Biomedical subjects

Ya-Ping Zhang

Publications and source records attributed to Ya-Ping Zhang.

At least 19 recordsLinked to original sources

PubMed2007

Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845).

The Northwestern Pacific has a unique tectonic and geographical history with several marginal seas separating Asia from the Pacific Ocean. During low sea level periods of Pleistocene glaciations, populations might have been isolated in three marginal seas: the Sea of Japan, East China Sea and South China Sea. Following postglacial sea level rise, we would expect the populations isolated in the three regions to have been homogenized by high dispersal potential. To assess these hypotheses, we explore the intraspecific phylogeographical patterns in redlip mullet, Chelon haematocheilus. Fragments of 435 bp at the 5' end of mitochondrial DNA control region were sequenced for 272 individuals from nine localities over most of the species' range. Three distinct lineages were detected, which might have diverged in the three marginal seas during Pleistocene low sea levels. Contrary to homogenization expectation, there were strong differences in the geographical distribution of the three lineages. Analyses of molecular variance and the population statistic Phi(ST) also revealed significant genetic structure among populations of the three marginal seas. These results indicate that gene flow in Chelon haematocheilus is far more restricted spatially than predicted by the potential dispersal capabilities of this species. The lack of phylogeographical structure in East China Sea may reflect a recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium.

Animals↗

PubMed2007

Relationship between COPD and polymorphisms of HOX-1 and mEPH in a Chinese population.

Recent studies have proposed that susceptibility to chronic obstructive pulmonary disease (COPD) might be related with the polymorphisms of some genes encoding antioxidant enzymes, such as heme oxygenase-1 (HOX-1) and microsomal epoxide hydrolase (mEPH). We examined these polymorphisms in 256 patients with COPD and 266 healthy smokers from Han population in Southwest China. The frequencies of each allele were compared both individually and in combination between patients and controls. Polymorphisms of HOX-1 gene could be grouped into three classes: S ( or=32 repeat). The allele frequencies of class L and the genotypic frequencies of the group with L were significantly higher in COPD than in controls. Our findings also showed that the proportion of slow mEPH activity was significantly higher in COPD than in controls. Conversely, the proportion of fast mEPH activity was significantly lower in COPD. In combined analysis, the frequency of the individuals having at least one L allele in the HOX-1 gene promoter and slow or very slow activity genotype for mEPH was higher in COPD than in control. Genetic polymorphisms in HOX-1 and mEPH genes are associated with the development of COPD in Southwest China.

Aged↗

PubMed2006

The role of climate in human mitochondrial DNA evolution: a reappraisal.

Previous studies have proposed that selection has been involved in the differentiation of human mitochondrial DNA (mtDNA) and climate was the main driving force. This viewpoint, however, gets no support from the subsequent studies and remains controversial thus far. To clarify this issue, a total of 237 complete mtDNA sequences belonging to autochthonous lineages from South Asia, Oceania, and East Asia were collected to seek for the imprint of selection. Based on nonsynonymous (N) and synonymous (S) substitutions analysis, our results confirmed that purifying selection was the predominant force during the evolution of human mtDNA. However, no significant and extensive difference was detected among these three regions, which did not support the climate adaptation hypothesis but preferred random genetic drift to be the main factor in shaping the current landscape of human mtDNA, at least those from Asian and Oceanian regions.

Amino Acid Substitution↗

PubMed2006

Haplotype frequency distribution and linkage disequilibrium analysis of single nucleotide polymorphisms at the human FMO3 gene locus.

We analyzed flavin-containing monooxygenase 3 (FMO3) polymorphisms, haplotype structure, and linkage disequilibrium (LD) in 256 Han Chinese and 50 African-American individuals to compare their haplotype frequencies and LD with other world populations. For the Han Chinese, genotyping of three haplotype tag single nucleotide polymorphisms (E158K, V257M, and E308G) was performed by polymerase chain reaction (PCR)-restriction fragment length polymorphism. For the African-Americans, genotyping of all coding exons was performed by modified PCR-single strand conformational polymorphism. Haplotype frequencies, LD, and evolutionary rates were inferred and estimated computationally. There were significant differences in haplotype frequency distribution and LD pattern among Han Chinese, African-Americans, and other world populations. Four major haplotypes of Han Chinese were EVE, KVE, EME, and EVG. Two major haplotypes of African-Americans were EVE and KVE. We found that sites 158 and 257 are in significant LD in both populations. This is the first report comparing FMO haplotypes and LD of Han Chinese with African-Americans. The data presented here justify further pharmacogenetic studies for potentially optimizing recommended drug dosages and evaluating relationships with disease processes.

Adult↗

PubMed2006

mtDNA mutation C1494T, haplogroup A, and hearing loss in Chinese.

Mutation C1494T in mitochondrial 12S rRNA gene was recently reported in two large Chinese families with aminoglycoside-induced and nonsyndromic hearing loss (AINHL) and was claimed to be pathogenic. This mutation, however, was first reported in a sample from central China in our previous study that was aimed to reconstruct East Asian mtDNA phylogeny. All these three mtDNAs formed a subclade defined by mutation C1494T in mtDNA haplogroup A. It thus seems that mutation C1494T is a haplogroup A-associated mutation and this matrilineal background may contribute a high risk for the penetrance of mutation C1494T in Chinese with AINHL. To test this hypothesis, we first genotyped mutation C1494T in 553 unrelated individuals from three regional Chinese populations and performed an extensive search for published complete or near-complete mtDNA data sets (>3000 mtDNAs), we then screened the C1494T mutation in 111 mtDNAs with haplogroup A status that were identified from 1823 subjects across China. The search for published mtDNA data sets revealed no other mtDNA besides the above-mentioned three carrying mutation C1494T. None of the 553 randomly selected individuals and the 111 haplogroup A mtDNAs was found to bear this mutation. Therefore, our results suggest that C1494T is a very rare event. The mtDNA haplogroup A background in general is unlikely to play an active role in the penetrance of mutation C1494T in AINHL.

Aminoglycosides↗

PubMed2006

Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations.

Knowledge about the world phylogeny of human mitochondrial DNA (mtDNA) is essential not only for evaluating the pathogenic role of specific mtDNA mutations but also for performing reliable association studies between mtDNA haplogroups and complex disorders. In the past few years, the main features of the East Asian portion of the mtDNA phylogeny have been determined on the basis of complete sequencing efforts, but representatives of several basal lineages were still lacking. Moreover, some recently published complete mtDNA sequences did apparently not fit into the known phylogenetic tree and conflicted with the established nomenclature. To refine the East Asian mtDNA tree and resolve data conflicts, we first completely sequenced 20 carefully selected mtDNAs--likely representatives of novel sub-haplogroups--and then, in order to distinguish diagnostic mutations of novel haplogroups from private variants, we applied a 'motif-search' procedure to a large sample collection. The novel information was incorporated into an updated East Asian mtDNA tree encompassing more than 1000 (near-) complete mtDNA sequences. A reassessment of the mtDNA data from a series of disease studies testified to the usefulness of such a refined mtDNA tree in evaluating the pathogenicity of mtDNA mutations. In particular, the claimed pathogenic role of mutations G3316A, T3394C, A4833G and G15497A appears to be most questionable as those initial claims were derived from anecdotal findings rather than e.g. appropriate association studies. Following a guideline based on the phylogenetic knowledge as proposed here could help avoiding similar problems in the future.

Asian People↗

PubMed2006

Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis).

Climatic oscillations during the Pleistocene ice ages produced great changes in species' geographical distribution and abundance, which could be expected to have genetic consequences. Living in the temperate upwelling zones of the northwestern Pacific, Japanese anchovy (Engraulis japonicus) might have been affected by these severe climatic oscillations. To investigate the effects of Pleistocene climatic changes on the evolution in Japanese anchovy, fragments of 522 bp at the 5' end of mitochondrial DNA control region were sequenced for 241 individuals from 13 localities and 37 individuals of Australian anchovy. Japanese anchovy and Australian anchovy are reciprocally monophyletic and a late Pleistocene transequatorial divergence between the two species was indicated. High levels of haplotype diversity (>0.99) were found for all samples, indicating a high level of genetic diversity. Analyses of molecular variance and the conventional population statistic F(ST) revealed no significant genetic structure throughout the range of Japanese anchovy. Both mismatch distribution analyses and neutrality tests suggested a late Pleistocene population expansion for both Japanese anchovy (79,000-317,000 years ago) and Australian anchovy (45,000-178,000 years ago).

Animals↗

PubMed2006

Origin, genetic diversity, and population structure of Chinese domestic sheep.

To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions.

Animal Migration↗

PubMed2006

Interleukin-1 beta up-regulates tissue inhibitor of matrix metalloproteinase-1 mRNA and phosphorylation of c-jun N-terminal kinase and p38 in hepatic stellate cells.

AIM: To study the relationship between interleukin-1beta (IL-1beta) up-regulating tissue inhibitor of matrix metalloproteinase-1 (TIMMP-1) mRNA expression and phosphorylation of both c-jun N-terminal kinase (JNK) and p38 in rat hepatic stellate cells (HSC). METHODS: RT-PCR was performed to measure the expression of TIMMP-1 mRNA in rat HSC. Western blot was performed to measure IL-1beta-induced JNK and p38 activities in rat HSC. RESULTS: TIMMP-1 mRNA expression (1.191+/-0.079) was much higher after treatment with IL-1beta (10 ng/mL) for 24 h than in control group (0.545+/-0.091) (P<0.01). IL-1beta activated JNK and p38 in a time-dependent manner. After stimulation with IL-1beta for 0, 5, 15, 30, 60 and 120 min,the JNK activity was 0.982+/-0.299,1.501+/-0.720, 2.133+/-0.882, 3.360+/-0.452, 2.181+/-0.789, and 1.385+/-0.368, respectively. There was a significant difference in JNK activity at 15 min (P<0.01), 30 min (P<0.01) and 60 min (P<0.01) in comparison to that at 0 min. The p38 activity was 1.061+/-0.310,2.050+/-0.863, 2.380+/-0.573, 2.973+/-0.953, 2.421+/-0.793, and 1.755+/-0.433 at the 6 time points (0, 5, 15, 30, 60 and 120 min) respectively. There was a significant difference in p38 activity at 5 min (P<0.05),15 min (P<0.01), 30 min (P<0.01) and 60 min (P<0.01) compared to that at 0 min.TIMMP-1 mRNA expression trended to decrease in 3 groups pretreated with different concentrations of SP600125 (10 micromol/L, 1.022+/-0.113; 20 micromol/L, 0.869+/-0.070; 40 micromol/L, 0.666+/-0.123). Their decreases were all significant (P<0.05, P<0.01, P<0.01) in comparison to control group (without SP600125 treatment, 1.163+/-0.107). In the other 3 groups pretreated with different concentrations of SB203580 (10 micromol/L, 1.507+/-0.099; 20 micromol/L, 1.698+/-0.107; 40 micromol/L,1.857+/-0.054), the expression of TIMMP-1 mRNA increased. Their levels were higher than those in the control group (without SB203580 treatment, 1.027+/-0.061) with a significant statistical significance (P<0.01). CONCLUSION: IL-1beta has a direct action on hepatic fibrosis by up-regulating TIMMP-1 mRNA expression in rat HSC. JNK and p38 mitogen-activated protein kinases (MAPKs) are involved in IL-1beta-induced TIMMP-1 gene expression,and play a distinct role in this process, indicating that p38 and JNK pathways cooperatively mediate TIMP-1 mRNA expression in rat HSC.

Animals↗

PubMed2006

Differential population structuring and demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus) and spotted sea bass (Lateolabrax maculatus) in Northwestern Pacific.

The Quaternary cold periods in the Northwestern Pacific are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in marine fishes. To estimate the demographic history and genetic structure of Lateolabrax maculatus and L. japonicus in the Northwestern Pacific, 256 individuals were sampled from 19 localities throughout the distribution range of the two species. Mitochondrial DNA variation was analyzed using DNA sequence data from the cytochrome b gene and control region. Nucleotide diversity was much higher in L. japonicus (0.030) than in L. maculatus (0.012). The demographic history of the two species was examined using neutrality tests and mismatch distribution analyses and results indicated Pleistocene population expansion in both species. Estimates of population expansion time suggested earlier population expansion in L. japonicus than in L. maculatus. Molecular variance analyses showed differential genetic structuring for these two closely related species. The results indicated that L. japonicus is panmictic throughout its range. In contrast, populations of L. maculatus showed statistically significant levels of genetic structuring. Pattern of isolation by distance was observed in L. maculatus, suggesting that L. maculatus is in genetic equilibrium. In contrast, L. japonicus did not exhibit isolation by distance.

Animals↗

PubMed2006

Mitochondrial data support an odd-nosed colobine clade.

To obtain a more complete understanding of the evolutionary history of the leaf-eating monkeys we have examined the mitochondrial genome sequence of two African and six Asian colobines. Although taxonomists have proposed grouping the "odd-nosed" colobines (proboscis monkey, douc langur, and the snub-nosed monkey) together, phylogenetic support for such a clade has not been tested using molecular data. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian methods support a monophyletic clade of odd-nosed colobines consisting of Nasalis, Pygathrix, and Rhinopithecus, with tentative support for Nasalis occupying a basal position within this clade. The African and Asian colobine lineages are inferred to have diverged by 10.8 million years ago (mya or Ma). Within the Asian colobines the odd-nosed clade began to diversify by 6.7 Ma. These results augment our understanding of colobine evolution, particularly the nature and timing of the colobine expansion into Asia. This phylogenetic information will aid those developing conservation strategies for these highly endangered, diverse, and unique primates.

Animals↗

PubMed2006

Comment on "Reconstructing the origin of Andaman islanders".

On the basis of mitochondrial DNA sequence analyses, Thangaraj et al. (Brevia, 13 May 2005, p. 996) proposed that Andaman islanders descended from the first humans to migrate out of Africa. We identified mitochondrial DNA from two northeast Indian Rajbanshi individuals that shares three specific mutations with the M31a lineage observed in the Great Andamanese, which suggests that the predecessor of haplogroup M31 originated on the Indian subcontinent.

Africa↗

PubMed2006

Molecular evolution of prolactin gene family in rodents.

In this study, we identified two novel members of prolactin gene family in rat by blast searches against the published genomic database. A further analysis showed that gene duplications leading to PRL gene family in rodents occurred after rodents diverged from other mammals. Major reorganization of the gene loci in rodents was largely completed before the split of rat and mouse. But PL-I and PL-II genes are the exceptions, which have clustered in a species-specific manner in the phylogenetic tree. By combining results from gene conversion testing, relative chromosomal location comparison and estimated time for gene duplication, we believe that rodent PL-1 and PL-II genes are species-specific and are the results of serial duplications which occurred after the divergence of mouse and rat. Our analysis also reveals that continual gene duplication and divergence occurred during the evolution of rodent PRL gene family.

Amino Acid Sequence↗

PubMed2006

[Phylogenomics--an attractive avenue to reconstruct "tree of life"].

The successive start-up of genome project in recent years has far-reaching impact on present phylogenetic studies. A new synthesized discipline--"Phylogenomics", combing genomics with phylogenetics together, is emerging, and becomes an attractive avenue to reconstruct "Tree of Life". In the review, the conception and analytic method of phylogenomics are summarized. The potential problems are also suggested.

Animals↗

PubMed2006

[Genetic diversity and population structure of BMY and brahman cattle revealed by six microsatellite loci].

The genetic variations and polymorphisms of six microsatellite loci were analyzed to determine the population structure and breeding progress of BMY and Brahman cattle. The range of polymorphic information content of six loci was 0.524-0.752. The unbiased expected and observed heterozygosity were similar and were 0.7376 and 0.7396, 0.6412 and 0.6537 for BMY and Brahman cattle, respectively. The expected heterozygosity was relatively high in the second generation of BMY in inter se breeding, which was congruent with the breeding progress. In addition, the value for Red Angus was 0.4609, which was lower and close to the Japanese Brown cattle (0.471), and may indicate its relative homogeneity.

Animals↗

PubMed2006

[Population genetics of Rhinopithecus bieti: a study of the mitochondrial control region].

Yunnan snub-nose monkey (Rhinopithecus bieti) is a famous endangered primate in China. So far, however, studies on its population genetics based on DNA sequences are not available. In this paper, the whole mitochondria control region of the samples from Weixi, Yunan Province as well as the whole cytochrome b gene in some individuals were sequenced. A deep divergence was observed within the Weixi population, which was confirmed after excluding the possibility of it being a nuclear pseudogene. Nonetheless, if the effects of population structure and migration are considered, the true level of polymorphism of the Weixi population may be not as high as observed.

Animals↗

PubMed2005

The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes.

Many efforts based on complete mitochondrial DNA (mtDNA) genomes have been made to depict the global mtDNA landscape, but the phylogeny of Indian macrohaplogroup M has not yet been resolved in detail. To fill this lacuna, we took the same strategy as in our recent analysis of Indian mtDNA macrohaplogroup N and selected 56 mtDNAs from over 1,200 samples across India for complete sequencing, with the intention to cover all Indian autochthonous M lineages. As a result, the phylogenetic status of previously identified haplogroups based on control-region and/or partial coding-region information, such as M2, M3, M4, M5, M6, M30, and M33, was solidified or redefined here. Moreover, seven novel basal M haplogroups (viz., M34-M40) were identified, and yet another five singular branches of the M phylogeny were discovered in the present study. The comparison of matrilineal components among India, East Asia, Southeast Asia, and Oceania at the deepest level yielded a star-like and nonoverlapping pattern, reflecting a rapid mode of modern human dispersal along the Asian coast after the initial "out-of-Africa" event.

DNA, Mitochondrial↗

PubMed2005

Multiple maternal origins of chickens: out of the Asian jungles.

Domestic chickens have long been important to human societies for food, religion, entertainment, and decorative uses, yet the origins and phylogeography of chickens through Eurasia remain uncertain. Here, we assessed their origins and phylogeographic history by analyzing the mitochondrial DNA hypervariable segment I (HVS-I) for 834 domestic chickens (Gallus gallus domesticus) across Eurasia as well as 66 wild red jungle fowls (Gallus gallus) from Southeast Asia and China. Phylogenetic analyses revealed nine highly divergent mtDNA clades (A-I) in which seven clades contained both the red jungle fowls and domestic chickens. There was no breed-specific clade in the chickens. The clades A, B, and E are distributed ubiquitously in Eurasia, while the other clades were restricted to South and Southeast Asia. Clade C was mainly distributed in Japan and Southeast China, while clades F and G were exclusive to Yunnan, China. The geographic distribution of clade D was closely related to the distribution of the pastime of cock fighting. Statistical tests detect population expansion within each subclade. These distinct distribution patterns and expansion signatures suggest that different clades may originate from different regions, such as Yunnan, South and Southwest China and/or surrounding areas (i.e., Vietnam, Burma, and Thailand), and the Indian subcontinent, respectively, which support the theory of multiple origins in South and Southeast Asia.

Amino Acid Sequence↗