the range sizes of 74,134 bacterial and archaeal taxa found in settled dust collected from 1,065 locations across the United States. We found that most microorganisms have small ranges and few have large ranges, a pattern similar to the range size distributions commonly observed for macrobes...
November 21, 2017: Ecology
https://www.readbyqxmd.com/read/29160859/the-role-of-rnf213-4810g-a-and-4950g-a-variants-in-patients-with-moyamoya-disease-in-korea
#8
Young Seok Park, Hui Jeong An, Jung Oh Kim, Won Seop Kim, In Bo Han, Ok Joon Kim, Nam Keun Kim, Dong-Seok Kim
Although a founder variant of RNF213 4810G>A is a major genetic risk factor for moyamoya disease (MMD) in East Asians, the frequency and disease susceptibility of RNF213 variants remain largely unknown. This study investigated the mutation analysis of RNF213 (4448, 4810, 4863, and 4950) between Korean MMD and healthy controls. We performed a polymerase chain reaction-restriction fragment length polymorphism analysis. To identify the association between RNF213 gene polymorphisms and MMD disease, we performed statistical analyses such as multivariable logistic regression and Fisher's exact test...
November 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29160840/cloning-and-molecular-characterization-of-an-alpha-glucosidase-malh-from-the-halophilic-archaeon-haloquadratum-walsbyi
#9
Mara F Cuebas-Irizarry, Ricardo A Irizarry-Caro, Carol López-Morales, Keyla M Badillo-Rivera, Carlos M Rodríguez-Minguela, Rafael Montalvo-Rodríguez
We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi. A 2349 bp region (Hqrw_2071) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated into plasmid pET28b(+), expressed in E. coli Rosetta cells, and the resulting protein purified by Ni-NTA affinity chromatography. The recombinant protein showed an estimated molecular mass of 87 kDa, consistent with the expected value of the annotated protein, and an optimal activity for the hydrolysis of α-PNPG was detected at 40 °C, and at pH 6...
November 21, 2017: Life
https://www.readbyqxmd.com/read/29160620/dna-methylation-of-mb-comt-in-malaysian-schizophrenia-patients
#10
Abd Rahim Nour El Huda, Ku Zaifah Norsidah, Rahim Mohd Nabil Fikri, Mohd Noor Hanisah, Abdullah Kartini, A Talib Norlelawati
AIM: This study examined catechol-O-methyltransferase (COMT) DNA methylation in the peripheral blood of schizophrenia patients and also in healthy controls to investigate its potential use as a peripheral biomarker of schizophrenia and its relationships with the clinical variables of schizophrenia patients. METHODS: We examined the DNA methylation levels of COMT using genomic DNA from the peripheral blood of schizophrenia patients (n = 138) and healthy control participants (n = 132); all were Malaysian Malays...
November 21, 2017: Psychiatry and Clinical Neurosciences
https://www.readbyqxmd.com/read/29160558/simpson-s-paradox-in-the-integrated-discrimination-improvement
#11
J Chipman, D Braun
The integrated discrimination improvement (IDI) is commonly used to compare two risk prediction models; it summarizes the extent a new model increases risk in events and decreases risk in non-events. The IDI averages risks across events and non-events and is therefore susceptible to Simpson's paradox. In some settings, adding a predictive covariate to a well calibrated model results in an overall negative (positive) IDI. However, if stratified by that same covariate, the strata-specific IDIs are positive (negative)...
December 10, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/29160301/new-insights-into-the-pharmacogenomics-of-antidepressant-response-from-the-gendep-and-star-d-studies-rare-variant-analysis-and-high-density-imputation
#12
C Fabbri, K E Tansey, R H Perlis, J Hauser, N Henigsberg, W Maier, O Mors, A Placentino, M Rietschel, D Souery, G Breen, C Curtis, L Sang-Hyuk, S Newhouse, H Patel, M Guipponi, N Perroud, G Bondolfi, M O'Donovan, G Lewis, J M Biernacka, R M Weinshilboum, A Farmer, K J Aitchison, I Craig, P McGuffin, R Uher, C M Lewis
Genome-wide association studies have generally failed to identify polymorphisms associated with antidepressant response. Possible reasons include limited coverage of genetic variants that this study tried to address by exome genotyping and dense imputation. A meta-analysis of Genome-Based Therapeutic Drugs for Depression (GENDEP) and Sequenced Treatment Alternatives to Relieve Depression (STAR*D) studies was performed at the single-nucleotide polymorphism (SNP), gene and pathway levels. Coverage of genetic variants was increased compared with previous studies by adding exome genotypes to previously available genome-wide data and using the Haplotype Reference Consortium panel for imputation...
November 21, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29160219/complete-sequences-of-4-viral-hemorrhagic-septicemia-virus-ivb-isolates-and-their-virulence-in-northern-pike-fry
#13
Rodman G Getchell, Emily R Cornwell, Steven Bogdanowicz, Jose Andrés, William N Batts, Gael Kurath, Rachel Breyta, Joanna G Choi, John M Farrell, Paul R Bowser
Four viral hemorrhagic septicemia virus (VHSV) genotype IVb isolates were sequenced, their genetic variation explored, and comparative virulence assayed with experimental infections of northern pike Esox lucius fry. In addition to the type strain MI03, the complete 11183 bp genome of the first round goby Neogobius melanostomus isolate from the St. Lawrence River, and the 2013 and 2014 isolates from gizzard shad Dorosoma cepedianum die-offs in Irondequoit Bay, Lake Ontario and Dunkirk Harbor, Lake Erie were all deep sequenced on an Illumina platform...
November 21, 2017: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/29160035/mosaic-uniparental-disomy-results-in-gm1-gangliosidosis-with-normal-enzyme-assay
#14
Kenneth A Myers, Mark F Bennett, Chung W Chow, Susan M Carden, Simone A Mandelstam, Melanie Bahlo, Ingrid E Scheffer
Inherited metabolic disorders are traditionally diagnosed using broad and expensive panels of screening tests, often including invasive skin and muscle biopsy. Proponents of next-generation genetic sequencing have argued that replacing these screening panels with whole exome sequencing (WES) would save money. Here, we present a complex patient in whom WES allowed diagnosis of GM1 gangliosidosis, caused by homozygous GLB1 mutations, resulting in β-galactosidase deficiency. A 10-year-old girl had progressive neurologic deterioration, macular cherry-red spot, and cornea verticillata...
November 21, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29160003/two-new-viruses-mcv1-and-mcv2-which-infect-marinitoga-bacteria-isolated-from-deep-sea-hydrothermal-vents-functional-and-genomic-analysis
#15
C Mercier, J Lossouarn, C L Nesbø, T H A Haverkamp, A C Baudoux, M Jebbar, N Bienvenu, S Thiroux, S Dupont, C Geslin
Viruses represent a driving force in the evolution of microorganisms including those thriving in extreme environments. However, our knowledge of the viral diversity associated to microorganisms inhabiting the deep-sea hydrothermal vents remains limited. The phylum of Thermotogae, including thermophilic bacteria, is well represented in this environment. Only one virus was described in this phylum, MPV1 carried by Marinitoga piezophila. In this study, we report on the functional and genomic characterization of two new bacterioviruses that infect bacteria from the Marinitoga genus...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29159924/using-the-icelandic-genealogical-database-to-define-the-familial-risk-of-primary-biliary-cholangitis
#16
K T Örnolfsson, S Olafsson, O M Bergmann, M E Gershwin, E S Björnsson
Hereditary factors in primary biliary cholangitis (PBC) have been well defined in genome wide-association studies but there is not much direct data available that define the relative risk for family members with an affected proband. An increased risk in first-degree relatives has been demonstrated in a variety of studies but data have been lacking on further detailed associations for subsequent generations. The objective of the study was to use the unique Icelandic genealogical database to study the familiality of PBC...
November 21, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29159508/comparative-genomics-and-transcriptome-analysis-of-lactobacillus-rhamnosus-atcc-11443-and-the-mutant-strain-sct-10-10-60-with-enhanced-l-lactic-acid-production-capacity
#17
Liang Sun, Zhilong Lu, Jianxiu Li, Feifei Sun, Ribo Huang
Mechanisms for high L-lactic acid production remain unclear in many bacteria. Lactobacillus rhamnosus SCT-10-10-60 was previously obtained from L. rhamnosus ATCC 11443 via mutagenesis and showed improved L-lactic acid production. In this study, the genomes of strains SCT-10-10-60 and ATCC 11443 were sequenced. Both genomes are a circular chromosome, 2.99 Mb in length with a GC content of approximately 46.8%. Eight split genes were identified in strain SCT-10-10-60, including two LytR family transcriptional regulators, two Rex redox-sensing transcriptional repressors, and four ABC transporters...
November 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29159421/qtl-mapping-of-downy-and-powdery-mildew-resistances-in-pi-197088-cucumber-with-genotyping-by-sequencing-in-ril-population
#18
Yuhui Wang, Kyle VandenLangenberg, Changlong Wen, Todd C Wehner, Yiqun Weng
Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'...
November 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29158986/comparative-analysis-of-prophages-in-streptococcus-mutans-genomes
#19
Tiwei Fu, Xiangyu Fan, Quanxin Long, Wanyan Deng, Jinlin Song, Enyi Huang
Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C...
2017: PeerJ
https://www.readbyqxmd.com/read/29158966/mitochondrial-genomes-of-three-tetrigoidea-species-and-phylogeny-of-tetrigoidea
#20
Li-Liang Lin, Xue-Juan Li, Hong-Li Zhang, Zhe-Min Zheng
The mitochondrial genomes (mitogenomes) of Formosatettix qinlingensis, Coptotettix longjiangensis and Thoradonta obtusilobata (Orthoptera: Caelifera: Tetrigoidea) were sequenced in this study, and almost the entire mitogenomes of these species were determined. The mitogenome sequences obtained for the three species were 15,180, 14,495 and 14,538 bp in length, respectively, and each sequence included 13 protein-coding genes (PCGs), partial sequences of rRNA genes (rRNAs), tRNA genes (tRNAs) and a A + T-rich region...
2017: PeerJ
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