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Comparative genomics

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https://www.readbyqxmd.com/read/28646637/ts-gene-polymorphisms-correlate-with-susceptibility-to-acute-lymphocytic-leukemia-in-children
#1
Runyin Zou, Xiangling He, Yanpeng Wu, Xin Tian, Yalan You, Mincui Zheng, Wanli Li, Hui Zou, Hua Liu, Xiujuan Zhu, Chengguang Zhu
BACKGROUND Acute lymphocytic leukemia (ALL) in children is a clonal disease of bone marrow hematopoietic stem cells. This study aimed to explore the associations between MTHFR or TS genetic polymorphisms and susceptibility to acute lymphocytic leukemia (ALL) in children. MATERIAL AND METHODS This case-control study included 79 ALL patients (case group) and 102 non-ALL patients (control group). Post-PCR genomic DNA sequencing revealed MTHFR C677T and MTHFR A1298C genotypes and TS polymorphisms. The χ² test was used to compare differences in MTHFR and TS polymorphisms (including genotypic and allelic distributions) between groups...
June 24, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28646502/the-liver-gut-microbiota-axis-modulates-hepatotoxicity-of-tacrine-in-the-rat
#2
Lian Yee Yip, Chiu Cheong Aw, Sze Han Lee, Yi Shuen Hong, Han Chen Ku, Winston Hecheng Xu, Jessalyn Mei Xuan Chan, Eleanor Jing Yi Cheong, Kern Rei Chng, Amanda Hui Qi Ng, Niranjan Nagarajan, Ratha Mahendran, Yuan Kun Lee, Edward R Browne, Eric Chun Yong Chan
The gut microbiota possesses diverse metabolic activities but its contribution towards heterogeneous toxicological responses is poorly understood. Here, we elucidate the role of the liver-gut microbiota axis in underpinning the hepatotoxicity of tacrine. We employed an integrated strategy combining pharmacokinetics, toxicology, metabonomics, genomics and metagenomics to elucidate and validate the mechanism of tacrine-induced hepatotoxicity in Lister hooded rats. Pharmacokinetic studies in rats demonstrated 3...
June 23, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28646115/genome-analysis-of-endomicrobium-proavitum-suggests-loss-and-gain-of-relevant-functions-during-the-evolution-of-intracellular-symbionts
#3
Hao Zheng, Carsten Dietrich, Andreas Brune
Bacterial endosymbionts of eukaryotes show progressive genome erosion, but detailed investigations of the evolutionary processes involved in the transition to an intracellular lifestyle are generally hampered by the lack of extant free-living lineages. Here, we characterize the genome of the recently isolated, free-living Endomicrobium proavitum, the second member of the Elusimicrobia phylum brought into pure culture, and compare it to the closely related "Candidatus Endomicrobium trichonymphae" strain Rs-D17, a previously described but uncultured endosymbiont of termite gut flagellates...
June 23, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28645872/two-obesity-susceptibility-loci-in-lyplal1-and-etv5-independently-associated-with-childhood-hypertension-in-chinese-population
#4
Duo Lv, Dan Zhou, Yan Zhang, Shuai Zhang, Yi-Min Zhu
AIMS: Genome-wide association studies have identified novel obesity-associated susceptibility loci. Associations of these variants with childhood obesity have been studied in our previous research. The purpose of this study is to investigate if these loci are associated with hypertension being independent of obesity in Chinese children and adolescents. METHODS: Nineteen candidate SNPs were genotyped using Sequenom MassARRAY platform among Chinese children (N=2954, 514 hypertension and 2440 controls, aged 7-17years)...
June 20, 2017: Gene
https://www.readbyqxmd.com/read/28645767/assessing-the-potential-of-rad-sequencing-to-resolve-phylogenetic-relationships-within-species-radiations-the-fly-genus-chiastocheta-diptera-anthomyiidae-as-a-case-study
#5
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic markers, which have been widely used notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies, but phylogenies for closely related species have been resolved at a much higher detail in the last couple of years with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation...
June 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28645745/dna-methylation-of-dlg4-and-gja-1-of-human-hippocampus-and-prefrontal-cortex-in-major-depression-is-unchanged-in-comparison-to-healthy-individuals
#6
Oliver Kaut, Amit Sharma, Ina Schmitt, René Hurlemann, Ullrich Wüllner
Epigenetic alterations provide a potential mechanism to account for the numerous gene-environment interactions that have been reported in association with neuropsychiatric phenotypes. In context to major depression disorder (MDD), where postmortem and neuroimaging studies provide insights into dysfunctional brain regions, involvement of genetic heterogeneity also revealed the complexity of this disorder. Despite intensive research during the past several decades and information from genome wide studies, pathophysiology of depressive disorders remained elusive...
June 20, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28645369/sequencing-dna-for-the-oxidatively-modified-base-8-oxo-7-8-dihydroguanine
#7
Aaron M Fleming, Yun Ding, Cynthia J Burrows
The DNA base guanine (G) can be oxidatively modified to 8-oxo-7,8-dihydroguanine (OG). Extraction of genomic DNA followed by nuclease digestion and mass spectrometry analysis has found OG is present at background levels of ~1 out of 10(6) Gs; however, this approach cannot determine the locations for the OGs in the genome. Thus, in this methods report, we outline three different methods (A, B, and C) for sequencing OG in DNA. Method A sequences OG by utilizing the base excision repair pathway to delete the OG nucleotide from the DNA that is then detected by Sanger sequencing as a deletion signature...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28645331/circadian-clock-gene-polymorphisms-in-relation-to-sleep-patterns-and-obesity-in-african-americans-findings-from-the-jackson-heart-study
#8
Pia Riestra, Samson Y Gebreab, Ruihua Xu, Rumana J Khan, Amadou Gaye, Adolfo Correa, Nancy Min, Mario Sims, Sharon K Davis
BACKGROUND: Circadian rhythms regulate key biological processes and the dysregulation of the intrinsic clock mechanism affects sleep patterns and obesity onset. The CLOCK (circadian locomotor output cycles protein kaput) gene encodes a core transcription factor of the molecular circadian clock influencing diverse metabolic pathways, including glucose and lipid homeostasis. The primary objective of this study was to evaluate the associations between CLOCK single nucleotide polymorphisms (SNPs) and body mass index (BMI)...
June 23, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28645290/establishment-of-an-orthotopic-patient-derived-xenograft-mouse-model-using-uveal-melanoma-hepatic-metastasis
#9
Ken Kageyama, Masahiro Ohara, Kengo Saito, Shinji Ozaki, Mizue Terai, Michael J Mastrangelo, Paolo Fortina, Andrew E Aplin, Takami Sato
BACKGROUND: Metastatic uveal melanoma is a highly fatal disease; most patients die from their hepatic metastasis within 1 year. A major drawback in the development of new treatments for metastatic uveal melanoma is the difficulty in obtaining appropriate cell lines and the lack of appropriate animal models. Patient-derived xenograft (PDX) tumor models, bearing ectopically implanted tumors at a subcutaneous site, have been developed. However, these ectopically implanted PDX models have obstacles to translational research, including a low engraftment rate, slow tumor growth, and biological changes after multiple passages due to the different microenvironment...
June 23, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28645264/molecular-cloning-structure-phylogeny-and-expression-analysis-of-the-invertase-gene-family-in-sugarcane
#10
Liming Wang, Yuexia Zheng, Shihui Ding, Qing Zhang, Youqiang Chen, Jisen Zhang
BACKGROUND: Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and their expression patterns are unknown in sugarcane due to its complex genome despite their significance in sucrose metabolism. RESULTS: In this study, based on comparative genomics, eleven cDNA and twelve DNA sequences belonging to 14 non-redundant members of the invertase gene family were successfully cloned from sugarcane...
June 23, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28645261/genome-wide-analysis-of-udp-glycosyltransferase-super-family-in-brassica-rapa-and-brassica-oleracea-reveals-its-evolutionary-history-and-functional-characterization
#11
Jingyin Yu, Fan Hu, Komivi Dossa, Zhaokai Wang, Tao Ke
BACKGROUND: Glycosyltransferases comprise a highly divergent and polyphyletic multigene family that is involved in widespread modification of plant secondary metabolites in a process called glycosylation. According to conserved domains identified in their amino acid sequences, these glycosyltransferases can be classified into a single UDP-glycosyltransferase (UGT) 1 superfamily. RESULTS: We performed genome-wide comparative analysis of UGT genes to trace evolutionary history in algae, bryophytes, pteridophytes, and angiosperms; then, we further investigated the expansion mechanisms and function characterization of UGT gene families in Brassica rapa and Brassica oleracea...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28645245/transcriptomic-dynamics-in-soybean-near-isogenic-lines-differing-in-alleles-for-an-aphid-resistance-gene-following-infestation-by-soybean-aphid-biotype-2
#12
Sungwoo Lee, Bryan J Cassone, Asela Wijeratne, Tae-Hwan Jun, Andrew P Michel, M A Rouf Mian
BACKGROUND: Genetic resistance of soybean [Glycine max (L.) Merr] against Aphis glycines provides effective management of this invasive pest, though the underlying molecular mechanisms are largely unknown. This study aimed to investigate genome-wide changes in gene expressions of soybean near-isogenic lines (NILs) either with the Rag5 allele for resistance or the rag5 allele for susceptibility to the aphid following infestation with soybean aphid biotype 2. RESULTS: The resistant (R)-NIL responded more rapidly to aphid infestation than the susceptible (S)-NIL, with differential expressions of 2496 genes during first 12 h of infestation (hai), compared to the aphid-free control...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28645144/increased-alignment-sensitivity-improves-the-usage-of-genome-alignments-for-comparative-gene-annotation
#13
Virag Sharma, Michael Hiller
Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28644986/designing-novel-inhibitors-against-histone-acetyltransferase-hat-%C3%A2-gcn5-of-plasmodium-falciparum
#14
Amarjeet Kumar, Krishanu Bhowmick, Kunwar Somesh Vikramdeo, Neelima Mondal, Naidu Subbarao, Suman Kumar Dhar
During active proliferation phase of intra-erythrocytic cycle, the genome of P. falciparum is regulated epigenetically and evolutionary conserved parasite-specific histone proteins are extensively acetylated. The reversible process of lysine acetylation, causing transcriptional activation and its deacetylation, causing transcriptional repression is regulated by balanced activities of HATs and HDACs. They are also known to regulate antigenic variations and gametocytic conversion in P. falciparum. These histone modifying enzymes have been identified as potential targets for development of anitmalarials in literature...
June 10, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28644509/comparative-transcriptomic-analysis-of-two-important-life-stages-of-angiostrongylus-cantonensis-fifth-stage-larvae-and-female-adults
#15
Liang Yu, Binbin Cao, Ying Long, Meks Tukayo, Chonglv Feng, Wenzhen Fang, Damin Luo
The mechanisms involved in the fast growth of Angiostrongylus cantonensis from fifth-stage larvae (L5) to female adults and how L5 breaks through the blood-brain barrier in a permissive host remain unclear. In this work, we compared the transcriptomes of these two life stages to identify the main factors involved in the rapid growth and transition to adulthood. RNA samples from the two stages were sequenced and assembled de novo. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of 1,346 differentially expressed genes between L5 and female adults was then undertaken...
April 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28644138/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#16
Danielle M Greenawalt, Winnie S Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enriquez, Rebecca Halperin, Ambar Ahmed, Vladislav Saveliev, John Carpten, David Craig, J Carl Barrett, Brian Dougherty, Michael Zinda, Stephen Fawell, Jonathan R Dry, Kate Byth
Current understanding of the mutation spectrum of relapsed/refractory (RR) tumors is limited. We performed whole exome sequencing (WES) on 47 diffuse large B cell lymphoma (DLBCL) tumors that persisted after R-CHOP treatment, 8 matched to primary biopsies. We compared genomic alterations from the RR cohort against two treatment-naïve DLBCL cohorts (n=112). While the overall number and types of mutations did not differ significantly, we identified frequency changes in DLBCL driver genes. The overall frequency of MYD88 mutant samples increased (12% to 19%), but we noted a decrease in p...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644126/extensive-horizontal-gene-transfer-in-cheese-associated-bacteria
#17
Kevin S Bonham, Benjamin E Wolfe, Rachel J Dutton
Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,844 protein coding genes...
June 23, 2017: ELife
https://www.readbyqxmd.com/read/28643740/telomere-length-variation-and-expression-analysis-of-shelterin-complex-genes-during-gallbladder-carcinogenesis
#18
Satish S Poojary, Gunja Mishra, Tekcham Dinesh Singh, Sanjiv Gupta, Braj Raj Shrivastav, Pramod Kumar Tiwari
BACKGROUND: Telomeres, which are bound with shelterin protein complex, play an important role in maintaining genomic stability and its dysfunction may lead to carcinogenesis. Here, we aimed to analyze whether shelterin complex gene expression and telomere length variation, play any role in gallbladder carcinogenesis. METHODS: Telomere length analysis was carried out by monochrome multiplex qPCR, whereas expression analysis of shelterin genes was carried out using RT-qPCR...
April 2017: Journal of Cancer Research and Therapeutics
https://www.readbyqxmd.com/read/28643628/real-time-whole-genome-sequencing-for-surveillance-of-listeria-monocytogenes-france
#19
Alexandra Moura, Mathieu Tourdjman, Alexandre Leclercq, Estelle Hamelin, Edith Laurent, Nathalie Fredriksen, Dieter Van Cauteren, Hélène Bracq-Dieye, Pierre Thouvenot, Guillaume Vales, Nathalie Tessaud-Rita, Mylène M Maury, Andreea Alexandru, Alexis Criscuolo, Emmanuel Quevillon, Marie-Pierre Donguy, Vincent Enouf, Henriette de Valk, Sylvain Brisse, Marc Lecuit
During 2015-2016, we evaluated the performance of whole-genome sequencing (WGS) as a routine typing tool. Its added value for microbiological and epidemiologic surveillance of listeriosis was compared with that for pulsed-field gel electrophoresis (PFGE), the current standard method. A total of 2,743 Listeria monocytogenes isolates collected as part of routine surveillance were characterized in parallel by PFGE and core genome multilocus sequence typing (cgMLST) extracted from WGS. We investigated PFGE and cgMLST clusters containing human isolates...
September 15, 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28643557/pooled-sample-testing-for-bonamia-ostreae-a-tale-of-two-sybr-green-real-time-pcr-assays
#20
Henry S Lane, J Brian Jones, Wendy L McDonald
Pooled testing of samples is a common laboratory practice to increase efficiency and reduce expenses. We investigated the efficacy of 2 published SYBR Green real-time PCR assays when used to detect the haplosporidian parasite Bonamia ostreae in pooled samples of infected oyster tissue. Each PCR targets a different gene within the B. ostreae genome: the actin 1 gene or the 18S rRNA gene. Tissue homogenates (150 mg) of the New Zealand flat oyster Ostrea chilensis were spiked with ~1.5 × 10(3) purified B. ostreae cells to create experimental pools of 3, 5, and 10...
June 1, 2017: Journal of Veterinary Diagnostic Investigation
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