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Search Results: 1 - 10 of 127512 matches for " Ya-Ping Zhang "
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Potential pitfalls in MitoChip detected tumor-specific somatic mutations: a call for caution when interpreting patient data
Malliya Palanichamy, Ya-Ping Zhang
BMC Cancer , 2010, DOI: 10.1186/1471-2407-10-597
Abstract: Published entire mitochondrial genomes from head and neck, adenoid cystic carcinoma, sessile serrated adenoma, and lung primary tumor from clinical patients were examined in a phylogenetic context and compared with known, naturally occurring mutations which characterize different populations.The phylogenetic linkage analysis of whole arrays of mtDNA mutations from patient cancerous and non-cancerous tissue confirmed that artificial recombination events occurred in studies of head and neck, adenoid cystic carcinoma, sessile serrated adenoma, and lung primary tumor. Our phylogenetic analysis of these tumor and control leukocyte mtDNA haplotype sequences shows clear cut evidence of mixed ancestries found in single individuals.Our study makes two prescriptions: both in the clinical situation and in research 1. more care should be taken in maintaining sample identity and 2. analysis should always be undertaken with respect to all the data available and within an evolutionary framework to eliminate artifacts and mix-ups.Mitochondrial DNA technology plays an exciting role in medical research especially the high throughput MitoChip for mtDNA mutation detection in cancer. In the past few years the MitoChip technique has uncovered a large number of mtDNA mutations in human head and neck, adenoid cystic carcinoma, sessile serrated adenoma, and lung primary tumors [1-6]. The majority of the MitoChip detected mutations were somatic (dominant in tumor cells) and it has been suggested that these mutations may be used as markers for the early diagnosis of cancer [2]. However, many of these early stages MitoChip detected cancer mutations require accurate validation before put into routine clinical practice. Many recorded mtDNA mutations in cancer samples are not fully reliable. Employing a phylogenetic analysis of mtDNA tumor profiles taken from a specific example in the literature, we demonstrate the pitfalls of using MitoChip identified mitochondrial mutations for clinical diagnos
Inferring the Population Expansions in Peopling of Japan
Min-Sheng Peng, Ya-Ping Zhang
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021509
Abstract: Background Extensive studies in different fields have been performed to reconstruct the prehistory of populations in the Japanese archipelago. Estimates the ancestral population dynamics based on Japanese molecular sequences can extend our understanding about the colonization of Japan and the ethnogenesis of modern Japanese. Methodology/Principal Findings We applied Bayesian skyline plot (BSP) with a dataset based on 952 Japanese mitochondrial DNA (mtDNA) genomes to depict the female effective population size (Nef) through time for the total Japanese and each of the major mtDNA haplogroups in Japanese. Our results revealed a rapid Nef growth since ~5 thousand years ago had left ~72% Japanese mtDNA lineages with a salient signature. The BSP for the major mtDNA haplogroups indicated some different demographic history. Conclusions/Significance The results suggested that the rapid population expansion acted as a major force in shaping current maternal pool of Japanese. It supported a model for population dynamics in Japan in which the prehistoric population growth initiated in the Middle Jomon Period experienced a smooth and swift transition from Jomon to Yayoi, and then continued through the Yayoi Period. The confounding demographic backgrounds of different mtDNA haplogroups could also have some implications for some related studies in future.
Different level of population differentiation among human genes
Dong-Dong Wu, Ya-Ping Zhang
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-16
Abstract: Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection.Our analysis demonstrates different level of population differentiation among human populations for different gene groups.After dispersal from Africa, humans have evolved to be characterized by substantial phenotypic variation, including variation in skin, hair, and eye color, body mass, height, diet, drug metabolism, susceptibility and resistance to disease, during the colonization of the World. Efforts to reveal the genetic bases of these variations should provide important insight into the history of human evolution, gene function, and the mechanisms of disease [1,2]. Indeed, with the advent of large scale comparative genomic and human polymorphism data, a flood of studies have identified many candidate g
Summary of Phylogeny in Mammalian Order Carnivora

YU Li,ZHANG Ya-ping,

动物学研究 , 2006,
Abstract: Tracing evolutionary relationships among organisms and re-constructing species phylogenetic trees is vital in evolutionary biology. Species in the mammalian order of Carnivora rank top in the animal food chain. Most carnivores have received great interest in the conservation of wild animals and are also crucial model animals for the study of the molecular mechanisms of adaptive evolution. As an order bearing important evolutionarily significance and conservation value, the phylogeny of Carnivora has received special attention. In this article, we reviewed higher-level (interfamilial) phylogeny of carnivores based on previous cytological, morphological and molecular evidence and indicated the existing phylogenetic problems. This review is expected to guide future research of carnivore phylogeny, and also provide theoretical evidence for the use of this order as a model in the study of adaptive evolution.
Ya-Ping Wang,Ning Zhang,Xiang He,Min Shao
Acta Crystallographica Section E , 2011, DOI: 10.1107/s1600536811017661
Abstract: The solvothermal reaction of Co(NO3)2 and 2,4,6-tris(4-pyridyl)-1,3,5-triazine in dimethylformamide/ethanol mixed solvent afforded the title coordination polymer, [Co(NO3)2(C18H12N6)]n, in which the CoII atom is seven-coordinated by pyridyl groups of three different ligands and two chelating nitrate anions. The complex displays a nano-sized porous metal–organic framework that belongs to a (10,3) topological network.
Cloning of Novel Pituitary Growth Hormone Gene from Rhinopithecus roxellanae
川金丝猴垂体生长激素基因的克隆与初步分析 Cloning of Novel Pituitary Growth Hormone Gene from Rhinopithecus roxellanae

Chun Ye,Ya-Ping Zhang,
,张亚平YE Chun,ZHANG Ya-Ping

遗传 , 2003,
Abstract: Putative pituitary growth hormone gene of Rhinopithecus roxellanae was cloned and sequenced. All exons sequences and deduced amino acid sequence (containing 26 residues signal peptide and 191 residues mature protein) were obtained. We constructed a phylogenetic tree,which well reflected the true evolutionary relationship of pituitary growth hormone genes from 7 primates species.From the results of amino acids sequence comparison and analysis of functionally important sites of growth hormone, pituitary growth hormone of macaque from Cercopithecidae and snub-nosed golden monkey from Colobidae show little difference. We indicated that pituitary growth hormone from Cercopithecoidea species have no apparently functional difference.
A Survey on Position-Based Routing Algorithms in Wireless Sensor Networks
Zhang Jin,Yu Jian-Ping,Zhou Si-Wang,Lin Ya-Ping,Li Guang
Algorithms , 2009, DOI: 10.3390/a2010158
Abstract: Wireless sensor networks (WSN) have attracted much attention in recent years for its unique characteristics and wide use in many different applications. Routing protocol is one of key technologies in WSN. In this paper, the position-based routing protocols are surveyed and classified into four categories: flooding-based, curve-based, grid-based and ant algorithm-based intelligent. To each category, the main contribution of related routing protocols is shown including the relationship among the routing protocols. The different routing algorithms in the same category and the different categories are compared based on popular metrics. Moreover, some open research directions in WSN are also discussed.
Absence of association between SERPINE2 genetic polymorphisms and chronic obstructive pulmonary disease in Han Chinese: a case-control cohort study
Li Zhong, Wei-Ping Fu, Chang Sun, Lu-Ming Dai, Ya-Ping Zhang
BMC Medical Genetics , 2009, DOI: 10.1186/1471-2350-10-66
Abstract: In this study, five proposed causal SNPs in SERPINE2 were genotyped in 327 COPD patients and 349 controls, all of which belonged to the Han population sampled from Southwest China. The frequency of each SNP was compared both individually and in combination between patients and controls. The potential relationship between these SNPs and severity of COPD was also investigated.Three SNPs (rs3795877, rs6747096, and rs3795879) showed complete linkage disequilibrium (r2 = 1), and the minor allele frequencies were 13.0% and 12.9% in case and control cohorts, respectively, with no significant difference observed (P = 0.96). We also failed to observe any significant correlation between these SNPs and COPD severity (P = 0.67). The other two SNPs (rs7579646 and rs840088) also presented a similar pattern. Moreover, four major haplotypes were observed in our sample but none showed a significant difference between case and control groups (P > 0.1).Our results failed to obtain the evidence that these SNPs in SERPINE2 contributed to the COPD susceptibility in the Han Chinese population.Chronic obstructive pulmonary disease (COPD, MIM# 606963), one of the major sources of morbidity all over the world [1], is characterized by airflow limitation that is not fully reversible and a chronic persistent inflammatory process [2]. Tobacco smoking has been proven to be the predominant environmental factor for COPD. However, only approximately 15% of smokers develop airway obstruction [3,4]. This phenomenon, together with the familial clustering in patients with COPD [5], suggested that genetic factors might play an important role in COPD development.Numerous studies have demonstrated that the balance between the serine proteases and serine protease inhibitors (SERPINs) is important in maintaining the matrix biology of the lung cells [6-8] and an imbalance between these two factors has been a long-standing hypothesis to explain lung destruction in emphysema during developing COPD [7]. However,
Exclusive gene mapping of congenital microphthalmia in a Chinese family
Yanan Yin,Hui Li,Ping Yu,Qiang Zhou,Luhang Zhao,Ya-Ping Zhang
Chinese Science Bulletin , 2006, DOI: 10.1007/s11434-006-2210-1
Abstract: Congenital microphthalmia is a developmental ocular disorder and might be caused by the mutations in the genes involved in eye development. To uncover the genetic cause in a six-generation Chinese pedigree with autosomal dominant congenital microphthalmia, we performed genescan and linkage analysis in this family. Fourteen microsatellite markers on chromosomes 3, 11, 14 and 15 were selected as genetic markers according to the five previously reported loci associated with microphthalmia (MITF, SOX2, PAX6, MCOP and NNO2). The genomic DNA of each member in the pedigree was amplified with 14 pairs of fluorescence labeled primers. Genome screening and genotyping were conducted on ABI377 DNA sequencer and linkage analysis was performed with Linkage software package. All two-point LOD scores of linkage analysis between the suggested disease genes and microsatellite markers were < 2, which indicated that none of the five genes were responsible for microphthalmia in this Chinese family. Microphthalmia in this family may be caused by mutation in a new gene which is essential in eye development.
Intriguing Balancing Selection on the Intron 5 Region of LMBR1 in Human Population
Fang He, Dong-Dong Wu, Qing-Peng Kong, Ya-Ping Zhang
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002948
Abstract: Background The intron 5 of gene LMBR1 is the cis-acting regulatory module for the sonic hedgehog (SHH) gene. Mutation in this non-coding region is associated with preaxial polydactyly, and may play crucial roles in the evolution of limb and skeletal system. Methodology/Principal Findings We sequenced a region of the LMBR1 gene intron 5 in East Asian human population, and found a significant deviation of Tajima's D statistics from neutrality taking human population growth into account. Data from HapMap also demonstrated extended linkage disequilibrium in the region in East Asian and European population, and significantly low degree of genetic differentiation among human populations. Conclusion/Significance We proposed that the intron 5 of LMBR1 was presumably subject to balancing selection during the evolution of modern human.
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