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ABSTRACT: The human body harbors numerous microbes, and here exists a close relationship between microbes and human health. The Human Microbiome Project has generated whole genome sequences of several hundred human microbes. In this study, we identified horizontal gene transfer (HGT) events in human microbes and tried to elucidate the relationships between the gene-transferring microbes. A total of 13,514 high confidence HGT genes were identified in 308 human microbes. The horizontally transferred genes were enriched for Gene Ontology terms pertaining to catalytic functions and metabolic processes. Construction of an HGT event network suggested that the human microbes could be divided into specific communities which only partly overlap their distribution in human body. Our research suggests that human microbiome may facilitate frequent horizontal gene transfer among bacteria in human body. Awareness of HGT in human microbiome may aid our understanding of the relationship between the human microbiome and human health.
Genomics 07/2012; · 3.02 Impact Factor
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Wei Xiong,
Tao Liu,
Yeshi Wang, Xiaowei Chen,
Lei Sun,
Ning Guo,
Hui Zheng,
Lianghong Zheng,
Martial Ruat,
Weiping Han,
Claire Xi Zhang,
Zhuan Zhou
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ABSTRACT: Neurotransmitter release is elicited by an elevation of intracellular Ca(2+) concentration ([Ca(2+)](i)). The action potential triggers Ca(2+) influx through Ca(2+) channels which causes local changes of [Ca(2+)](i) for vesicle release. However, any direct role of extracellular Ca(2+) (besides Ca(2+) influx) on Ca(2+)-dependent exocytosis remains elusive. Here we set out to investigate this possibility on rat dorsal root ganglion (DRG) neurons and chromaffin cells, widely used models for studying vesicle exocytosis.
Using photolysis of caged Ca(2+) and caffeine-induced release of stored Ca(2+), we found that extracellular Ca(2+) inhibited exocytosis following moderate [Ca(2+)](i) rises (2-3 µM). The IC(50) for extracellular Ca(2+) inhibition of exocytosis (ECIE) was 1.38 mM and a physiological reduction (∼30%) of extracellular Ca(2+) concentration ([Ca(2+)](o)) significantly increased the evoked exocytosis. At the single vesicle level, quantal size and release frequency were also altered by physiological [Ca(2+)](o). The calcimimetics Mg(2+), Cd(2+), G418, and neomycin all inhibited exocytosis. The extracellular Ca(2+)-sensing receptor (CaSR) was not involved because specific drugs and knockdown of CaSR in DRG neurons did not affect ECIE.
As an extension of the classic Ca(2+) hypothesis of synaptic release, physiological levels of extracellular Ca(2+) play dual roles in evoked exocytosis by providing a source of Ca(2+) influx, and by directly regulating quantal size and release probability in neuronal cells.
PLoS ONE 01/2011; 6(10):e24573. · 4.09 Impact Factor
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ABSTRACT: Housekeeping genes (HKGs) generally have fundamental functions in basic biochemical processes in organisms, and usually have relatively steady expression levels across various tissues. They play an important role in the normalization of microarray technology. Using Fourier analysis we transformed gene expression time-series from a Hela cell cycle gene expression dataset into Fourier spectra, and designed an effective computational method for discriminating between HKGs and non-HKGs using the support vector machine (SVM) supervised learning algorithm which can extract significant features of the spectra, providing a basis for identifying specific gene expression patterns. Using our method we identified 510 human HKGs, and then validated them by comparison with two independent sets of tissue expression profiles. Results showed that our predicted HKG set is more reliable than three previously identified sets of HKGs.
PLoS ONE 01/2011; 6(6):e21012. · 4.09 Impact Factor
