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Genes & Genetic Systems

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27980240/characterization-of-a-heat-activated-retrotransposon-in-natural-accessions-of-arabidopsis-thaliana
#16
Seiji Masuda, Kosuke Nozawa, Wataru Matsunaga, Yukari Masuta, Akira Kawabe, Atsushi Kato, Hidetaka Ito
Natural accessions are used for studying intraspecies genetic variation in the model plant Arabidopsis thaliana in order to address fundamental questions of evolution. Transposable elements are responsible for a wide range of mutations and play significant roles in shaping a genome over evolutionary time. In the present study, we aimed to characterize ONSEN, a heat-activated long terminal repeat (LTR) retrotransposon, in natural A. thaliana accessions. Southern blot analysis demonstrated that ONSEN was present in all the studied accessions, but the copy number was diverse...
December 14, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27941309/gene-interaction-at-seed-awning-loci-in-the-genetic-background-of-wild-rice
#17
Mai Ikemoto, Mitsuharu Otsuka, Pham Thien Thanh, Phuong Dang Thai Phan, Ryo Ishikawa, Takashige Ishii
Seed awning is one of the important traits for successful propagation in wild rice. During the domestication of rice by ancient humans, plants with awnless seeds may have been selected because long awns hindered collection and handling activities. To investigate domestication of awnless rice, QTL analysis for seed awning was first carried out using backcross recombinant inbred lines between Oryza sativa Nipponbare (recurrent parent) and O. rufipogon W630 (donor parent). Two strong QTLs were detected in the same regions as known major seed-awning loci, An-1 and RAE2...
December 9, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27452040/development-of-a-multiplex-methylight-assay-for-the-detection-of-dapk1-and-sox1-methylation-in-epithelial-ovarian-cancer-in-a-north-indian-population
#18
Manpreet Kaur, Alka Singh, Kiran Singh, Sameer Gupta, Manisha Sachan
Ovarian cancer is the fourth most common cancer in women worldwide. It is very heterogeneous at the clinical, histopathological and molecular levels and is caused by the accumulation of genetic and epigenetic changes in regulatory genes. More than 90% of ovarian cancers are epithelial in origin. Ovarian cancer is typically asymptomatic in its early stages, and, due to difficulties in early detection, most ovarian cancers are diagnosed at an advanced stage. The positive predictive value of CA-125, a routinely used serum protein marker, is < 30%; therefore, for effective screening, there is a need to develop a marker with high sensitivity for early detection...
November 26, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27321190/construction-and-characterization-of-a-bacterial-artificial-chromosome-library-for-mandarin-fish-siniperca-chuatsi-basilewsky
#19
Liyuan Lv, Xu-Fang Liang, Changxu Tian, Ling Li, Shan He, Wenjie Guo
Siniperca chuatsi (Basilewsky), a demersal piscivore, is an endemic freshwater fish species in China. For the purpose of genomics research, we have constructed the first bacterial artificial chromosome (BAC) library for S. chuatsi. The BAC library comprised a total of 84,480 clones with an average insert size of 124.6 kb and less than 2.5% empty clones, corresponding to a 10.5-fold coverage of the S. chuatsi genome. The probability of isolating genes of interest was more than 99%. To validate the library, we screened 220 superpools and found that 1-19 were positive for six SSR markers, while none was positive for two mitochondrial gene markers...
November 26, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27301280/gic1-is-a-novel-heterochromatin-boundary-protein-in-vivo
#20
Risa Mitsumori, Kaori Shinmyozu, Jun-Ichi Nakayama, Hiroyuki Uchida, Masaya Oki
In Saccharomyces cerevisiae, HMR/HML, telomeres and ribosomal DNA are heterochromatin-like regions in which gene transcription is prevented by the silent information regulator (Sir) complex. The Sir complex (Sir2, Sir3 and Sir4) can spread through chromatin from the silencer. Boundaries prevent Sir complex spreading, and we previously identified 55 boundary genes among all ~6,000 yeast genes. These boundary proteins can be distinguished into two types: those that activate transcription to prevent spreading of silencing, and those that prevent gene silencing by forming a boundary...
November 26, 2016: Genes & Genetic Systems
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