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Search Results: 1 - 10 of 32572 matches for " Xiaoqiu Huang "
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Horizontal transfer generates genetic variation in an asexual pathogen
Xiaoqiu Huang
PeerJ , 2015, DOI: 10.7717/peerj.650
Abstract: There are major gaps in the understanding of how genetic variation is generated in the asexual pathogen Verticillium dahliae. On the one hand, V. dahliae is a haploid organism that reproduces clonally. On the other hand, single-nucleotide polymorphisms and chromosomal rearrangements were found between V. dahliae strains. Lineage-specific (LS) regions comprising about 5% of the genome are highly variable between V. dahliae strains. Nonetheless, it is unknown whether horizontal gene transfer plays a major role in generating genetic variation in V. dahliae. Here, we analyzed a previously sequenced V. dahliae population of nine strains from various geographical locations and hosts. We found highly homologous elements in LS regions of each strain; LS regions of V. dahliae strain JR2 are much richer in highly homologous elements than the core genome. In addition, we discovered, in LS regions of JR2, several structural forms of nonhomologous recombination, and two or three homologous sequence types of each form, with almost each sequence type present in an LS region of another strain. A large section of one of the forms is known to be horizontally transferred between V. dahliae strains. We unexpectedly found that 350 kilobases of dynamic LS regions were much more conserved than the core genome between V. dahliae and a closely related species (V. albo-atrum), suggesting that these LS regions were horizontally transferred recently. Our results support the view that genetic variation in LS regions is generated by horizontal transfer between strains, and by chromosomal reshuffling reported previously.
Association between Experiences and Representations: Memory, Dreaming, Dementia and Consciousness
Xiaoqiu Huang
Quantitative Biology , 2013,
Abstract: The mechanisms underlying major aspects of the human brain remain a mystery. It is unknown how verbal episodic memory is formed and integrated with sensory episodic memory. There is no consensus on the function and nature of dreaming. Here we present a theory for governing neural activity in the human brain. The theory describes the mechanisms for building memory traces for entities and explains how verbal memory is integrated with sensory memory. We infer that a core function of dreaming is to move charged particles such as calcium ions from the hippocampus to association areas to primary areas. We link a high level of calcium ions concentrations to Alzheimer's disease. We present a more precise definition of consciousness. Our results are a step forward in understanding the function and health of the human brain and provide the public with ways to keep a healthy brain.
Some General Inequalities for Choquet Integral  [PDF]
Xiuli Yang, Xiaoqiu Song, Leilei Huang
Applied Mathematics (AM) , 2015, DOI: 10.4236/am.2015.614201
Abstract: With the development of fuzzy measure theory, the integral inequalities based on Sugeno integral are extensively investigated. We concern on the inequalities of Choquuet integral. The main purpose of this paper is to prove the H?lder inequality for any arbitrary fuzzy measure-based Choquet integral whenever any two of these integrated functions f, g and h are comonotone, and there are three weights. Then we prove Minkowski inequality and Lyapunov inequality for Choquet integral. Moreover, when any two of these integrated functions f1, f2, , fn are comonotone, we also obtain the Hölder inequality, Minkowski inequality and Lyapunov inequality hold for Choquet integral.
A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage
Jianmin Wang, Xiaoqiu Huang
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-220
Abstract: We describe a computational method for finding common SNPs with allele frequencies in single-pass sequences of deep coverage. The method enhances a widely used program named PolyBayes in several aspects. We present results from our method and PolyBayes on eighteen data sets of human expressed sequence tags (ESTs) with deep coverage. The results indicate that our method used almost all single-pass sequences in computation of the allele frequencies of SNPs.The new method is able to handle single-pass sequences of deep coverage efficiently. Our work shows that it is possible to analyze sequences of deep coverage by using pairwise alignments of the sequences with the finished genome sequence, instead of multiple sequence alignments.Information concerning the allele frequencies of single-nucleotide polymorphisms (SNPs) is needed to select an optimal subset of common SNPs for use in association studies [1]. One approach to finding common SNPs with allele frequencies is to generate DNA sequences from a sufficient number of samples in a population. This approach requires that computational methods have an ability to handle thousands of sequences from the same genome location (sequences of deep coverage). In this paper, we describe a computational method for finding common SNPs with allele frequencies in sequences of deep coverage. We present results from the method on human expressed sequence tags (ESTs) of deep coverage, which are currently a major source of DNA sequences of deep coverage. The method is also expected to be useful for finding common mutations in sequences of deep coverage produced in a cancer genome project [2].The PolyBayes program is widely used to find SNPs in redundant DNA sequences [3,4]. It first constructs a multiple sequence alignment based on pairwise alignments of each sequence with a high-quality genomic sequence called an anchor. Then it identifies and removes paralogous sequences that have a high number of observed differences with the anchor s
Obesity Induced by Neonatal Overfeeding Worsens Airway Hyperresponsiveness and Inflammation
Zehui Ye, Ying Huang, Dan Liu, Xiaoyi Chen, Dongjuan Wang, Daochao Huang, Li Zhao, Xiaoqiu Xiao
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047013
Abstract: Background Obesity is a risk factor for the development of certain respiratory diseases, and neonatal overfeeding results in an early onset of obesity in adulthood. However, the influence of neonatal overfeeding on respiratory diseases has rarely been studied. Therefore, this paper is aimed at investigating the effect of neonatal overfeeding on airway responsiveness and inflammation. Methodology/Principal Findings The neonatal overfeeding was induced by reducing litter size to three pups per litter (small litter, SL) in contrast to the normal litter size with ten pups per litter (NL) on postnatal day 3 (P3) in male ICR mice. On P21, mice were weaned to standard chow diet. Airway responsiveness to methacholine was measured either on P21 or P150. Total and classified inflammatory cells in bronchoalveolar lavage fluid (BALF) were counted, lung inflammatory cells were evaluated through staining with hematoxylin & eosin and F4/80 immunohistochemistry; lung fibrosis was evaluated through staining with Masson and α-SAM immunohistochemistry. Leptin levels in serum were measured by RIA; TNF-α levels in serum and BALF were quantified by ELISA; mRNA levels of TNF-α, CTGF and TGF-β1 in lung tissues were measured using real-time PCR. Mice from SL exhibited accelerated body weight gain, impaired glucose tolerance and hyperleptinemia. Enhanced airway responsiveness to methacholine was observed in SL mice on P150, but not on P21. Pulmonary inflammation was evident in SL mice on P150, as reflected by inflammatory cells especially macrophages around bronchi and interstitium. BALF and serum TNF-α levels and lung TNF-α mRNA expression were significantly increased in SL mice on P150. More collagen accumulated surrounding the bronchi on P150; lung mRNA levels of TGF-β1 and CTGF were also increased on P150. Conclusion In addition to inducing a variety of metabolic defects, neonatal overfeeding enhanced lung inflammation, which may lead to airway remodeling and airway hyperresponsiveness in adulthood.
Engaging hospitals to meet tuberculosis control targets in China: using the Internet as a tool to put policy into practice
Wang,Lixia; Liu,Xiaoqiu; Huang,Fei; Hennig,Cornelia; Uplekar,Mukund; Jiang,Shiwen;
Bulletin of the World Health Organization , 2010, DOI: 10.1590/S0042-96862010001200015
Abstract: tuberculosis (tb) services in china are provided through a large network of tb dispensaries. even though hospitals are not as well placed to follow recommended standards of tb care, a significant proportion of people with tb symptoms seek care from hospitals. in spite of having a policy and mandate in place, the ministry of health had little success in encouraging hospitals to refer suspected tb cases to dispensaries. following the epidemic of severe acute respiratory syndrome in 2003, the government set up a nationwide internet-based communicable diseases reporting system. this achieved productive collaboration between hospitals and tb dispensaries. from 2004 to 2007, the percentage of tb suspects and patients needing referral from hospitals who arrived in tb dispensaries increased substantially from 58.7% to 77.8% and the contribution of hospitals to diagnosing sputum smear-positive tb cases doubled from 16.3% to 32.9%. using the internet-based reporting system, hospitals in china contributed to finding about one third of all sputu m smear-positive tb cases and helped meet the global tb control target of detecting 70% of such cases. based on the data available from routine surveillance facilitated by this internet-based system, this paper details the process and outcomes of strengthening collaboration between hospitals and tb dispensaries using the internet as a tool and its potential application to other country settings.
The Genome Sequence of the Fungal Pathogen Fusarium virguliforme That Causes Sudden Death Syndrome in Soybean
Subodh K. Srivastava, Xiaoqiu Huang, Hargeet K. Brar, Ahmad M. Fakhoury, Burton H. Bluhm, Madan K. Bhattacharyya
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0081832
Abstract: Fusarium virguliforme causes sudden death syndrome (SDS) of soybean, a disease of serious concern throughout most of the soybean producing regions of the world. Despite the global importance, little is known about the pathogenesis mechanisms of F. virguliforme. Thus, we applied Next-Generation DNA Sequencing to reveal the draft F. virguliforme genome sequence and identified putative pathogenicity genes to facilitate discovering the mechanisms used by the pathogen to cause this disease. Methodology/Principal Findings We have generated the draft genome sequence of F. virguliforme by conducting whole-genome shotgun sequencing on a 454 GS-FLX Titanium sequencer. Initially, single-end reads of a 400-bp shotgun library were assembled using the PCAP program. Paired end sequences from 3 and 20 Kb DNA fragments and approximately 100 Kb inserts of 1,400 BAC clones were used to generate the assembled genome. The assembled genome sequence was 51 Mb. The N50 scaffold number was 11 with an N50 Scaffold length of 1,263 Kb. The AUGUSTUS gene prediction program predicted 14,845 putative genes, which were annotated with Pfam and GO databases. Gene distributions were uniform in all but one of the major scaffolds. Phylogenic analyses revealed that F. virguliforme was closely related to the pea pathogen, Nectria haematococca. Of the 14,845 F. virguliforme genes, 11,043 were conserved among five Fusarium species: F. virguliforme, F. graminearum, F. verticillioides, F. oxysporum and N. haematococca; and 1,332 F. virguliforme-specific genes, which may include pathogenicity genes. Additionally, searches for candidate F. virguliforme pathogenicity genes using gene sequences of the pathogen-host interaction database identified 358 genes. Conclusions The F. virguliforme genome sequence and putative pathogenicity genes presented here will facilitate identification of pathogenicity mechanisms involved in SDS development. Together, these resources will expedite our efforts towards discovering pathogenicity mechanisms in F. virguliforme. This will ultimately lead to improvement of SDS resistance in soybean.
A Genome-Wide Survey of Highly Expressed Non-Coding RNAs and Biological Validation of Selected Candidates in Agrobacterium tumefaciens
Keunsub Lee, Xiaoqiu Huang, Chichun Yang, Danny Lee, Vincent Ho, Kan Nobuta, Jian-Bing Fan, Kan Wang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0070720
Abstract: Agrobacterium tumefaciens is a plant pathogen that has the natural ability of delivering and integrating a piece of its own DNA into plant genome. Although bacterial non-coding RNAs (ncRNAs) have been shown to regulate various biological processes including virulence, we have limited knowledge of how Agrobacterium ncRNAs regulate this unique inter-Kingdom gene transfer. Using whole transcriptome sequencing and an ncRNA search algorithm developed for this work, we identified 475 highly expressed candidate ncRNAs from A. tumefaciens C58, including 101 trans-encoded small RNAs (sRNAs), 354 antisense RNAs (asRNAs), 20 5′ untranslated region (UTR) leaders including a RNA thermosensor and 6 riboswitches. Moreover, transcription start site (TSS) mapping analysis revealed that about 51% of the mapped mRNAs have 5′ UTRs longer than 60 nt, suggesting that numerous cis-acting regulatory elements might be encoded in the A. tumefaciens genome. Eighteen asRNAs were found on the complementary strands of virA, virB, virC, virD, and virE operons. Fifteen ncRNAs were induced and 7 were suppressed by the Agrobacterium virulence (vir) gene inducer acetosyringone (AS), a phenolic compound secreted by the plants. Interestingly, fourteen of the AS-induced ncRNAs have putative vir box sequences in the upstream regions. We experimentally validated expression of 36 ncRNAs using Northern blot and Rapid Amplification of cDNA Ends analyses. We show functional relevance of two 5′ UTR elements: a RNA thermonsensor (C1_109596F) that may regulate translation of the major cold shock protein cspA, and a thi-box riboswitch (C1_2541934R) that may transcriptionally regulate a thiamine biosynthesis operon, thiCOGG. Further studies on ncRNAs functions in this bacterium may provide insights and strategies that can be used to better manage pathogenic bacteria for plants and to improve Agrobacterum-mediated plant transformation.
Dispersive liquid-liquid microextraction coupled with high performance liquid chromatography for the determination of polynuclear aromatic hydrocarbons in environmental water samples

ZHANG Jianhua,HUANG Ying,CHEN Xiaoqiu,CHEN Jinhua,LI Hui,CHEN Guonan,

色谱 , 2009,
Abstract: A simple, rapid and effective method, the dispersive liquid-liquid microextraction coupled with high performance liquid chromatography-fluorescence detection (DLLME-HPLC-FLD), has been developed for the extraction and determination of polynuclear aromatic hydro-carbons (PAHs) in environmental water samples. The factors relevant to the microextraction efficiency, such as type and volume of dispersion agent and extraction solvents and the extrac-tion time were investigated and optimized. Under the optimized extraction conditions, the relia-bility of the proposed method was evaluated. The linear response of this method was in the range of 0. 01-10 μg/L (r≥0.991 3), the relative standard deviations (RSDs) of peak area for 0.05 μg/L PAHs were in the range of 2.3%-4. 7% (n = 6). At room temperature, the method exhibited excellent enrichment factors and good recoveries, 674-1 032 and 67. 4%-103. 2% respectively. The detection limits (S/N = 3) were in the range of 0. 000 3-0. 002 μg/L. The developed method was applied to the determination of 15 PAHs in the water from Aojiang river, the average recoveries were 79. 5%-92. 3% with RSD of 4. 3%-6. 7% (n=5). The developed method is suitable for the analysis of trace PAHs in environmental water samples.
Establishment of the Academic Value Judging System of the Science and Research Works

Tong Xiaoqiu,

中国科技期刊研究 , 2000,
Abstract: 人事部门的职评工作与年度考核工作改革的深化,呼唤科研成果和学术论著的科学合理透明及时且可操作性强的精确的学术价值评判体系,并最终实现这两项工作的科学的动态管理。
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