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1.
Toru Sugita Yukari Semi Hiromasa Sawada Yumi Utoyama Yuko Hosomi Eri Yoshimoto Yuki Maehata Hiroyuki Fukuoka Ryutaro Nagata Akio Ohyama 《Molecular breeding : new strategies in plant improvement》2013,31(4):909-920
To facilitate marker-assisted breeding and genetic analyses of pepper (Capsicum annuum), we developed non-redundant 2- or 3-base simple sequence repeat (SSR) markers from enriched C. annuum genomic libraries and from C. annuum cDNA sequences in public databases. The SSR-enriched libraries were constructed using combinations of three restriction enzymes (AluI, HaeIII, and RsaI) and two biotinylated oligonucleotides [b(GA)15 and b(CA)15]. Ultimately, we obtained 1,736 genomic SSR markers and 1,344 cDNA-derived SSR markers from 6,528 clones and 13,003 sequences, respectively. We mapped 597 markers, including 265 of the newly developed SSR markers, onto a linkage map by using doubled-haploid (DH) lines derived from an intraspecific cross of two pure lines of C. annuum (K9-11 × MZC-180). The map, designated as the KL-DH map, consisted of 12 linkage groups. The map covered a genetic distance of 2,028 cM, and the average distance between markers was less than 4 cM. The frame structure of the KL-DH map was compared with the published standard conserved ortholog set II (COSII) map, which was derived from an interspecific F2 population (C. frutescens × C. annuum), by using tomato (Solanum lycopersicum) chromosomal sequences to bridge the two maps. The intraspecific KL-DH map constructed in this study and the interspecific COSII map were similar in map length and marker distribution, suggesting that the KL-DH map covers nearly the whole genome of C. annuum. 相似文献
2.
Wayne Reeve Rui Tian Sofie De Meyer Vanessa Melino Jason Terpolilli Julie Ardley Ravi Tiwari John Howieson Ronald Yates Graham O’Hara Mohamed Ninawi Hazuki Teshima David Bruce Chris Detter Roxanne Tapia Cliff Han Chia-Lin Wei Marcel Huntemann James Han I-Min Chen Konstantinos Mavromatis Victor Markowitz Natalia Ivanova Galina Ovchinnikova Ioanna Pagani Amrita Pati Lynne Goodwin Sam Pitluck Tanja Woyke Nikos Kyrpides 《Standards in genomic sciences》2013,9(2):243-253
Rhizobium leguminosarum bv. trifolii strain TA1 is an aerobic, motile, Gram-negative, non-spore-forming rod that is an effective nitrogen fixing microsymbiont on the perennial clovers originating from Europe and the Mediterranean basin. TA1 however is ineffective with many annual and perennial clovers originating from Africa and America. Here we describe the features of R. leguminosarum bv. trifolii strain TA1, together with genome sequence information and annotation. The 8,618,824 bp high-quality-draft genome is arranged in a 6 scaffold of 32 contigs, contains 8,493 protein-coding genes and 83 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. 相似文献
3.
Hazuki Tamada Hisao Naito Kazuya Kitamori Yumi Hayashi Nozomi Yamagishi Masashi Kato Tamie Nakajima 《PloS one》2016,11(1)
Nonalcoholic steatohepatitis is related to lifestyle, particularly to dietary habits. We developed diet-induced fibrotic steatohepatitis model stroke-prone spontaneously hypertensive 5/Dmcr (SHRSP5/Dmcr) rats showing steatosis, hepatic inflammation, and severe fibrosis induced by high-fat and -cholesterol (HFC) diet feeding. We aimed to clarify the efficacy of dietary intervention on the disease before and after the appearance of fibrosis. Male SHRSP5/Dmcr rats were divided into 9 groups; of these, 6 groups were fed control or HFC diet for several weeks and the remaining 3 groups represented the dietary intervention groups, which were fed the control diet after HFC diet feeding for 2 (before the appearance of fibrosis) or 8 (after the appearance of fibrosis) weeks. Dietary intervention before the appearance of fibrosis significantly improved the steatosis and reset the increased serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), and serum total cholesterol (TC) levels. However, dietary intervention after the appearance of fibrosis was unable to reset the levels of hepatic TC, serum ALT, and fibrogenesis-related markers and had only a minor influence on hepatic fibrosis, although it reset the increased expression of transforming growth factor (TGF)-β1 and α-smooth muscle actin (SMA). It was noted that dietary intervention improved the increased AST levels; however, aggregated CD68-positive cells were still observed around the fibrosis area, which may be related to the findings of inflammatory cytokine mRNAs. Taken together, dietary intervention for fibrotic steatohepatitis improved steatosis, although it could not completely improve fibrosis. 相似文献
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5.
Yoko Nishimura Taisuke Ohtsuka Kohei Yoshiyama Daisuke Nakai Fujiyoshi Shibahara Masayoshi Maehata 《Ecological Research》2011,26(3):615-626
Effects of fish predation propagate through aquatic food webs, where the classical grazing food chain and microbial loop are
interwoven by trophic interactions. The overall impact on aquatic food webs is further complicated because fish may also exert
bottom-up controls through nutrient regeneration. Yet, we still have limited information about cascading effects among fish,
zooplankton, phytoplankton, and microbes. In this study, we performed a mesocosm experiment to evaluate effects of fish introduction
on plankton communities. Six plots were set in factorial combination with fish introduction and rice straw plowing in a paddy
field, and the experiment was continued for 4 weeks. Introduction of fish significantly increased chlorophyll a concentrations in smaller size fractions (<15 μm) and abundances of filamentous bacteria (>5 μm in length) and heterotrophic
nanoflagellates in 3–15 μm fraction. Microbes in 0.8–3 μm fraction showed increasing but not significant trends in response
to fish introduction. These results indicate cascading effects of fish predation operating via two pathways, one through grazing
food chain and the other through microbial food web. Phytoplankton community compositions shifted in similar fashion in all
plots until 1 week after fish introduction, and then diverged between plots with and without fish thereafter. Bottom-up effects
of fish introduction were suggested by increases of total chlorophyll a and inedible phytoplankton species in response to fish introduction. This study provides an example of how fish predation
regulates biomass and structure of phytoplankton and microbial communities. 相似文献
6.
Sikorski J Teshima H Nolan M Lucas S Hammon N Deshpande S Cheng JF Pitluck S Liolios K Pagani I Ivanova N Huntemann M Mavromatis K Ovchinikova G Pati A Tapia R Han C Goodwin L Chen A Palaniappan K Land M Hauser L Ngatchou-Djao OD Rohde M Pukall R Spring S Abt B Göker M Detter JC Woyke T Bristow J Markowitz V Hugenholtz P Eisen JA Kyrpides NC Klenk HP Lapidus A 《Standards in genomic sciences》2011,4(3):331-341
Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
7.
Lang E Teshima H Lucas S Lapidus A Hammon N Deshpande S Nolan M Cheng JF Pitluck S Liolios K Pagani I Mikhailova N Ivanova N Mavromatis K Pati A Tapia R Han C Goodwin L Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Brambilla EM Kopitz M Rohde M Göker M Tindall BJ Detter JC Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Klenk HP Kyrpides NC 《Standards in genomic sciences》2011,4(1):81-90
8.
Hazuki E. Miwa Thomas A. Gerken Oliver Jamison Lawrence A. Tabak 《The Journal of biological chemistry》2010,285(2):1208-1219
Mucin-type O-glycan biosynthesis is regulated by the family of UDP-GalNAc polypeptide:N-acetylgalactosaminlytransfersases (ppGalNAcTs) that catalyzes the first step in the pathway by transferring GalNAc to Ser or Thr residues in a protein from the sugar donor UDP-GalNAc. Because not all Ser/Thr residues are glycosylated, rules must exist that signal which hydroyxamino acids acquire sugar. To date, no universal consensus signal has emerged. Therefore, strategies to deduce the subset of proteins that will be glycosylated by distinct ppGalNAcTs must be developed. Mucin-type O-glycoproteins are present abundantly in bone, where we found multiple ppGalNAcT isoforms, including ppGalNAcT-1, to be highly expressed. Thus, we compared glycoproteins expressed in wild-type and Galnt1-null mice to identify bone-associated proteins that were glycosylated in a ppGalNAcT-1-dependent manner. A reduction in the apparent molecular masses of two SIBLINGs (small integrin binding ligand N-linked glycoproteins), osteopontin (OPN) and bone sialoprotein (BSP) in the Galnt1-null mice relative to those of the wild-type was observed. Several synthetic peptides derived from OPN and BSP sequences were designed to include either known or predicted (in silico) glycosylation sites. In vitro glycosylation assays of these peptides with recombinant ppGalNAcT-1, ppGalNAcT-2, or ppGalNAcT-3 demonstrated that both SIBLINGs contained Thr/Ser residues that were preferentially glycosylated by ppGalNAcT-1. In addition, lysates prepared from wild-type, but not those from Galnt1-null derived osteoblasts, could glycosylate these peptides efficiently, suggesting that OPN and BSP contain sites that are specific for ppGalNAcT-1. Our study presents a novel and systematic approach for identification of isoform-specific substrates of the ppGalNAcT family and suggests ppGalNAcT-1 to be indispensable for O-glycosylation at specific sites of the bone glycoproteins OPN and BSP. 相似文献
9.
Yamaguchi T Saneyoshi M Takahashi H Hirokawa S Amano R Liu X Inomata M Maruyama T 《Nucleosides, nucleotides & nucleic acids》2006,25(4-6):539-551
Telomerase, responsible for telomere synthesis, is expressed in approximately 90% of human tumor cells but seldom in normal somatic cells. In this study, inhibition by carbocyclic oxetanocin G triphosphate (C. OXT-GTP) and its analogues was investigated in order to clarify the susceptibility of telomerase to various nucleotide analogues. C. OXT-GTP competitively inhibited telomerase activity with respect to dGTP However, C. OXT-GTP had a potent inhibitory effect on DNA polymerase alpha. It was examined whether the nucleoside (C. OXT-G) was able to alter telomere length in cultured human HL60 cells. Contrary to expectation, long-term treatment with 10 microM C. OXT-G was found to cause telomere lengthening. 相似文献
10.
AimsAs the clinical use of induced pluripotent stem (iPS) cells may have the potential to overcome current obstacles in stem cell-based therapy, the molecular mechanisms that regulate the proliferation of iPS cells are of great interest. However, to our knowledge, no previous studies have examined whether stimulation with nicotinic acetylcholine receptor (nAchR) enhances the growth of iPS cells. In the present study, we examined the involvement of nAchR in the proliferation of mouse iPS cells.Main methodsWe performed immunofluorescence staining to determine whether mouse iPS cells could express nAchRs. Mouse iPS cells were treated with nicotine for 24 h under feeder-free conditions in the presence of leukemia inhibitory factor (LIF). The DNA synthesis was examined by the BrdU incorporation assay. Intracellular calcium levels were measured using Fluo-4-acetoxymethyl (a cell-permeable calcium indicator). In addition, we examined the involvement of the CaMKП pathway in nicotine-enhanced proliferation of mouse iPS cells.Key findingsThe fluorescence images revealed that α4-nAchR and α7-nAchR are expressed on mouse iPS cells. Treatment of the cells with 300 nM nicotine significantly increases DNA synthesis. This is significantly inhibited by pretreatment with antagonists of α4-nAchR and α7-nAchR or a CaMKП inhibitor. In addition, treatment with nicotine increases the intracellular Ca2+ level dose-dependently in mouse iPS cells. Treatment with nicotine significantly enhances CaMKП phosphorylation.SignificanceThe present study indicates that stimulation of α4-nAchR and α7-nAchR may lead to a significant increase in the rate of mouse iPS cell proliferation through enhancement of the CaMKП signaling pathway. 相似文献