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Genes & Genetic Systems

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https://www.readbyqxmd.com/read/30416149/structural-and-sequence-diversity-of-eukaryotic-transposable-elements
#1
Kenji K Kojima
The majority of eukaryotic genomes contain a large fraction of repetitive sequences that primarily originate from transpositional bursts of transposable elements (TEs). Repbase serves as a database for eukaryotic repetitive sequences and has now become the largest collection of eukaryotic TEs. During the development of Repbase, many new superfamilies/lineages of TEs, which include Helitron, Polinton, Ginger and SINEU, were reported. The unique composition of protein domains and DNA motifs in TEs sometimes indicates novel mechanisms of transposition, replication, anti-suppression or proliferation...
November 9, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30381610/spontaneous-de-novo-germline-mutations-in-humans-and-mice-rates-spectra-causes-and-consequences
#2
Mizuki Ohno
Germline mutations are the origin of genetic variation and are widely considered to be the driving force of genome evolution. The rates and spectra of de novo mutations (DNMs) directly affect evolutionary speed and direction and thereby establish species-specific genomic futures in the long term. This has resulted in a keen interest in understanding the origin of germline mutations in mammals. Accumulating evidence from next-generation sequencing and family-based analysis indicates that the frequency of human DNMs varies according to sex, age and local genomic context...
November 1, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30369561/regulation-of-mcm2-7-function
#3
Yukio Ishimi
Recently published structural and functional analyses of the CMG complex have provided insight into the mechanism of its DNA helicase function and into the distinct roles of its central six component proteins MCM2-MCM7 (MCM2-7). To activate CMG helicase, the two protein kinases CDK and DDK, as well as MCM10, are required. In addition to the initiation of DNA replication, MCM function must be regulated at the DNA replication steps of elongation and termination. Polyubiquitylation of MCM7 is involved in terminating MCM function...
October 23, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30333384/functional-characterization-of-cynoglossus-semilaevis-r-spondin2-and-its-role-in-muscle-development-during-embryogenesis
#4
Bo Wang, Fan Yang, Rui Li, Xuemei Li, Xiaolong Wu, Zheng Sun, Jieming Zhai, Yan He, Jie Qi
R-spondin2 (Rspo2) is a member of the R-spondin family, which plays important roles in cell proliferation, cell fate determination and organogenesis. Rspo2 exhibits important functions during embryonic development and muscle maintenance in adult human, mouse and Xenopus. In the present study, the tongue sole Cynoglossus semilaevis Rspo2 (CsRspo2) gene was isolated and characterized, and its role in muscle development during embryogenesis was studied. Our results showed that CsRspo2 expression was abundant during gastrulation and significantly high during somite formation, but then decreased markedly after hatching...
October 18, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30270233/a-new-inference-method-for-detecting-an-ongoing-selective-sweep
#5
Naoko T Fujito, Yoko Satta, Toshiyuki Hayakawa, Naoyuki Takahata
A simple method was developed to detect signatures of ongoing selective sweeps in single nucleotide polymorphism (SNP) data. Based largely on the traditional site frequency spectrum (SFS), the method additionally incorporates linkage disequilibrium (LD) between pairs of SNP sites and uniquely represents both SFS and LD information as hierarchical "barcodes." This barcode representation allows the identification of a hitchhiking genomic region surrounding a putative target site of positive selection, or a core site...
September 30, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30185720/dsh5-a-dihydrosphingosine-c4-hydroxylase-gene-family-member-shows-spatially-restricted-expression-in-rice-and-is-lethal-when-expressed-ectopically
#6
Tomohiro Imamura, Chihiro Obata, Kazuyoshi Yoneyama, Masatoshi Ichikawa, Akane Ikura, Hiromi Mutsuro-Aoki, Toshiki Ishikawa, Maki Kawai-Yamada, Tadamasa Sasaki, Hiroaki Kusano, Hiroaki Shimada
Dihydrosphingosine C4 hydroxylase (DSH), a diiron-binding membrane enzyme, catalyzes the hydration of dihydrosphingosine and acyl-sphinganine to produce phytosphingosine and phytoceramide, respectively. Rice has two types of DSH homologs: general DSHs, namely DSH1, DSH2 and DSH4, and others that show spatial expression profiles, namely DSH3 and DSH5. The general DSHs exist in many plant species. These DSHs showed similarity in their functions and complemented the yeast sur2D mutation. In contrast, homologs of DSH3 and DSH5 were found only in monocot plants...
September 4, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30175721/identification-of-a-novel-myo6-mutation-associated-with-autosomal-dominant-non-syndromic-hearing-loss-in-a-chinese-family-by-whole-exome-sequencing
#7
Tao Tian, Yajie Lu, Jun Yao, Xin Cao, Qinjun Wei, Qi Li
Autosomal dominant non-syndromic hearing loss (ADNSHL) is characterized by postlingual progressive onset. Due to its high genetic heterogeneity, it is difficult to perform a molecular diagnosis for most patients with ADNSHL. In our study, whole-exome sequencing (WES) was used to screen pathogenic gene candidates by analyzing genomic DNA samples from a large Chinese family (JSNY-067), including the proband and her father, who suffered from non-syndromic hearing loss. The pathogenicity of candidate nonsynonymous variants in ADNSHL genes was evaluated by co-segregation analysis in family members by direct PCR and Sanger sequencing...
August 31, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30158334/an-albino-mutant-of-the-japanese-rat-snake-elaphe-climacophora-carries-a-nonsense-mutation-in-the-tyrosinase-gene
#8
Shuzo Iwanishi, Shohei Zaitsu, Hiroki Shibata, Eiji Nitasaka
The Japanese rat snake (Elaphe climacophora) is a common species in Japan and is widely distributed across the Japanese islands. An albino mutant of the Japanese rat snake ("pet trade" albino) has been bred and traded by hobbyists for around two decades because of its remarkable light-yellowish coloration with red eyes, attributable to a lack of melanin. Another albino Japanese rat snake mutant found in a natural population of the Japanese rat snake at high frequency in Iwakuni City, Yamaguchi Prefecture is known as "Iwakuni no Shirohebi"...
August 30, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30135335/the-mitochondrial-genome-of-an-asymmetrically-cell-fused-rapeseed-brassica-napus-containing-a-radish-derived-cytoplasmic-male-sterility-associated-gene
#9
Shin-Ichi Arimura, Shungo Yanase, Nobuhiro Tsutsumi, Nobuya Koizuka
Cytoplasmic male sterility (CMS) is an agronomically important trait whose causative genes are located in the mitochondrial genome. A CMS rapeseed, Brassica napus 'SW18', was made 25 years ago by an asymmetric (or "donor-recipient") cell fusion between B. napus 'Westar' and a CMS radish (Raphanus sativus 'Kosena'), in order to transfer the radish CMS-associated gene without disturbing the rapeseed features. Here, we determined the nucleotide sequences of the mitochondrial genomes of Kosena radish and SW18...
August 23, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30089747/cytological-observation-of-chromosome-breakage-in-wheat-male-gametophytes-caused-by-gametocidal-action-of-aegilops-triuncialis-derived-chromosome-3c-t
#10
Kazuki Murata, Shota Watanabe, Hisashi Tsujimoto, Shuhei Nasuda
In this study, we investigated the chromosome breakage caused by gametocidal (Gc) chromosome 3Ct and its interaction with the suppressor gene Igc1 (inhibitor of gametocidal gene 1) on wheat chromosome 3B. We demonstrated cytologically that patterns of 3Ct -induced chromosomal fragmentation in microspores differed from patterns observed for other Gc genes. Uninuclear microspores of the monosomic 3Ct addition line had high frequencies of micronuclei, possibly explaining its low fertility. Chromosome fragmentation was observed in prometaphase and metaphase of the first pollen mitosis in the monosomic 3Ct addition line...
October 30, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/30078824/two-polymorphisms-rs2046210-and-rs3803662-are-associated-with-breast-cancer-risk-in-a-vietnamese-case-control-cohort
#11
Nguyen Thi Ngoc Thanh, Nguyen Thi Tuyet Lan, Phan Thanh Phat, Nguyen Dien Thanh Giang, Nguyen Thi Hue
Breast cancer is the most common cancer in women worldwide. Breast tumorigenesis encompasses both extrinsic and intrinsic factors. Among intrinsic aspects, the appearance of DNA variation can cause genetic instability, which may lead to carcinogenesis. Genome-wide association studies have found several potential breast cancer-associated single nucleotide polymorphisms (SNPs) in many different populations. Among these, seven (rs2046210, rs1219648, rs3817198, rs3803662, rs889312, rs10941679 and rs13281615) have been shown to be significantly associated with breast cancer risk in various populations including those very similar to the Vietnamese...
October 30, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29998908/light-is-required-for-proper-female-mate-choice-between-winged-and-wingless-males-in-drosophila
#12
Kazuki Watanabe, Yuki Suzuki, Show Inami, Hirono Ohashi, Takaomi Sakai
In many animal species, females choose potential mating partners according to their own preferences. Thus, female preference-based mate choice affects intraspecific mating success and prevents interspecific mating. To clarify the neuronal basis of female mate choice, it is essential to identify the important relevant sensory cues. In the fruitfly Drosophila melanogaster, the courtship song of males promotes female sexual receptivity. When wild-type virgin females can freely choose one of two types of courting males (winged or wingless males), they prefer to mate with winged males...
October 30, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29998907/the-scallop-igf2-mrna-binding-protein-gene-pyimp-and-association-of-a-synonymous-mutation-with-growth-traits
#13
Xianhui Ning, Liying Feng, Xue Li, Shuyue Wang, Mengran Zhang, Shi Wang, Lingling Zhang, Xiaoli Hu, Zhenmin Bao
Insulin-like growth factor 2 mRNA-binding proteins (IMPs) function in localization, stability and translational control of their target RNAs. In this study, we identified an IMP gene (PyIMP) from Yesso scallop, Patinopecten yessoensis. The complete DNA sequence of PyIMP was 22,875 bp, consisting of seventeen exons and sixteen introns. The full-length cDNA sequence was 3,293 bp, with an open reading frame of 1,776 bp, encoding 592 amino acids. PyIMP exhibited characters typical of IMPs, namely two RNA recognition motifs and four hnRNP K homology domains...
October 30, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28993555/complete-chloroplast-genome-and-45s-nrdna-sequences-of-the-medicinal-plant-species-glycyrrhiza-glabra-and-glycyrrhiza-uralensis
#14
Sang-Ho Kang, Jeong-Hoon Lee, Hyun Oh Lee, Byoung Ohg Ahn, So Youn Won, Seong-Han Sohn, Jung Sun Kim
Glycyrrhiza uralensis and G. glabra, members of the Fabaceae, are medicinally important species that are native to Asia and Europe. Extracts from these plants are widely used as natural sweeteners because of their much greater sweetness than sucrose. In this study, the three complete chloroplast genomes and five 45S nuclear ribosomal (nr)DNA sequences of these two licorice species and an interspecific hybrid are presented. The chloroplast genomes of G. glabra, G. uralensis and G. glabra × G. uralensis were 127,895 bp, 127,716 bp and 127,939 bp, respectively...
October 30, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29343671/development-of-microsatellite-markers-for-the-endangered-orchid-calanthe-izu-insularis-orchidaceae
#15
Naoyuki Nakahama, Azusa Ito, Shingo Kaneko, Yu Matsuki, Yoshihisa Suyama, Azusa Hayano, Miho Murayama, Yuji Isagi
Microsatellite markers were developed for the endangered orchid Calanthe izu-insularis (Orchidaceae). This species is unique to the Izu Islands in Japan. Unfortunately, its population size has decreased because of excessive collection for horticultural purposes. In addition, although natural hybridization between C. izu-insularis and C. discolor var. discolor has been reported, morphological differences between C. izu-insularis and the hybridized individuals remain unclear. Using next-generation sequencing, 11 polymorphic microsatellite markers were developed...
July 13, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29343669/direct-interaction-between-vrn1-protein-and-the-promoter-region-of-the-wheat-ft-gene
#16
Chihiro Tanaka, Takafumi Itoh, Yukimoto Iwasaki, Nobuyuki Mizuno, Shuhei Nasuda, Koji Murai
The wheat florigen gene Wheat FLOWERING LOCUS T (WFT, which is identical to VRN3) is an integrator of the vernalization, photoperiod and autonomous pathways in wheat flowering. Many studies have indicated that VERNALIZATION 1 (VRN1) directly or indirectly up-regulates WFT expression in leaves. VRN1 encodes an APETALA1/FRUITFULL-like MADS box transcription factor that is up-regulated by vernalization and aging, leading to promotion of flowering. In this study, the VRN1 protein was expressed as a His-Tag fusion protein in Escherichia coli and used in an electrophoretic mobility shift assay (EMSA)...
July 13, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29343667/genotypic-effects-on-sugar-and-by-products-of-liquid-hydrolysates-and-on-saccharification-of-acid-insoluble-residues-from-wheat-straw
#17
Ryoko Ohno, Hiroshi Teramura, Chiaki Ogino, Akihiko Kondo, Shigeo Takumi
Wheat straw is one of the major attractive resources for low-cost raw materials for renewable energy, biofuels and biochemicals. However, like other sources of lignocellulosic biomass, straw is a heterogeneous material due to its mixed origin from different tissue and cell types. Here, to examine the genotypic effects on biorefinery usage of wheat straw, straw obtained from different wheat cultivars and experimental lines was pretreated with dilute acid. Significant differences between cultivars were observed in the concentrations of glucose and toxic by-products of the liquid hydrolysates...
July 13, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29343666/the-c-terminal-extension-domain-of-saccharomyces-cerevisiae-mrpl32-a-homolog-of-ribosomal-protein-l32-functions-in-trans-to-support-mitochondrial-translation
#18
Ivo Ngundu Woogeng, Madoka Kitakawa
Mitochondrial ribosomal protein L32 (MrpL32) of Saccharomyces cerevisiae is homologous to the bacterial L32 ribosomal protein. MrpL32 carries an N-terminal mitochondrion-targeting sequence (MTS) and is about 60 amino acid residues longer at the C-terminus. Adding to its function as a leader sequence, the MTS of MrpL32 has been reported to regulate ribosome biogenesis through its processing by m-AAA protease. However, the function of the C-terminal extension (CE) remains totally unknown. Therefore, we constructed a series of C-terminally truncated mrpl32 (mrpl32ΔC) genes and expressed them in a Δmrpl32 mutant to examine their function...
July 13, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29343665/molecular-characterization-of-gliadins-of-chinese-spring-wheat-in-relation-to-celiac-disease-elicitors
#19
Kanako Kawaura, Mayuko Miura, Yoko Kamei, Tatsuya M Ikeda, Yasunari Ogihara
The wheat seed storage proteins gliadin and glutenin are encoded by multigenes. Gliadins are further classified into α-, γ-, δ- and ω-gliadins. Genes encoding α-gliadins belong to a large multigene family, whose members are located on the homoeologous group 6 chromosomes at the Gli-2 loci. Genes encoding other gliadins are located on the homoeologous group 1 chromosomes at the Gli-1 loci. Two-dimensional polyacrylamide gel electrophoresis (2-DE) was used to characterize and profile the gliadins. The gliadins in aneuploid Chinese Spring wheat lines were then compared in this study...
July 13, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29151455/piggybac-and-phic31-integrase-mediated-transgenesis-in-drosophila-prolongata
#20
Ayumi Kudo, Takeshi Awasaki, Yukio Ishikawa, Takashi Matsuo
The development of transgenesis systems in non-model organisms provides a powerful tool for molecular analysis and contributes to the understanding of phenomena that are not observed in model organisms. Drosophila prolongata is a fruit fly that has unique morphology and behavior not found in other Drosophila species including D. melanogaster. In this study, we developed a phiC31 integrase-mediated transgenesis system for D. prolongata. First, using piggyBac-mediated transgenesis, 37 homozygous attP strains were established...
May 3, 2018: Genes & Genetic Systems
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