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1.
Kazuhiro Ishibashi Natsuki Mawatari Shuhei Miyashita Hirohisa Kishino Tetsuo Meshi Masayuki Ishikawa 《PLoS pathogens》2012,8(10)
During antagonistic coevolution between viruses and their hosts, viruses have a major advantage by evolving more rapidly. Nevertheless, viruses and their hosts coexist and have coevolved, although the processes remain largely unknown. We previously identified Tm-1 that confers resistance to Tomato mosaic virus (ToMV), and revealed that it encodes a protein that binds ToMV replication proteins and inhibits RNA replication. Tm-1 was introgressed from a wild tomato species Solanum habrochaites into the cultivated tomato species Solanum lycopersicum. In this study, we analyzed Tm-1 alleles in S. habrochaites. Although most part of this gene was under purifying selection, a cluster of nonsynonymous substitutions in a small region important for inhibitory activity was identified, suggesting that the region is under positive selection. We then examined the resistance of S. habrochaites plants to ToMV. Approximately 60% of 149 individuals from 24 accessions were resistant to ToMV, while the others accumulated detectable levels of coat protein after inoculation. Unexpectedly, many S. habrochaites plants were observed in which even multiplication of the Tm-1-resistance-breaking ToMV mutant LT1 was inhibited. An amino acid change in the positively selected region of the Tm-1 protein was responsible for the inhibition of LT1 multiplication. This amino acid change allowed Tm-1 to bind LT1 replication proteins without losing the ability to bind replication proteins of wild-type ToMV. The antiviral spectra and biochemical properties suggest that Tm-1 has evolved by changing the strengths of its inhibitory activity rather than diversifying the recognition spectra. In the LT1-resistant S. habrochaites plants inoculated with LT1, mutant viruses emerged whose multiplication was not inhibited by the Tm-1 allele that confers resistance to LT1. However, the resistance-breaking mutants were less competitive than the parental strains in the absence of Tm-1. Based on these results, we discuss possible coevolutionary processes of ToMV and Tm-1. 相似文献
2.
H Kido Y Yokogoshi K Sakai M Tashiro Y Kishino A Fukutomi N Katunuma 《The Journal of biological chemistry》1992,267(19):13573-13579
A novel trypsin-like protease associated with rat bronchiolar epithelial Clara cells, named Tryptase Clara, was purified to homogeneity from rat lung by a series of standard chromatographic procedures. The enzyme has apparent molecular masses of 180 +/- 16 kDa on gel filtration and 30 +/- 1.5 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions. Its isoelectric point is pH 4.75. Studies with model peptide substrates showed that the enzyme preferentially recognizes a single arginine cleavage site, cleaving Boc-Gln-Ala-Arg-4-methylcoumaryl-7-amide most efficiently and having a pH optimum of 7.5 with this substrate. The enzyme is strongly inhibited by aprotinin, diisopropylfluorophosphate, antipain, leupeptin, and Kunitz-type soybean trypsin inhibitor, but inhibited only slightly by Bowman-Birk soybean trypsin inhibitor, benzamidine, and alpha 1-antitrypsin. Immunohistochemical studies indicated that the enzyme is located exclusively in the bronchiolar epithelial Clara cells and colocalized with surfactant. An immunoreactive protein with a molecular mass of 28.5 kDa was also detected in airway secretions by Western blotting analyses, suggesting that the 30-kDa protease in Clara cells is processed before or after its secretion. Proteolytic cleavage of the hemagglutinin of influenza virus is a prerequisite for the virus to become infectious. Tryptase Clara was shown to cleave the hemagglutinin and activate infectivity of influenza A virus in a dose-dependent way. These results suggest that the enzyme is a possible activator of inactive viral fusion glycoprotein in the respiratory tract and thus responsible for pneumopathogenicity of the virus. 相似文献
3.
Cow-calf pairs of southern right whales on the South African coast have been photographed in aerial surveys in October each year since 1979. In this paper 469 resightings of 177 individually identified cows photographed in the first six years of surveys have been analyzed in two ways to produce estimates of natural mortality rate. Both methods assume that all females calve either two, three, or four years after their previous calf. In Method A there is assumed to be no systematic trend with time in the probability of a female being photographed on each calving occasion. Natural logarithms of the numbers photographed 2-4, 5-7, 8-10, etc. yr after being first seen are regressed against time, the slope of which provides an estimate of natural mortality rate of 0.0255 ± 0.0071. The intercept value for this regression provides an estimate of the detection probability, or 0.769 ± 0.011. In Method B it is assumed that if a female has not been photographed for at least nine years then it is dead. Annual mortality estimates are obtained from the proportional reduction in the numbers of females known to be alive at each three-year interval after being first photographed, up to at least 6-8 yr from the present. Method B produces an estimate of natural mortality of 0.0260 ± 0.0190 (corrected to 0.0227 ± 0.0192 using the average detection probability). Both methods may be subject to various biases that tend to inflate estimates of natural mortality. 相似文献
4.
Johnstone Julia W. Lunden Jay J. Waller Rhian G. Poulton Nicole J. Togami Hanae 《Coral reefs (Online)》2022,41(5):1495-1510
Coral Reefs - The Western Antarctic Peninsula is home to a diverse assemblage of deep-sea species and is warming faster than any other region in the Southern Hemisphere. This study investigated how... 相似文献
5.
Hanae Shimo Satya Nanda Vel Arjunan Hiroaki Machiyama Taiko Nishino Makoto Suematsu Hideaki Fujita Masaru Tomita Koichi Takahashi 《PLoS computational biology》2015,11(6)
Oxidative stress mediated clustering of membrane protein band 3 plays an essential role in the clearance of damaged and aged red blood cells (RBCs) from the circulation. While a number of previous experimental studies have observed changes in band 3 distribution after oxidative treatment, the details of how these clusters are formed and how their properties change under different conditions have remained poorly understood. To address these issues, a framework that enables the simultaneous monitoring of the temporal and spatial changes following oxidation is needed. In this study, we established a novel simulation strategy that incorporates deterministic and stochastic reactions with particle reaction-diffusion processes, to model band 3 cluster formation at single molecule resolution. By integrating a kinetic model of RBC antioxidant metabolism with a model of band 3 diffusion, we developed a model that reproduces the time-dependent changes of glutathione and clustered band 3 levels, as well as band 3 distribution during oxidative treatment, observed in prior studies. We predicted that cluster formation is largely dependent on fast reverse reaction rates, strong affinity between clustering molecules, and irreversible hemichrome binding. We further predicted that under repeated oxidative perturbations, clusters tended to progressively grow and shift towards an irreversible state. Application of our model to simulate oxidation in RBCs with cytoskeletal deficiency also suggested that oxidation leads to more enhanced clustering compared to healthy RBCs. Taken together, our model enables the prediction of band 3 spatio-temporal profiles under various situations, thus providing valuable insights to potentially aid understanding mechanisms for removing senescent and premature RBCs. 相似文献
6.
Hanae Takatsuki Katsuya Satoh Kazunori Sano Takayuki Fuse Takehiro Nakagaki Tsuyoshi Mori Daisuke Ishibashi Ban Mihara Masaki Takao Yasushi Iwasaki Mari Yoshida Ryuichiro Atarashi Noriyuki Nishida 《PloS one》2015,10(6)
The infectious agents of the transmissible spongiform encephalopathies are composed of amyloidogenic prion protein, PrPSc. Real-time quaking-induced conversion can amplify very small amounts of PrPSc seeds in tissues/body fluids of patients or animals. Using this in vitro PrP-amyloid amplification assay, we quantitated the seeding activity of affected human brains. End-point assay using serially diluted brain homogenates of sporadic Creutzfeldt–Jakob disease patients demonstrated that 50% seeding dose (SD50) is reached approximately 1010/g brain (values varies 108.79–10.63/g). A genetic case (GSS-P102L) yielded a similar level of seeding activity in an autopsy brain sample. The range of PrPSc concentrations in the samples, determined by dot-blot assay, was 0.6–5.4 μg/g brain; therefore, we estimated that 1 SD50 unit was equivalent to 0.06–0.27 fg of PrPSc. The SD50 values of the affected brains dropped more than three orders of magnitude after autoclaving at 121°C. This new method for quantitation of human prion activity provides a new way to reduce the risk of iatrogenic prion transmission. 相似文献
7.
The diversity of marine communities is in striking contrast with the diversity of terrestrial communities. In all oceans, species richness is low in tropical areas and high at latitudes between 20 and 40°. While species richness is a primary metric used in conservation and management strategies, it is important to take into account the complex phylogenetic patterns of species compositions within communities. We measured the phylogenetic skew and diversity of shark communities throughout the world. We found that shark communities in tropical seas were highly phylogenetically skewed, whereas temperate sea communities had phylogenetically diversified species compositions. Interestingly, although geographically distant from one another, tropical sea communities were all highly skewed toward requiem sharks (Carcharhinidae), hammerhead sharks (Sphyrnidae), and whale sharks (Rhincodon typus). Worldwide, the greatest phylogenetic evenness in terms of clades was found in the North Sea and coastal regions of countries in temperate zones, such as the United Kingdom, Ireland, southern Australia, and Chile. This study is the first to examine patterns of phylogenetic diversity of shark communities on a global scale. Our findings suggest that when establishing conservation activities, it is important to take full account of phylogenetic patterns of species composition and not solely use species richness as a target. Protecting areas of high phylogenetic diversity in sharks, which were identified in this study, could form a broader strategy for protecting other threatened marine species. 相似文献
8.
Ulrich Dobramysl Iris Katharina Jarsch Yoshiko Inoue Hanae Shimo Benjamin Richier Jonathan R. Gadsby Julia Mason Alicja Szaapak Pantelis Savvas Ioannou Guilherme Pereira Correia Astrid Walrant Richard Butler Edouard Hannezo Benjamin D. Simons Jennifer L. Gallop 《The Journal of cell biology》2021,220(4)
Assemblies of actin and its regulators underlie the dynamic morphology of all eukaryotic cells. To understand how actin regulatory proteins work together to generate actin-rich structures such as filopodia, we analyzed the localization of diverse actin regulators within filopodia in Drosophila embryos and in a complementary in vitro system of filopodia-like structures (FLSs). We found that the composition of the regulatory protein complex where actin is incorporated (the filopodial tip complex) is remarkably heterogeneous both in vivo and in vitro. Our data reveal that different pairs of proteins correlate with each other and with actin bundle length, suggesting the presence of functional subcomplexes. This is consistent with a theoretical framework where three or more redundant subcomplexes join the tip complex stochastically, with any two being sufficient to drive filopodia formation. We provide an explanation for the observed heterogeneity and suggest that a mechanism based on multiple components allows stereotypical filopodial dynamics to arise from diverse upstream signaling pathways. 相似文献
9.
Modulation of Rat Cecal Microbiota by Administration of Raffinose and Encapsulated Bifidobacterium breve 总被引:1,自引:0,他引:1 下载免费PDF全文
Achmad Dinoto Akarat Suksomcheep Satoshi Ishizuka Hanae Kimura Satoshi Hanada Yoichi Kamagata Kozo Asano Fusao Tomita Atsushi Yokota 《Applied microbiology》2006,72(1):784-792
To investigate the effects of administration of raffinose and encapsulated Bifidobacterium breve JCM 1192T cells on the rat cecal microbiota, in a preclinical synbiotic study groups of male WKAH/Hkm Slc rats were fed for 3 weeks with four different test diets: basal diet (group BD), basal diet supplemented with raffinose (group RAF), basal diet supplemented with encapsulated B. breve (group CB), and basal diet supplemented with both raffinose and encapsulated B. breve (group RCB). The bacterial populations in cecal samples were determined by fluorescence in situ hybridization (FISH) and terminal restriction fragment length polymorphism (T-RFLP). B. breve cells were detected only in the RCB group and accounted for about 6.3% of the total cells as determined by FISH analysis. B. breve was also detected only in the RCB group by T-RFLP analysis. This was in contrast to the CB group, in which no B. breve signals were detected by either FISH or T-RFLP. Increases in the sizes of the populations of Bifidobacterium animalis, a Bifidobacterium indigenous to the rat, were observed in the RAF and RCB groups. Principal-component analysis of T-RFLP results revealed significant alterations in the bacterial populations of rats in the RAF and RCB groups; the population in the CB group was similar to that in the control group (group BD). To the best of our knowledge, these results provide the first clear picture of the changes in the rat cecal microbiota in response to synbiotic administration. 相似文献
10.
Yosuke Suzuki Hiroki Itoh Fuminori Sato Kanako Kawasaki Yukie Sato Takashi Fujioka Yuhki Sato Keiko Ohno Hiromitsu Mimata Satoshi Kishino 《Journal of lipid research》2013,54(9):2568-2572
Several previous studies have shown that renal failure decreases not only renal elimination but also metabolic clearance of drugs, particularly those metabolized by CYP3A. However, whether recovery of renal function results in recovery of hepatic CYP3A activity remains unknown. In this study, we evaluated the effect of renal function on CYP3A activity after kidney transplantation in patients with end-stage renal disease (ESRD) by measuring the change in CYP3A activity using plasma concentration of 4β-hydroxycholesterol as a biomarker. The study enrolled 13 patients with ESRD who underwent the first kidney allograft transplantation. Morning blood samples were collected before and 3, 7, 10, 14, 21, 30, 60, 90, 120, 150 and 180 days after kidney transplantation. Plasma concentration of 4β-hydroxycholesterol was measured using GC-MS. Compared with before kidney transplantation, creatinine clearance increased significantly from day 3 after kidney transplantation and stabilized thereafter. Plasma concentration of 4β-hydroxycholesterol was elevated significantly on days 90 and 180 after kidney transplantation. In conclusion, this study suggests the recovery of CYP3A activity with improvement in renal function after kidney transplantation in patients with ESRD. 相似文献