Sat-BSA: an NGS-based method using local de novo assembly of long reads for rapid identification of genomic structural variations associated with agronomic traits     

Tenta Segawa  Chisato Nishiyama  Muluneh Tamiru-Oli  Yu Sugihara  Akira Abe  Hinako Sone  Noriaki Itoh  Mayu Asukai  Aiko Uemura  Kaori Oikawa  Hiroe Utsushi  Ayako Ikegami-Katayama  Tomohiro Imamura  Masashi Mori  Ryohei Terauchi  Hiroki Takagi 《Breeding Science》2021,71(3):299

Advances in next generation sequencing (NGS)-based methodologies have accelerated the identifications of simple genetic variants such as point mutations and small insertions/deletions (InDels). Structural variants (SVs) including large InDels and rearrangements provide vital sources of genetic diversity for plant breeding. However, their analysis remains a challenge due to their complex nature. Consequently, novel NGS-based approaches are needed to rapidly and accurately identify SVs. Here, we present an NGS-based bulked-segregant analysis (BSA) technique called Sat-BSA (SVs associated with traits) for identifying SVs controlling traits of interest in crops. Sat-BSA targets allele frequencies at all SNP positions to first identify candidate genomic regions associated with a trait, which is then reconstructed by long reads-based local de novo assembly. Finally, the association between SVs, RNA-seq-based gene expression patterns and trait is evaluated for multiple cultivars to narrow down the candidate genes. We applied Sat-BSA to segregating F₂ progeny obtained from crosses between turnip cultivars with different tuber colors and successfully isolated two genes harboring SVs that are responsible for tuber phenotypes. The current study demonstrates the utility of Sat-BSA for the identification of SVs associated with traits of interest in species with large and heterozygous genomes.  相似文献   

Acute responses of gill mitochondria-rich cells in Mozambique tilapia Oreochromis mossambicus following transfer from normal freshwater to deionized freshwater     

Jeong Hyun Choi  Kyung Mi Lee  Mayu Inokuchi  Toyoji Kaneko 《Fisheries Science》2010,76(1):101-109

Acute responses of gill mitochondria-rich (MR) cells to direct transfer from freshwater to deionized freshwater were examined in Mozambique tilapia. Scanning electron microscopic observations showed that apical openings of MR cells were morphologically classified into a small apical pit, a convex apical surface, and a concave apical surface. Following transfer from normal freshwater to deionized freshwater, the sizes of convex and concave apical surfaces were significantly increased at 24 and 6 h, respectively. Meanwhile, whole-mount immunocytochemistry revealed that freshwater-type, ion-absorbing MR cells were functionally classified into MR cells with apical Na⁺/Cl^? cotransporter (NCC) and those with apical Na⁺/H⁺ exchanger 3 (NHE3). On transfer to deionized freshwater, the intensity and size of apical-NHE3 immunoreaction were increased at 6 h, whereas the apical-NCC immunoreaction became enlarged and intense at 24 h. Considering that convex and concave MR cells are activated forms of apical-NCC cells and apical-NHE3 cells, respectively, our findings indicate that preexisting concave MR cells with apical NHE3 enlarge their apical surfaces as an acute response to exposure to deionized freshwater, followed by activation of convex MR cells with apical NCC.  相似文献   

Prevention of hypermelanosis by rearing Japanese flounder Paralichthys olivaceus in net-lined tanks     

Mizutani  Koei  Yamada  Toshiyuki  Suzuki  Keita W.  Masuda  Reiji  Nakata  Kuniaki  Tagawa  Masatomo 《Fisheries Science》2020,86(1):127-136

Fisheries Science - In artificially reared flatfish, especially the Japanese flounder Paralichthys olivaceus, pigmented skin (hypermelanosis) frequently appears on the fish’s blind side after...  相似文献   

Effect of the methoxyiminoacetamide fungicide,SSF129, on respiratory activity in Botrytis cinerea     

Hiroto Tamura  Akira Mizutani  Hideo Yukioka  Nobuo Miki  Katsuaki Ohba  Michio Masuko 《Pest management science》1999,55(7):681-686

(E)-2-Methoxyimino-N-methyl-2-[2-(2,5-dimethylphenoxymethyl)phenyl]acetamide (SSF129) has been developed as a broad-spectrum systemic fungicide for control of cereal and fruit diseases. This compound inhibited NADH-oxidation by submitochondrial particles from mycelial cells of Botrytis cinerea, with an EC₅₀ value of 14.5 nM , due to blockage of electron transport through the cytochrome bc₁ complex in the mitochondrial respiratory chain. However, SSF129 did not suppress, but rather increased, oxygen consumption by mycelial cells of the fungus. This was because mycelial cells contain an alternative oxidase protein and the cells have the ability to rapidly switch electron flux from the main cytochrome pathway to the alternative pathway on blockage of the former by SSF129. The alternative pathway of the mycelia seems not to be operative when the cytochrome pathway is functional. Naturally occurring flavonoids inhibited the alternative oxidase of the mycelial cells in a dose-dependent manner, with EC₅₀ values of 68.4 µM for flavone and 63.7 µM for flavanone. These observations suggested that plant components play an important role in control of gray mould by SSF129. © 1999 Society of Chemical Industry  相似文献   

Reverse transcription-nested polymerase chain reaction for detecting p40 RNA of Borna disease virus, without risk of plasmid contamination     

Mizutani T  Nishino Y  Kariwa H  Takashima I 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》1999,61(1):77-80

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The difference of chows affects mouse physiological conditions     

Taiki WATANABE  Shuhei TAKADA  Mayu ONOZATO  Takeshi FUKUSHIMA  Ryushin MIZUTA 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2022,84(4):582

Acetaminophen-induced liver injury in mice is a model system of human acetaminophen overdose and oxidative stress in vivo. The system is technically established, and we usually obtain severe liver damage in the treated mice; however, it is possible that the degree of liver damage is affected by the type of chow fed to mice. Thus, in this experiment, we investigated the effect of different chows on mice by comparing acetaminophen-induced liver damage, liver antioxidant level, and serum amino-acid concentrations. The results showed that differences in chows, even standard ones, affected mouse physiological conditions, with the response to oxidative stress greatly affected.  相似文献   

The binding of curcumin to various types of canine amyloid proteins     

Tei M  Uchida K  Mutsuga M  Chambers JK  Nakayama H 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2012,74(4):481-483

Curcumin is a constituent phenol compound of turmeric, and has been used as a dietary spice and Indian medicine. Curcumin has been reported to inhibit the formation of amyloid β fibrils and aggregation. In this study, the binding activity of curcumin to various types of canine amyloid was examined. Tissue samples used were lesions of AA, AL, amyloid of canine amyloid-producing odontogenic tumor (Aapot), and senile cardiovascular amyloid (ScA). Curcumin stained all types of amyloid. The binding of curcumin to AA, ScA, and AL was lost by the KMnO(4) treatment, but Aapot maintained the binding. These findings indicate that curcumin binds several types of amyloid, while the binding sites of amyloid molecules might be different from that of Congo red.  相似文献   

Efficient generation of canine bone marrow-derived dendritic cells     

Isotani M  Katsuma K  Tamura K  Yamada M  Yagihara H  Azakami D  Ono K  Washizu T  Bonkobara M 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2006,68(8):809-814

Because of their unsurpassed potency in presenting antigens to naive T cells, dendritic cells are considered to be an important candidate in the development of immunotherapeutic strategies. Despite the high potential of dendritic cell-based immunotherapy, as a so-called dendritic cell vaccination, few clinical approaches using dendritic cell vaccination have been performed in the dog because of very limited information regarding the generation of canine dendritic cells and their functional properties. We therefore established a protocol for the efficient generation of dendritic cells from canine bone marrow cells using recombinant feline granulocyte-macrophage colony-stimulating factor and canine interleukin-4. Dendritic cells were generated efficiently: a yield of 1-9 x 10(6) cells per approximately 0.5 ml of canine bone marrow aspiration was achieved. These dendritic cells showed features shared with mouse and human dendritic cells: dendrite morphology, expression of surface markers MHC class II and CD11c, and up-regulation of molecules related to antigen presentation (MHC class II, B7-1, and B7-2) by activation with lipopolysaccharide. Moreover, the dendritic cells demonstrated phagocytic activity, processing activity of pinocytosed proteins, and activation of allogeneic T cells far more potent than that by macrophages. Our findings suggest that the bone marrow-derived dendritic cells are functional for the capturing and processing of antigens and the initiation of T cell responses.  相似文献   

Imatinib elicited a favorable response in a dog with a mast cell tumor carrying a c-kit c.1523A>T mutation via suppression of constitutive KIT activation     

Yamada O  Kobayashi M  Sugisaki O  Ishii N  Ito K  Kuroki S  Sasaki Y  Isotani M  Ono K  Washizu T  Bonkobara M 《Veterinary immunology and immunopathology》2011,142(1-2):101-106

Target therapy using the tyrosine kinase inhibitor imatinib is one of the new therapeutic approaches for canine mast cell tumors (MCTs). In the present report, we demonstrate a clinical response to imatinib in a dog with MCT carrying a c-kit c.1523A>T mutation. Moreover, the effect of this mutation on the phosphorylation status of KIT and the inhibitory potency of imatinib on the phosphorylation of the mutant KIT were examined in vitro. A dog with a MCT tumor mass on the right forelimb sole with lymph node metastasis and mastocytemia was treated with imatinib. The MCT mass markedly shrank and mastocytemia became undetectable with 2 weeks of treatment. The lymph node enlarged by metastasis became normal in size with 5 weeks of treatment. From the sequencing analysis of c-kit in tumor cells, a substitution mutation c.1523A>T that alters the amino acid composition (p.Asn508Ile) within the extracellular domain of KIT was identified. The mutant KIT expressed on 293 cells showed ligand-independent phosphorylation and imatinib suppressed this phosphorylation in a dose-dependent manner. From these findings, imatinib was considered to elicit a clinical response in a canine case of MCT via inhibition of the constitutively activated KIT caused by a c-kit c.1523A>T mutation.  相似文献   

Cytoskeletal abnormalities in relation with meiotic competence and ageing in porcine and bovine oocytes during in vitro maturation     

Somfai T  Kikuchi K  Kaneda M  Akagi S  Watanabe S  Mizutani E  Haraguchi S  Dang-Nguyen TQ  Inaba Y  Geshi M  Nagai T 《Anatomia, histologia, embryologia》2011,40(5):335-344

We investigated the frequencies of cytoskeletal anomalies in metaphase-II (M-II) and incompetent [arrested at an immature metaphase (IM) stage] porcine and bovine oocytes during in vitro maturation (IVM) in relation with ageing by immunostaining and confocal microscopy. In porcine oocytes, meiotic arrest at the IM stage was associated with abnormalities of cortical actin but not with abnormal spindles. Prolongation of IVM culture to 52 h did not affect microfilament and spindle abnormalities, but reduced the microfilament-rich area overlaying the spindle. Meiotic arrest of bovine oocytes at the IM stage was associated with degenerations of microfilaments, and the frequencies of abnormal spindles were also higher than those of M-II oocytes. Ageing of bovine oocytes (IVM for 30 h) did not affect cortical microfilaments but increased the frequency of spindle alterations in both M-II and IM bovine oocytes. These results suggest that, in both species, altered ability of oocytes to polymerize F-actin might be a possible reason for the failure of polar body extrusion during IVM. Also, there seem to be differences between the two species in the sensitivity of oocytes to suffer ageing-related spindle damages.  相似文献