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Genes & Genetic Systems

Jung Eun Hwang, Duk-Soo Jang, Kyung Jun Lee, Joon-Woo Ahn, Sang Hoon Kim, Si-Yong Kang, Dong Sub Kim, Jin-Baek Kim
A high-salt environment represents environmental stress for most plants. Those that can grow and thrive in such an environment must have membrane transport systems that can respond effectively. Plant roots absorb Na(+) from the soil, and the plant must maintain Na(+) homeostasis to survive salt stress. A major mechanism by which salt-tolerant plants adapt to salt stress is through modulation of ion transport genes. We have subjected a population of rice plants to mutagenesis, and identified lines with both single-nucleotide polymorphisms (SNPs) in membrane transport genes and altered responses to salt stress...
September 1, 2016: Genes & Genetic Systems
Pin Huan, Hongxia Wang, Baozhong Liu
The early development of mollusks exhibits important characteristics from the developmental and evolutionary perspective. With the increasing number of genome-wide studies, accurate analyses of quantitative gene expression during development are impeded by the lack of validated reference genes. To improve the situation, in this study, we analyzed the expression stability of seven candidate housekeeping genes during early development of the Pacific oyster Crassostrea gigas: actin, glyceraldehyde-3 phosphate-dehydrogenase (gapdh), α subunit of elongation factor 1 (elf1α), adp-ribosylation factor 1 (arf1), heterogeneous nuclear ribonucleoprotein q, ubiquitin-conjugating enzyme e2d2 and ribosomal protein s18...
August 31, 2016: Genes & Genetic Systems
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...
August 31, 2016: Genes & Genetic Systems
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...
August 23, 2016: Genes & Genetic Systems
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...
August 12, 2016: Genes & Genetic Systems
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...
August 12, 2016: Genes & Genetic Systems
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
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
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...
July 25, 2016: Genes & Genetic Systems
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)...
July 25, 2016: Genes & Genetic Systems
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...
July 25, 2016: Genes & Genetic Systems
Haruki Nishio, Diana Mihaela Buzas, Atsushi J Nagano, Yutaka Suzuki, Sumio Sugano, Motomi Ito, Shin-Ichi Morinaga, Hiroshi Kudoh
Gene regulatory mechanisms are often defined in studies performed in the laboratory but are seldom validated for natural habitat conditions, i.e., in natura. Vernalization, the promotion of flowering by winter cold, is a prominent naturally occurring phenomenon, so far best characterized using artificial warm and cold treatments. The floral inhibitor FLOWERING LOCUS C (FLC) gene of Arabidopsis thaliana has been identified as the central regulator of vernalization. FLC shows an idiosyncratic pattern of histone modification at different stages of cold exposure, believed to regulate transcriptional responses of FLC...
July 20, 2016: Genes & Genetic Systems
Takahiro Kawanabe, Kenji Osabe, Etsuko Itabashi, Keiichi Okazaki, Elizabeth S Dennis, Ryo Fujimoto
Epigenetic regulation is crucial for the development of plants and for adaptation to a changing environment. Recently, genome-wide profiles of histone modifications have been determined by a combination of chromatin immunoprecipitation (ChIP) and genomic tiling arrays (ChIP on chip) or ChIP and high-throughput sequencing (ChIP-seq) in species including Arabidopsis thaliana, rice and maize. Validation of ChIP analysis by PCR or qPCR using positive and negative regions of histone modification is necessary. In contrast, information about histone modifications is limited in Chinese cabbage, Brassica rapa...
July 20, 2016: Genes & Genetic Systems
Atsushi Hoshino, Yoshiaki Yoneda, Tsutomu Kuboyama
Floricultural cultivars of the Japanese morning glory (Ipomoea nil) carry transposons of the Tpn1 family as active spontaneous mutagens. Half of the characterized mutations related to floricultural traits were caused by insertion of Tpn1 family elements. In addition, mutations comprising insertions of several bp, presumed to be footprints generated by transposon excisions, were also found. Among these, ca-1 and ca-2 are 7-bp insertions at the same position in the InWDR1 gene, which encodes a multifunctional transcription regulator...
July 20, 2016: Genes & Genetic Systems
Koichiro Tsunewaki
Sakamura (1918) reported the discovery of a polyploid series among eight species of the genus Triticum; this series consisted of 2x, 4x and 6x species with 2n = 14, 28 and 42 chromosomes, respectively. He mentioned in this article that all the materials he used were gifted by T. Minami of the same department of Hokkaido University, Japan. In addition to carrying out an extensive collection of cereal germplasms in the period 1914 to 1916, Minami wrote on October 7, 1915 to K. A. Flaksberger, a wheat taxonomist at the Bureau of Applied Botany, Saint Petersburg, Russia, requesting seeds of Russian wheat and other cereals...
July 20, 2016: Genes & Genetic Systems
Qi-Fang Geng, Jie Yang, Jia He, Dan-Bi Wang, En Shi, Wei-Xiang Xu, Nasreen Jeelani, Zhong-Sheng Wang, Hong Liu
The Anhui elm Ulmus gaussenii is listed as a critically endangered species by the International Union for Conservation of Nature and is endemic to China, where its only population is restricted to Langya Mountain in Chuzhou, Anhui Province. To better understand the population genetics of U. gaussenii, we developed 12 microsatellite markers using an improved technique. The 12 markers were polymorphic, with the number of alleles per locus ranging from two to nine. Observed and expected heterozygosities ranged from 0...
July 20, 2016: Genes & Genetic Systems
Yuko Nakashima, Asako Higashiyama, Ayana Ushimaru, Nozomi Nagoda, Yoshinori Matsuo
A subset of histone genes (H1, H2A, H2B and H4), which are encoded along with H3 within repeating units, were analyzed in Drosophila lutescens, D. takahashii and D. pseudoobscura to investigate the evolutionary mechanisms influencing this multigene family and its GC content. Nucleotide divergence among species was more marked in the less functional regions. A strong inverse relationship was observed between the extent of evolutionary divergence and GC content within the repeating units; this finding indicated that the functional constraint on a region must be associated with both divergence and GC content...
July 20, 2016: Genes & Genetic Systems
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...
June 20, 2016: Genes & Genetic Systems
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...
June 10, 2016: Genes & Genetic Systems
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...
June 10, 2016: Genes & Genetic Systems
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