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Search Results: 1 - 10 of 39859 matches for " Qing-Peng Kong "
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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.
Mitochondrial DNA Content Contributes to Climate Adaptation Using Chinese Populations as a Model
Yao-Ting Cheng, Jia Liu, Li-Qin Yang, Chang Sun, Qing-Peng Kong
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0079536
Abstract: Maintaining a balance between ATP synthesis and heat generation is crucial for adapting to changes in climate. Variation in the mitochondrial DNA (mtDNA), which encodes 13 subunits of the respiratory chain complexes, may contribute to climate adaptation by regulating thermogenesis and the use of bioenergy. However, studies looking for a relationship between mtDNA haplogroups and climate have obtained mixed results, leaving unresolved the role of mtDNA in climate adaptation. Since mtDNA content can regulate human bioenergy processes and is known to influence many physiological traits and diseases, it is possible that mtDNA content contributes to climate adaptation in human populations. Here, we analyze the distribution of mtDNA content among 27 Chinese ethnic populations residing across China and find a significant association between mtDNA content and climate, with northern populations having significantly higher mtDNA content than southern populations. Functional studies have shown that high mtDNA content correlates with an increase in the expression of energy metabolism enzymes, which may accelerate thermogenesis. This suggests that the significantly higher mtDNA content observed in northern populations may confer a selective advantage in adapting to colder northern climates
Huan WU,Yong-Han HE,Tian-Rui XU,Qing-Peng KONG
动物学研究 , 2015,
Distilling Artificial Recombinants from Large Sets of Complete mtDNA Genomes
Qing-Peng Kong, Antonio Salas, Chang Sun, Noriyuki Fuku, Masashi Tanaka, Li Zhong, Cheng-Ye Wang, Yong-Gang Yao, Hans-Jürgen Bandelt
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003016
Abstract: Background Large-scale genome sequencing poses enormous problems to the logistics of laboratory work and data handling. When numerous fragments of different genomes are PCR amplified and sequenced in a laboratory, there is a high immanent risk of sample confusion. For genetic markers, such as mitochondrial DNA (mtDNA), which are free of natural recombination, single instances of sample mix-up involving different branches of the mtDNA phylogeny would give rise to reticulate patterns and should therefore be detectable. Methodology/Principal Findings We have developed a strategy for comparing new complete mtDNA genomes, one by one, to a current skeleton of the worldwide mtDNA phylogeny. The mutations distinguishing the reference sequence from a putative recombinant sequence can then be allocated to two or more different branches of this phylogenetic skeleton. Thus, one would search for two (or three) near-matches in the total mtDNA database that together best explain the variation seen in the recombinants. The evolutionary pathway from the mtDNA tree connecting this pair together with the recombinant then generate a grid-like median network, from which one can read off the exchanged segments. Conclusions We have applied this procedure to a large collection of complete human mtDNA sequences, where several recombinants could be distilled by our method. All these recombinant sequences were subsequently corrected by de novo experiments – fully concordant with the predictions from our data-analytical approach.
The Phylogeny of the Four Pan-American MtDNA Haplogroups: Implications for Evolutionary and Disease Studies
Alessandro Achilli, Ugo A. Perego, Claudio M. Bravi, Michael D. Coble, Qing-Peng Kong, Scott R. Woodward, Antonio Salas, Antonio Torroni, Hans-Jürgen Bandelt
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001764
Abstract: Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs. In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception) using the conventional calibration. The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America. In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds.
Uncovering the Profile of Somatic mtDNA Mutations in Chinese Colorectal Cancer Patients
Cheng-Ye Wang, Hui Li, Xiao-Dan Hao, Jia Liu, Jia-Xin Wang, Wen-Zhi Wang, Qing-Peng Kong, Ya-Ping Zhang
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021613
Abstract: In the past decade, a high incidence of somatic mitochondrial DNA (mtDNA) mutations has been observed, mostly based on a fraction of the molecule, in various cancerous tissues; nevertheless, some of them were queried due to problems in data quality. Obviously, without a comprehensive understanding of mtDNA mutational profile in the cancerous tissue of a specific patient, it is unlikely to disclose the genuine relationship between somatic mtDNA mutations and tumorigenesis. To achieve this objective, the most straightforward way is to directly compare the whole mtDNA genome variation among three tissues (namely, cancerous tissue, para-cancerous tissue, and distant normal tissue) from the same patient. Considering the fact that most of the previous studies on the role of mtDNA in colorectal tumor focused merely on the D-loop or partial segment of the molecule, in the current study we have collected three tissues (cancerous, para-cancerous and normal tissues) respectively recruited from 20 patients with colorectal tumor and completely sequenced the mitochondrial genome of each tissue. Our results reveal a relatively lower incidence of somatic mutations in these patients; intriguingly, all somatic mutations are in heteroplasmic status. Surprisingly, the observed somatic mutations are not restricted to cancer tissues, for the para-cancer tissues and distant normal tissues also harbor somatic mtDNA mutations with a lower frequency than cancerous tissues but higher than that observed in the general population. Our results suggest that somatic mtDNA mutations in cancerous tissues could not be simply explained as a consequence of tumorigenesis; meanwhile, the somatic mtDNA mutations in normal tissues might reflect an altered physiological environment in cancer patients.
Mitochondrial DNA Haplogroup Background Affects LHON, but Not Suspected LHON, in Chinese Patients
A-Mei Zhang, Xiaoyun Jia, Rui Bi, Antonio Salas, Shiqiang Li, Xueshan Xiao, Panfeng Wang, Xiangming Guo, Qing-Peng Kong, Qingjiong Zhang, Yong-Gang Yao
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027750
Abstract: Recent studies have shown that mtDNA background could affect the clinical expression of Leber hereditary optic neuropathy (LHON). We analyzed the mitochondrial DNA (mtDNA) variation of 304 Chinese patients with m.11778G>A (sample #1) and of 843 suspected LHON patients who lack the three primary mutations (sample #2) to discern mtDNA haplogroup effect on disease onset. Haplogroup frequencies in the patient group was compared to frequencies in the general Han Chinese population (n = 1,689; sample #3). The overall matrilineal composition of the suspected LHON population resembles that of the general Han Chinese population, suggesting no association with mtDNA haplogroup. In contrast, analysis of these LHON patients confirms mtDNA haplogroup effect on LHON. Specifically, the LHON sample significantly differs from the general Han Chinese and suspected LHON populations by harboring an extremely lower frequency of haplogroup R9, in particular of its main sub-haplogroup F (#1 vs. #3, P-value = 1.46×10?17, OR = 0.051, 95% CI: 0.016–0.162; #1 vs. #2, P-value = 4.44×10?17, OR = 0.049, 95% CI: 0.015–0.154; in both cases, adjusted P-value <10?5) and higher frequencies of M7b (#1 vs. #3, adjusted P-value = 0.001 and #1 vs. #2, adjusted P-value = 0.004). Our result shows that mtDNA background affects LHON in Chinese patients with m.11778G>A but not suspected LHON. Haplogroup F has a protective effect against LHON, while M7b is a risk factor.
The neck-region polymorphism of DC-SIGNR in peri-centenarian from Han Chinese Population
Hui Li, Cheng-Ye Wang, Jia-Xin Wang, Nelson Tang, Liang Xie, Yuan-Ying Gong, Zhao Yang, Liang-You Xu, Qing-Peng Kong, Ya-Ping Zhang
BMC Medical Genetics , 2009, DOI: 10.1186/1471-2350-10-134
Abstract: Here we collected 361 peri-centenarian individuals (age ≥94 for female and age ≥90 for male) and 342 geographically matched controls (age 22-53, mean 35.0 ± 12.0) from Han Chinese. The VNTR polymorphism of the neck region was determined by PCR and genotype was called by separating the PCR products in agarose gel.A total of 11 genotypes and 5 alleles were found in our population. The genotype distribution, allele frequencies and homozygote proportion did not show a significant difference between peri-centenarian and control group. As gender differences in lifespan are ubiquitously observed throughout the animal kingdom, we then stratified the samples by gender. There was more 6/7 genotypes in female peri-centenarian group than that in female control group, at a marginal level of significance (5.56 vs. 1.28%, p = 0.041). The difference was not significant after correction by Bonferroni method. It suggests a possible differential effect of DC-SIGNR VNTR genotypes between sexes. Further studies are warranted to confirm our preliminary findings and investigate the mechanisms of the underlying functions.Our study indicated that there was absence of association between the neck region polymorphism of DC-SIGNR and longevity in Han Chinese population. But the question of whether the DC-SIGNR could affect longevity in a gender-specific pattern remains open.Dendritic cell-specific intracellular adhesion molecular-3-grabbing nonintegrin (DC-SIGN) and DC-SIGN related (DC-SIGNR) are C-type lectins involved in both innate and adaptive immunity. As DC-SIGN and DC-SIGNR originated from the duplication of the same ancestral gene, they are located side-by-side within a ~26-kb segment of chromosome 19p13.2-3 and they share similar functions as cell adhesion receptors and pathogen recognition receptors[1]. A large number of their binding targets are of clinical significance, including bacteria such as Mycobacterium tuberculosis, Helicobacter pylori, and certain Klebsiela pneumonia strai
Restudy on Dark Matter Time-Evolution in the Littlest Higgs model with T-parity
Qiao, Qing-Peng;Tang, Jian;Li, Xue-Qian
High Energy Physics - Phenomenology , 2007, DOI: 10.1088/0253-6102/50/5/40
Abstract: Following previous study, in the Littlest Higgs model (LHM), the heavy photon is supposed to be a possible dark matter candidate and its relic abundance of the heavy photon is estimated in terms of the Boltzman-Lee-Weinberg time-evolution equation. The effects of the T-parity violation is also considered. Our calculations show that when Higgs mass $M_H$ taken to be 300 GeV and don't consider T-parity violation, only two narrow ranges $133
1,5-Bis[1-(2,4-dihydroxyphenyl)ethylidene]carbonohydrazide dimethylformamide disolvate
Qing-Peng He,Bo Tan,Ze-Hua Lu
Acta Crystallographica Section E , 2010, DOI: 10.1107/s1600536810043151
Abstract: In the title compound, C17H18N4O5·2C3H7NO, two solvent molecules are linked to the main molecule via N—H...O and O—H...O hydrogen bonds, forming a hydrogen-bonded trimer. Intramolecular O—H...N hydrogen bonds influence the molecular conformation of the main molecule, and the two benzene rings form a dihedral angle of 10.55 (18)°. In the crystal, intermolecular O—H...O hydrogen bonds link hydrogen-bonded trimers into ribbons extending along the b axis.
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