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441.
Yoji Nakamura Yuya Shigenobu Takuma Sugaya Tadahide Kurokawa Kenji Saitoh 《Ichthyological Research》2013,60(2):184-187
In recent years, massive sequencing approaches have allowed us to determine genomic structures of various organisms rapidly, raising novel applicability of the high-throughput sequence data obtained to various fields of biological studies. We present here a pipeline to search for microsatellite DNA and design PCR primers encompassing the microsatellites on genomic sequence data produced by 454 pyrosequencing. We tested this pipeline, called ‘Auto-primer’, on several fish genomic sequences and obtained many and various candidates for microsatellite DNA loci useful for detecting intraspecies genetic variability. This in silico search for microsatellite DNA is superior to conventional cloning methods, since any sequence patterns of repeat unit can be screened. 相似文献
442.
Xiao-Long Yang Toshiyuki Wakimoto Yuya Takeshige Rui He Yoko Egami Takayoshi Awakawa Ikuro Abe 《Bioorganic & medicinal chemistry letters》2013,23(13):3810-3813
New indole–porphyrin hybrid molecules were isolated from Escherichia coli harboring metagenomic DNA from the Japanese marine sponge Discodermia calyx. The indole was appended to the reactive vinyl substituent of the harderoporphyrin chromophore, encoded by the insert DNA. Thus, the chimeric pathway between the heterologously expressed porphyrins and the endogenous indole generated new indole-conjugated chiral porphyrins in E. coli. 相似文献
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In various ectotherms, it is well-known that high-latitude individuals grow faster at any temperature than do low-latitude
individuals as an adaptation to shorter growing seasons. The submaximal growth of low-latitude ectotherms implies that there
exist trade-offs with fast growth. Although there is accumulating evidence for latitudinal variation in growth capacity, however,
few studies have demonstrated these trade-offs. In this study, using a freshwater fish Oryzias latipes as a model organism, we tested whether there is an acquisition trade-off in which the higher growth capacity of high-latitude
individuals is realized by foraging more intensively, despite the risk of predation. Foraging experiments revealed that higher-latitude
O. latipes juveniles captured more prey per unit time than lower-latitude juveniles at any temperature. In addition, predation experiments
revealed that higher-latitude juveniles were more frequently killed by dragonfly larvae. Observations of swimming behaviors
demonstrated that the higher vulnerability to predation in high-latitude O. latipes is probably caused by lower steady- and burst-swimming performances due to the larger meal size, and partially by reduced
caution due to a greater willingness to forage. We conclude that acquisition trade-offs may be the primary constraint on growth
evolution across latitudes among fishes. This implies that growth capacity evolves in response not only to the length of the
growing season but also to predation pressures. 相似文献
445.
Akihiro Sonoda Sosuke Yoshinaga Kaori Yunoki Soichiro Ezaki Kotaro Yano Mitsuhiro Takeda Etsuko Toda Yuya Terashima Kouji Matsushima Hiroaki Terasawa 《Molecular biotechnology》2017,59(4-5):141-150
FROUNT is a cytoplasmic protein that binds to the membrane-proximal C-terminal regions (Pro-Cs) of chemokine receptors, CCR2 and CCR5. The FROUNT–chemokine receptor interactions play a pivotal role in the migration of inflammatory immune cells, indicating the potential of FROUNT as a drug target for inflammatory diseases. To provide the foundation for drug development, structural information of the Pro-C binding region of FROUNT is desired. Here, we defined the novel structural domain (FNT-CB), which mediates the interaction with the chemokine receptors. A recombinant GST-tag-fused FNT-CB protein expression system was constructed. The protein was purified by affinity chromatography and then subjected to in-gel protease digestion of the GST-tag. The released FNT-CB was further purified by anion-exchange and size-exclusion chromatography. Purified FNT-CB adopts a helical structure, as indicated by CD. NMR line-broadening indicated that weak aggregation occurred at sub-millimolar concentrations, but the line-broadening was mitigated by using a deuterated sample in concert with transverse relaxation-optimized spectroscopy. The specific binding of FNT-CB to CCR2 Pro-C was confirmed by the fluorescence-based assay. The improved NMR spectral quality and the retained functional activity of FNT-CB support the feasibility of further structural and functional studies targeted at the anti-inflammatory drug development. 相似文献
446.
Kengo Hamamura Naoya Matsunaga Eriko Ikeda Hideaki Kondo Hisako Ikeyama Kazutaka Tokushige Kazufumi Itcho Yoko Furuichi Yuya Yoshida Masaki Matsuda Kaori Yasuda Atsushi Doi Yoshifumi Yokota Toshiaki Amamoto Hironori Aramaki Yasuhiro Irino Satoru Koyanagi Shigehiro Ohdo 《The Journal of biological chemistry》2016,291(10):4913-4927
Chronic kidney disease (CKD) is associated with an increase in serum retinol; however, the underlying mechanisms of this disorder are poorly characterized. Here, we found that the alteration of hepatic metabolism induced the accumulation of serum retinol in 5/6 nephrectomy (5/6Nx) mice. The liver is the major organ responsible for retinol metabolism; accordingly, microarray analysis revealed that the hepatic expression of most CYP genes was changed in 5/6Nx mice. In addition, D-box-binding protein (DBP), which controls the expression of several CYP genes, was significantly decreased in these mice. Cyp3a11 and Cyp26a1, encoding key proteins in retinol metabolism, showed the greatest decrease in expression in 5/6Nx mice, a process mediated by the decreased expression of DBP. Furthermore, an increase of plasma transforming growth factor-β1 (TGF-β1) in 5/6Nx mice led to the decreased expression of the Dbp gene. Consistent with these findings, the alterations of retinol metabolism and renal dysfunction in 5/6Nx mice were ameliorated by administration of an anti-TGF-β1 antibody. We also show that the accumulation of serum retinol induced renal apoptosis in 5/6Nx mice fed a normal diet, whereas renal dysfunction was reduced in mice fed a retinol-free diet. These findings indicate that constitutive Dbp expression plays an important role in mediating hepatic dysfunction under CKD. Thus, the aggravation of renal dysfunction in patients with CKD might be prevented by a recovery of hepatic function, potentially through therapies targeting DBP and retinol. 相似文献
447.
Eric Capo Benjamin D. Peterson Minjae Kim Daniel S. Jones Silvia G. Acinas Marc Amyot Stefan Bertilsson Erik Björn Moritz Buck Claudia Cosio Dwayne A. Elias Cynthia Gilmour Marisol Goñi-Urriza Baohua Gu Heyu Lin Yu-Rong Liu Katherine McMahon John W. Moreau Jarone Pinhassi Mircea Podar Fernando Puente-Sánchez Pablo Sánchez Veronika Storck Yuya Tada Adrien Vigneron David A. Walsh Marine Vandewalle-Capo Andrea G. Bravo Caitlin M. Gionfriddo 《Molecular ecology resources》2023,23(1):190-204
Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes. 相似文献
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