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Some DNA data show patterns of variation not expected under the neutral theory. Here, the independent multicodon (IMC) model, a nearly neutral mutation model assuming no interaction among codons, was studied when population size changes using computer simulation. Patterns of variation expected under the model were investigated using statistics for the neutrality tests. The average dispersion index is more than one when population size changes slowly but it never becomes large. The diversity at linked silent site decreases when the strength of selection is intermediate and the reduction is larger when population size changes slowly. Tajima's (1989. Genetics 123, 585-595) D is generally negative. Rejections by the Tajima's test occur more frequently if population size changes quickly but the effect of selection is confounded with the size change itself in this case. If we apply the test of McDonald and Kreitman (1991. Nature 351, 652-654), the rejection is always in the direction of excess replacement polymorphisms. The rejection probability decreases as the rate of population size changes decreases. These results show that the predictions of the IMC model are consistent with the pattern observed in mitochondrial DNA data but not consistent with some data of nuclear DNA. Interaction among codons or variable selection would be necessary to explain such cases. 相似文献
44.
Evidence for recent invasion of the medaka fish genome by the Tol2 transposable element 总被引:1,自引:0,他引:1
Tol2 is a transposable element of the terminal-inverted-repeat class, residing in the genome of the medaka fish Oryzias latipes. The genus Oryzias contains more than 10 species for which phylogenetic relationships have previously been estimated. To infer the history of Tol2 in this genus we performed genomic Southern blots and PCR analyses of 10 of the species. It was revealed that Tol2 occurs in 2 of the 10 species (O. curvinotus and O. latipes) and that the length and the restriction map structure of Tol2 are identical in the two cases. Further, sequencing analysis revealed an extremely low level of divergence compared with that in a nuclear gene. These results suggest recent incorporation of Tol2 into one or both of the two species, implying horizontal transfer of Tol2 from one species to the other or into them both from a common source. 相似文献
45.
Yuriko Uehara Katsutoshi Oda Yuji Ikeda Takahiro Koso Shingo Tsuji Shogo Yamamoto Kayo Asada Kenbun Sone Reiko Kurikawa Chinami Makii Otoe Hagiwara Michihiro Tanikawa Daichi Maeda Kosei Hasegawa Shunsuke Nakagawa Osamu Wada-Hiraike Kei Kawana Masashi Fukayama Keiichi Fujiwara Tetsu Yano Yutaka Osuga Tomoyuki Fujii Hiroyuki Aburatani 《PloS one》2015,10(6)
Ovarian clear cell carcinoma (CCC) is generally associated with chemoresistance and poor clinical outcome, even with early diagnosis; whereas high-grade serous carcinomas (SCs) and endometrioid carcinomas (ECs) are commonly chemosensitive at advanced stages. Although an integrated genomic analysis of SC has been performed, conclusive views on copy number and expression profiles for CCC are still limited. In this study, we performed single nucleotide polymorphism analysis with 57 epithelial ovarian cancers (31 CCCs, 14 SCs, and 12 ECs) and microarray expression analysis with 55 cancers (25 CCCs, 16 SCs, and 14 ECs). We then evaluated PIK3CA mutations and ARID1A expression in CCCs. SNP array analysis classified 13% of CCCs into a cluster with high frequency and focal range of copy number alterations (CNAs), significantly lower than for SCs (93%, P < 0.01) and ECs (50%, P = 0.017). The ratio of whole-arm to all CNAs was higher in CCCs (46.9%) than SCs (21.7%; P < 0.0001). SCs with loss of heterozygosity (LOH) of BRCA1 (85%) also had LOH of NF1 and TP53, and LOH of BRCA2 (62%) coexisted with LOH of RB1 and TP53. Microarray analysis classified CCCs into three clusters. One cluster (CCC-2, n = 10) showed more favorable prognosis than the CCC-1 and CCC-3 clusters (P = 0.041). Coexistent alterations of PIK3CA and ARID1A were more common in CCC-1 and CCC-3 (7/11, 64%) than in CCC-2 (0/10, 0%; P < 0.01). Being in cluster CCC-2 was an independent favorable prognostic factor in CCC. In conclusion, CCC was characterized by a high ratio of whole-arm CNAs; whereas CNAs in SC were mainly focal, but preferentially caused LOH of well-known tumor suppressor genes. As such, expression profiles might be useful for sub-classification of CCC, and might provide useful information on prognosis. 相似文献
46.
Eriko Simamura Tomohiro Arikawa Takayuki Ikeda Hiroki Shimada Hiroki Shoji Hiroko Masuta Yuriko Nakajima Hiroki Otani Hideto Yonekura Toshihisa Hatta 《PloS one》2015,10(4)
In this study, we showed that adrenocorticotropic hormone (ACTH) promoted erythroblast differentiation and increased the enucleation ratio of erythroblasts. Because ACTH was contained in hematopoietic medium as contamination, the ratio decreased by the addition of anti-ACTH antibody (Ab). Addition of neutralizing Abs (nAbs) for melanocortin receptors (MCRs) caused erythroblast accumulation at specific stages, i.e., the addition of anti-MC2R nAb led to erythroblast accumulation at the basophilic stage (baso-E), the addition of anti-MC1R nAb caused accumulation at the polychromatic stage (poly-E), and the addition of anti-MC5R nAb caused accumulation at the orthochromatic stage (ortho-E). During erythroblast differentiation, ERK, STAT5, and AKT were consecutively phosphorylated by erythropoietin (EPO). ERK, STAT5, and AKT phosphorylation was inhibited by blocking MC2R, MC1R, and MC5R, respectively. Finally, the phosphorylation of myosin light chain 2, which is essential for the formation of contractile actomyosin rings, was inhibited by anti-MC5R nAb. Taken together, our study suggests that MC2R and MC1R signals are consecutively required for the regulation of EPO signal transduction in erythroblast differentiation, and that MC5R signal transduction is required to induce enucleation. Thus, melanocortin induces proliferation and differentiation at baso-E, and polarization and formation of an actomyosin contractile ring at ortho-E are required for enucleation. 相似文献
47.
Yoshida Takanori Nagai Hisako Yahara Tetsukazu Tachida Hidenori 《Journal of plant research》2010,123(4):607-616
Zanthoxylum ailanthoides Siebold & Zucc. is one of the most frequently encountered pioneer trees in Japanese warm–temperate evergreen oak forests.
Our previous study in one region of Japan suggested high levels of population differentiation and putative natural selection
acting on one of the nuclear loci analyzed. Here, we extend our analysis to study the genetic structure of 10 populations
of Z. ailanthoides across Japan using 9 simple sequence repeat (SSR) loci for a better understanding of its genetic structure. First, the southernmost
population (Kagoshima) in the samples was found to have the highest genetic diversity, suggesting there was a glacial refugium
at or near the location of the population. Second, relatively strong genetic differentiation was found among populations,
and there was a positive correlation between genetic distances and geographic distances (Mantel test; P < 0.001). Based on this information, we analyzed nucleotide variation at the putatively selected locus homologous to the
gene encoding the ADP-glucose pyrophosphorylase large subunit (agpL). Despite the strong genetic differentiation among populations suggested by the SSR loci, the agpL locus was monomorphic in almost all populations analyzed. The results of this study strongly supported the possibility of
a selective sweep at or near the agpL locus. 相似文献
48.
Typical omega 3 polyunsaturated fatty acids (n-3 PUFAs) are docosahexaenoic acid and eicosapentaenoic acid in the form of fish oils and α linolenic acid from flaxseed oil. Epidemiological studies suggested the benefits of n-3 PUFA on cardiovascular health. Intervention studies confirmed that the consumption of n-3 PUFA provided benefits for primary and secondary prevention of cardiovascular disease. Evidence from cellular and molecular research studies indicates that the cardioprotective effects of n-3 PUFA result from a synergism between multiple, intricate mechanisms that involve antiinflammation, proresolving lipid mediators, modulation of cardiac ion channels, reduction of triglycerides, influence on membrane microdomains and downstream cell signaling pathways and antithrombotic and antiarrhythmic effects. n-3 PUFAs inhibit inflammatory signaling pathways (nuclear factor-κ B activity) and down-regulate fatty acid (FA) synthesis gene expression (sterol regulatory element binding protein-1c) and up-regulate gene expression involved in FA oxidation (peroxisome proliferator-activated receptor α). This review examines the various mechanisms by which n-3 PUFA exert beneficial effects against CVD. 相似文献
49.
Xia Y Chackalamannil S Greenlee WJ Wang Y Hu Z Root Y Wong J Kong J Ahn HS Boykow G Hsieh Y Kurowski S Chintala M 《Bioorganic & medicinal chemistry letters》2010,20(22):6676-6679
An analog of the thrombin receptor antagonist vorapaxar (SCH 530348) with increased aqueous solubility, compound 9c (SCH 602539), was discovered through incorporation of polar substituents on the pyridine ring of the himbacine-derived lead series. This analog retained the excellent potency, pharmacokinetic and safety properties of vorapaxar while increasing the aqueous solubility by 20-fold. Also presented are in vivo evaluations of this compound in a cynomolgus monkey platelet aggregation assay and in a Folts model of thrombosis in anesthetized monkeys. 相似文献
50.
Kitanishi K Kobayashi K Kawamura Y Ishigami I Ogura T Nakajima K Igarashi J Tanaka A Shimizu T 《Biochemistry》2010,49(49):10381-10393
YddV from Escherichia coli (Ec) is a novel globin-coupled heme-based oxygen sensor protein displaying diguanylate cyclase activity in response to oxygen availability. In this study, we quantified the turnover numbers of the active [Fe(III), 0.066 min(-1); Fe(II)-O(2) and Fe(II)-CO, 0.022 min(-1)] [Fe(III), Fe(III)-protoporphyrin IX complex; Fe(II), Fe(II)-protoporphyrin IX complex] and inactive forms [Fe(II) and Fe(II)-NO, <0.01 min(-1)] of YddV for the first time. Our data indicate that the YddV reaction is the rate-determining step for two consecutive reactions coupled with phosphodiesterase Ec DOS activity on cyclic di-GMP (c-di-GMP) [turnover number of Ec DOS-Fe(II)-O(2), 61 min(-1)]. Thus, O(2) binding and the heme redox switch of YddV appear to be critical factors in the regulation of c-di-GMP homeostasis. The redox potential and autoxidation rate of heme of the isolated heme domain of YddV (YddV-heme) were determined to be -17 mV versus the standard hydrogen electrode and 0.0076 min(-1), respectively. The Fe(II) complexes of Y43A and Y43L mutant proteins (residues at the heme distal side of the isolated heme-bound globin domain of YddV) exhibited very low O(2) affinities, and thus, their Fe(II)-O(2) complexes were not detected on the spectra. The O(2) dissociation rate constant of the Y43W protein was >150 s(-1), which is significantly larger than that of the wild-type protein (22 s(-1)). The autoxidation rate constants of the Y43F and Y43W mutant proteins were 0.069 and 0.12 min(-1), respectively, which are also markedly higher than that of the wild-type protein. The resonance Raman frequencies representing ν(Fe-O(2)) (559 cm(-1)) of the Fe(II)-O(2) complex and ν(Fe-CO) (505 cm(-1)) of the Fe(II)-CO complex of Y43F differed from those (ν(Fe-O(2)), 565 cm(-1); ν(Fe-CO), 495 cm(-1)) of the wild-type protein, suggesting that Tyr43 forms hydrogen bonds with both O(2) and CO molecules. On the basis of the results, we suggest that Tyr43 located at the heme distal side is important for the O(2) recognition and stability of the Fe(II)-O(2) complex, because the hydroxyl group of the residue appears to interact electrostatically with the O(2) molecule bound to the Fe(II) complex in YddV. Our findings clearly support a role of Tyr in oxygen sensing, and thus modulation of overall conversion from GTP to pGpG via c-di-GMP catalyzed by YddV and Ec DOS, which may be applicable to other globin-coupled oxygen sensor enzymes. 相似文献