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Genes & Genetic Systems

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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
#1
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
#2
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
#3
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/28003573/a-novel-missense-variant-in-the-diaph1-gene-in-a-korean-family-with-autosomal-dominant-nonsyndromic-hearing-loss
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27301279/engineering-of-chimeric-eukaryotic-bacterial-rubisco-large-subunits-in-escherichia-coli
#13
Teng Wei Koay, Hann Ling Wong, Boon Hoe Lim
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a rate-limiting photosynthetic enzyme that catalyzes carbon fixation in the Calvin cycle. Much interest has been devoted to engineering this ubiquitous enzyme with the goal of increasing plant growth. However, experiments that have successfully produced improved Rubisco variants, via directed evolution in Escherichia coli, are limited to bacterial Rubisco because the eukaryotic holoenzyme cannot be produced in E. coli. The present study attempts to determine the specific differences between bacterial and eukaryotic Rubisco large subunit primary structure that are responsible for preventing heterologous eukaryotic holoenzyme formation in E...
November 26, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27150717/systematic-identification-of-synthetic-lethal-mutations-with-reduced-genome-escherichia-coli-synthetic-genetic-interactions-among-yoaa-xtha-and-holc-related-to-survival-from-mms-exposure
#14
Keisuke Watanabe, Kento Tominaga, Maiko Kitamura, Jun-Ichi Kato
Reduced-genome Escherichia coli strains lacking up to 38.9% of the parental chromosome have been constructed by combining large-scale chromosome deletion mutations. Functionally redundant genes involved in essential processes can be systematically identified using these reduced-genome strains. One large-scale chromosome deletion mutation could be introduced into the wild-type strain but not into the largest reduced-genome strain, suggesting a synthetic lethal interaction between genes removed by the deletion and those already absent in the reduced-genome strain...
November 26, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27074981/diversity-evaluation-based-on-morphological-physiological-and-isozyme-variation-in-genetic-resources-of-garlic-allium-sativum-l-collected-worldwide
#15
Sho Hirata, Mostafa Abdelrahman, Naoki Yamauchi, Masayoshi Shigyo
The aim of this study was to obtain primary information about the global diversity of garlic (Allium sativum L.) by evaluating morphological, physiological and isozyme variation. A total of 107 garlic accessions collected worldwide were grown in Yamaguchi, Japan. Five morphological traits (bulb weight, bulb diameter, number of cloves per bulb, number of bulbils and scape length) and one physiological trait (bolting period) of the collected garlic showed wide variation. Meanwhile, a total of 140 garlic accessions, including the 107 mentioned above, were characterized by leucine aminopeptidase (LAP) and phosphoglucoisomerase (PGI) isozyme analyses; they clearly showed polymorphisms in putative isozyme loci (Lap-1, Lap-2 and Pgi-1)...
November 26, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27853052/co-evolution-in-a-putative-bundling-signal-of-bluetongue-and-epizootic-hemorrhagic-disease-viruses
#16
Yoshiyuki Suzuki
Bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV) possess a genome of 10 segmented RNAs (S1-S10), one copy of each of which is considered to be packaged in a virion. This selective packaging is thought to be mediated by supramolecular complex formation of the 10 RNAs, through intermolecular base pairing of complementary nucleotide sequences termed the bundling signal. Here, the whole genomic sequences of BTV and EHDV isolates were analyzed to identify co-evolving pairs of complementary nucleotide sequences within and between genomic segments...
November 15, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27853051/expression-efficiency-of-nat2-haplotypes-in-a-korean-population
#17
Han Sung Na, Jin Sol Lee, Hyun Sub Cheong, Hee Jung Shin, Tae Sun Kang, Hyun Joo Park, Hyoung Doo Shin, Myeon Woo Chung
Since NAT2 single-nucleotide polymorphisms (SNPs) are responsible for the efficacy of arylamines and hydrazine drugs, defining the effects of these SNPs in various ethnicities is an important factor in the development of personalized medicine. In the present study, we examined the expression efficiency of NAT2 using promoter haplotypes identified in a Korean population. To construct NAT2 promoter haplotypes, seven NAT2 promoter SNPs (rs4646241, rs4646242, rs4646243, rs4646267, rs4345600, rs4271002, and rs4646246) were genotyped in a total of 192 Korean subjects...
November 15, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27628130/interspecific-hybrids-of-dwarf-hamsters-and-phasianidae-birds-as-animal-models-for-studying-the-genetic-and-developmental-basis-of-hybrid-incompatibility
#18
REVIEW
Satoshi Ishishita, Yoichi Matsuda
Hybrid incompatibility is important in speciation as it prevents gene flow between closely related populations. Reduced fitness from hybrid incompatibility may also reinforce prezygotic reproductive isolation between sympatric populations. However, the genetic and developmental basis of hybrid incompatibility in higher vertebrates remains poorly understood. Mammals and birds, both amniotes, have similar developmental processes, but marked differences in development such as the XY/ZW sex determination systems and the presence or absence of genomic imprinting...
October 13, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27592684/emerging-links-between-iron-sulfur-clusters-and-5-methylcytosine-base-excision-repair-in-plants
#19
REVIEW
Diana Mihaela Buzas
Iron-sulfur (Fe-S) clusters are ancient cofactors present in all kingdoms of life. Both the Fe-S cluster assembly machineries and target apoproteins are distributed across different subcellular compartments. The essential function of Fe-S clusters in nuclear enzymes is particularly difficult to study. The base excision repair (BER) pathway guards the integrity of DNA; enzymes from the DEMETER family of DNA glycosylases in plants are Fe-S cluster-dependent and extend the BER repertowere to excision of 5-methylcytosine (5mC)...
October 13, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27301281/toward-conservation-of-genetic-and-phenotypic-diversity-in-japanese-sticklebacks
#20
REVIEW
Jun Kitano, Seiichi Mori
Stickleback fishes have been established as a leading model system for studying the genetic mechanisms that underlie naturally occurring phenotypic diversification. Because of the tremendous diversification achieved by stickleback species in various environments, different geographical populations have unique phenotypes and genotypes, which provide us with unique opportunities for evolutionary genetic research. Among sticklebacks, Japanese species have several unique characteristics that have not been found in other populations...
October 13, 2016: Genes & Genetic Systems
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