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Genes & Genetic Systems

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https://www.readbyqxmd.com/read/28408727/single-nucleotide-polymorphisms-of-the-il-12-gene-lead-to-a-higher-cancer-risk-a-meta-analysis-based-on-22-670-subjects
#1
Xiaohan Shi, Yingxian Jia, Xiaochuan Xie, Shangwei Li
The associations between interleukin-12 (IL-12) gene polymorphisms and cancer risk have been discussed extensively, with controversial results. Therefore, we conducted the present meta-analysis to better assess the potential roles of IL-12 gene variation in cancer occurrence. Eligible articles were found via PubMed, Medline, EMBASE, Google Scholar and CNKI. Odds ratios and 95% confidence intervals were used to evaluate the associations between IL-12 gene polymorphisms and cancer risk. Thirty-one studies with 10,749 cancer patients and 11,921 healthy subjects were included in the analyses...
April 12, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28381656/homologous-recombination-is-required-for-recovery-from-oxidative-dna-damage
#2
Michio Hayashi, Keiko Umezu
We have been studying the genetic events, including chromosome loss, chromosome rearrangements and intragenic point mutations, that are responsible for the deletion of a URA3 marker in a loss of heterozygosity (LOH) assay in the yeast Saccharomycess cerevisiae. With this assay, we previously showed that homologous recombination plays an important role in genome maintenance in response to DNA lesions that occur spontaneously in normally growing cells. Here, to investigate DNA lesions capable of triggering homologous recombination, we examined the effects of oxidative stress, a prominent cause of endogenous DNA damage, on LOH events...
April 3, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28381655/establishment-of-a-genome-wide-and-quantitative-protocol-for-assessment-of-transcriptional-activity-at-human-retrotransposon-l1-antisense-promoters
#3
Koichi Ishiguro, Saneyuki Higashino, Hideki Hirakawa, Shusei Sato, Yasunori Aizawa
Long interspersed element 1 (L1) retrotransposon sequences are widespread in the human genome, occupying ~500,000 locations. The majority of L1s have lost their retrotransposition capability, although a significant population of human L1s maintains bidirectional transcriptional activity from the internal promoter. While the sense promoter drives transcription of the entire L1 mRNA and leads to L1 retrotransposition, the antisense promoter (ASP) transcribes L1-gene chimeric RNAs that include neighboring exon sequences...
April 3, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28344191/transposition-of-insertion-sequence-is256bsu1-in-bacillus-subtilis-168-is-strictly-dependent-on-reca
#4
Motohiro Akashi, Shota Harada, Syunsuke Moki, Yuki Okouji, Kiwamu Takahashi, Shigeki Kada, Keigo Yamagami, Yasuhiko Sekine, Satoru Watanabe, Taku Chibazakura, Hirofumi Yoshikawa
We developed an insertion sequence transposition detection system called the "jumping cat assay" and applied it to the Bacillus subtilis chromosome using IS256Bsu1 derived from B. subtilis natto. The high frequency of transposition enabled us to explore host factors; combining the assay and genetic analyses revealed that recA is essential for the transposition of IS256Bsu1. Detailed analyses using various domain mutants of recA demonstrated that this essentiality is not related to the function of recA in homologous recombination...
March 24, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28344190/an-artificial-intelligence-approach-fit-for-trna-gene-studies-in-the-era-of-big-sequence-data
#5
Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura
Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions...
March 24, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28239025/the-role-of-single-nucleotide-variants-of-the-energy-metabolism-linked-genes-sirt3-ppargc1a-and-apoe-in-amyotrophic-lateral-sclerosis-risk
#6
Diego Albani, Elisabetta Pupillo, Elisa Bianchi, Armando Chierchia, Rosalba Martines, Gianluigi Forloni, Ettore Beghi
Amyotrophic lateral sclerosis (ALS) is a multifactorial disease, possibly with contributions from genetics and lifestyle. We examined variants in genes relevant to energy metabolism and physical activity in a case-control association study, with the aim of assessing genetics and physical activity as contributors to ALS risk. A well-characterized sample of Italian ALS patients (101) and controls (101) from the EURALS Consortium underwent a questionnaire interview on demographic, physical and other lifestyle habits, and venipuncture for DNA extraction...
February 24, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28228607/analysis-of-nuclear-mitochondrial-dnas-and-factors-affecting-patterns-of-integration-in-plant-species
#7
Takanori Yoshida, Hazuka Y Furihata, Akira Kawabe
Sequences homologous to organellar DNA that have been integrated into nuclear genomes are referred to as nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs). NUMTs in nine plant species were analyzed to reveal the integration patterns and possible factors involved. The cumulative lengths of NUMTs in two-thirds of species analyzed were greater than those of NUPTs observed in a previous study. The age distribution of NUMTs was similar to that of NUPTs, suggesting similar mechanisms for integration and degradation of both NUPTs and NUMTs...
February 22, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28216511/global-kinetoplastea-phylogeny-inferred-from-a-large-scale-multigene-alignment-including-parasitic-species-for-better-understanding-transitions-from-a-free-living-to-a-parasitic-lifestyle
#8
Euki Yazaki, Sohta A Ishikawa, Keitaro Kume, Akira Kumagai, Takashi Kamaishi, Goro Tanifuji, Tetsuo Hashimoto, Yuji Inagaki
All members of the order Trypanosomatida known to date are parasites that are most likely descendants of a free-living ancestor. Trypanosomatids are an excellent model to assess the transition from a free-living to a parasitic lifestyle, because a large amount of experimental data has been accumulated for well-studied members that are harmful to humans and livestock (Trypanosoma spp. and Leishmania spp.). However, recent advances in our understanding of the diversity of trypanosomatids and their close relatives (i...
February 20, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28216510/the-amount-of-dna-polymorphism-when-population-size-changes-linearly
#9
Takuya Takahashi, Fumio Tajima
Population size is one of the main factors that determine the amount of DNA polymorphism. We examined a model under which the population size changed linearly. Because of the simplicity of this model, we could analytically obtain the expectation of nucleotide diversity, E(π), and the expectation of the amount of DNA polymorphism, E(θ), based on the number of segregating sites. The results suggest that E(π) is larger than E(θ) when the population size decreased and that E(π) is smaller than E(θ) when the population size increased...
February 20, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28216509/development-of-microsatellite-markers-for-partially-and-putative-fully-mycoheterotrophic-varieties-of-pyrola-japonica-sensu-lato-ericaceae
#10
Kohtaroh Shutoh, Ayako Izuno, Yuji Isagi, Takahide Kurosawa, Shingo Kaneko
We developed microsatellite markers to compare the genetic variation and reproductive biology between the partially mycoheterotrophic Pyrola japonica var. japonica and the putative fully mycoheterotrophic P. japonica var. subaphylla. Fifteen primer pairs were developed for P. japonica sensu lato and they were tested on 77 ramets from three populations of the two varieties. Thirteen loci were polymorphic in at least one of the two var. japonica populations, whereas only four loci were polymorphic in the var...
February 20, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27582048/fudr-extends-the-lifespan-of-the-short-lived-ap-endonuclease-mutant-in-caenorhabditis-elegans-in-a-fertility-dependent-manner
#11
Yuichi Kato, Masahiro Miyaji, Qiu-Mei Zhang-Akiyama
The anticancer drug 5-fluorouracil (5-FU) and its metabolite 5-fluoro-2'-deoxyuridine (FUdR) inhibit thymidylate synthase and induce uracil bases in DNA. FUdR is commonly used for inhibiting fertility when measuring the lifespan of the nematode Caenorhabditis elegans. However, it is not known whether DNA damage induced by FUdR affects lifespan. EXO-3 is an apurinic/apyrimidinic endonuclease in C. elegans, and we reported previously that deletion of the exo-3 gene causes reproductive abnormalities and decreased lifespan...
March 17, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27557976/cretaceous-origin-of-giant-rhinoceros-beetles-dynastini-coleoptera-and-correlation-of-their-evolution-with-the-pangean-breakup
#12
Haofei Jin, Takahiro Yonezawa, Yang Zhong, Hirohisa Kishino, Masami Hasegawa
The giant rhinoceros beetles (Dynastini, Scarabaeidae, Coleoptera) are distributed in tropical and temperate regions in Asia, America and Africa. Recent molecular phylogenetic studies have revealed that the giant rhinoceros beetles can be divided into three clades representing Asia, America and Africa. Although a correlation between their evolution and the continental drift during the Pangean breakup was suggested, there is no accurate divergence time estimation among the three clades based on molecular data...
March 17, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27522959/genetic-analysis-of-rice-mutants-responsible-for-narrow-leaf-phenotype-and-reduced-vein-number
#13
Fumika Clara Kubo, Yukiko Yasui, Toshihiro Kumamaru, Yutaka Sato, Hiro-Yuki Hirano
Leaves are a major site for photosynthesis and a key determinant of plant architecture. Rice produces thin and slender leaves, which consist of the leaf blade and leaf sheath separated by the lamina joint. Two types of vasculature, the large and small vascular bundles, run in parallel, together with a strong structure, the midrib. In this paper, we examined the function of four genes that regulate the width of the leaf blade and the vein number: NARROW LEAF1 (NAL1), NAL2, NAL3 and NAL7. We backcrossed original mutants of these genes with the standard wild-type rice, Taichung 65...
March 17, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27522958/polar-patterning-of-the-spikelet-is-disrupted-in-the-two-opposite-lemma-mutant-in-rice
#14
Shige-Hiro Sugiyama, Wakana Tanaka, Hiro-Yuki Hirano
Angiosperms produce diverse flowers and the pattern of floral symmetry is a major factor for flower diversification. Bilaterally symmetric flowers have evolved multiple times in different angiosperm lineages from radially symmetric ancestors. Whereas most monocots produce radially symmetric flowers, grasses such as rice (Oryza sativa) and maize (Zea mays) generate bilaterally symmetric flowers and spikelets. In this paper, we focused on the two opposite lemma (tol) mutant, which displays a pleiotropic phenotype in the spikelet...
March 17, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27452042/inter-and-intra-specific-genetic-divergence-of-asian-tiger-frogs-genus-hoplobatrachus-with-special-reference-to-the-population-structure-of-h-tigerinus-in-bangladesh
#15
Nasrin Sultana, Takeshi Igawa, Mohammed Mafizul Islam, Mahmudul Hasan, Mohammad Shafiqul Alam, Shohei Komaki, Kensuke Kawamura, Md Mukhlesur Rahman Khan, Masayuki Sumida
The five frog species of the genus Hoplobatrachus are widely distributed in Asia and Africa, with Asia being considered the genus' origin. However, the evolutionary relationships of Asian Hoplobatrachus species remain ambiguous. Additionally, genetic diversity and fundamental differentiation processes within species have not been studied. We conducted molecular phylogenetic analysis on Asian Hoplobatrachus frogs and population genetic analysis on H. tigerinus in Bangladesh using the mitochondrial CYTB gene and 21 microsatellite markers...
March 17, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27452041/amap-a-pipeline-for-whole-genome-mutation-detection-in-arabidopsis-thaliana
#16
Kotaro Ishii, Yusuke Kazama, Tomonari Hirano, Michiaki Hamada, Yukiteru Ono, Mieko Yamada, Tomoko Abe
Detection of mutations at the whole-genome level is now possible by the use of high-throughput sequencing. However, determining mutations is a time-consuming process due to the number of false positives provided by mutation-detecting programs. AMAP (automated mutation analysis pipeline) was developed to overcome this issue. AMAP integrates a set of well-validated programs for mapping (BWA), removal of potential PCR duplicates (Picard), realignment (GATK) and detection of mutations (SAMtools, GATK, Pindel, BreakDancer and CNVnator)...
March 17, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28003573/a-novel-missense-variant-in-the-diaph1-gene-in-a-korean-family-with-autosomal-dominant-nonsyndromic-hearing-loss
#17
Tae-Hun Kang, Jeong-In Baek, Borum Sagong, Hong-Joon Park, Chan Ik Park, Kyu-Yup Lee, Un-Kyung Kim
Hair cells in the cochlea display highly regulated actin polymerization, which is mediated by the human diaphanous-related formin 1 gene (DIAPH1; also called DFNA1, DIA1). DFNA1, the first type of autosomal dominant nonsyndromic hearing loss (ADNSHL), is known to be associated with mutations in DIAPH1. However, no genetic study of DFNA1 in Koreans with hearing loss has yet been reported. A 51-year-old patient in a Korean family with ADNSHL was examined by pure-tone audiometry, and genetic analysis of DIAPH1 was performed...
December 21, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28003572/geographical-variation-in-soil-bacterial-community-structure-in-tropical-forests-in-southeast-asia-and-temperate-forests-in-japan-based-on-pyrosequencing-analysis-of-16s-rrna
#18
Natsumi Ito, Hiroko Iwanaga, Suliana Charles, Bibian Diway, John Sabang, Lucy Chong, Satoshi Nanami, Koichi Kamiya, Shawn Lum, Ulfah J Siregar, Ko Harada, Naohiko T Miyashita
Geographical variation in soil bacterial community structure in 26 tropical forests in Southeast Asia (Malaysia, Indonesia and Singapore) and two temperate forests in Japan was investigated to elucidate the environmental factors and mechanisms that influence biogeography of soil bacterial diversity and composition. Despite substantial environmental differences, bacterial phyla were represented in similar proportions, with Acidobacteria and Proteobacteria the dominant phyla in all forests except one mangrove forest in Sarawak, although highly significant heterogeneity in frequency of individual phyla was detected among forests...
December 21, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28003571/identification-of-%C3%AE-globin-haplotypes-linked-to-sickle-hemoglobin-hb-s-alleles-in-mazandaran-province-iran
#19
Faeghe Aghajani, Mohammad Reza Mahdavi, Mehrnoush Kosaryan, Mehrad Mahdavi, Mohaddese Hamidi, Hossein Jalali
Carrier frequency of the β(S) allele has been reported to be 0.19% in Mazandaran province, northern Iran. Haplotype analysis of the β(S) allele helps trace the origin of its encoded hemoglobin (Hb) variant, Hb S, in a region. The aim of this study was to investigate the haplotypes associated with β(S) alleles in Mazandaran province. Capillary electrophoresis was carried out to detect individuals suspected to have a βS allele(s). DNA analysis (PCR-RFLP) was used for final confirmation. To identify 5\' to 3\' β-globin gene cluster haplotypes associated with β(S) alleles, family linkage analysis was applied...
December 21, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27990012/characterization-of-the-traf3ip1-gene-in-yesso-scallop-patinopecten-yessoensis-and-its-expression-in-response-to-bacterial-challenge
#20
Jie Cheng, Jing Wang, Shuyue Wang, Ruojiao Li, Xianhui Ning, Qiang Xing, Xiaoli Ma, Lingling Zhang, Shi Wang, Xiaoli Hu, Zhenmin Bao
Tumor necrosis factor receptor-associated factor 3 (TRAF3) is an important adaptor that transmits upstream activation signals to induce innate immune responses. TRAF3 interacting protein 1 (TRAF3IP1) interacts specifically with TRAF3, but its function in innate immunity remains unclear, especially in marine invertebrates. In this study, to better understand the functions of TRAFs in innate immune responses, we identified and characterized the first bivalve TRAF3IP1 gene, PyTRAF3IP1, from Yesso scallop (Patinopecten yessoensis), one of the most important mollusk species for aquaculture...
December 19, 2016: Genes & Genetic Systems
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