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Search Results: 1 - 10 of 16071 matches for " Zhengchang Su "
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A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs
Minli Xu,Zhengchang Su
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008797
Abstract: Transcription factor binding site (TFBS) motifs can be accurately represented by position frequency matrices (PFM) or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs. In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described.
Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes
Minli Xu, Zhengchang Su
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-23
Abstract: We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution.The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The loss of CRPs in these species leads to the rapid loss of their binding sites in the genomes.Cyclic AMP receptor protein (CRP), also known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in a variety of bacterial groups [1,2]. The biological processes under the regulation of CRP are highly diverse, including energy metabolism [3,4], cell division and development [5], toxin production [1], competence development [6], quorum sensing [7] and cellular motility [8,9]. CRP belongs to the CRP/FNR transcription factor (TF) superfamily [10], which are generally believed to function as global regulators throughout the eubacteria [11]. Each member of the CRP/FNR superfamily contains an N-terminal effector binding domain a
Computational prediction of Pho regulons in cyanobacteria
Zhengchang Su, Victor Olman, Ying Xu
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-156
Abstract: We have predicted and analyzed the Pho regulons in 19 sequenced cyanobacterial genomes using a highly effective scanning algorithm that we have previously developed. Our results show that different cyanobacterial species/ecotypes may encode diverse sets of genes responsible for the utilization of various sources of phosphorus, ranging from inorganic phosphate, phosphodiester, to phosphonates. Unlike in E. coli, some cyanobacterial genes that are directly involved in phosphorus assimilation seem to not be under the regulation of the regulator SphR (orthologue of PhoB in E coli.) in some species/ecotypes. On the other hand, SphR binding sites are found for genes known to play important roles in other biological processes. These genes might serve as bridging points to coordinate the phosphorus assimilation and other biological processes. More interestingly, in three cyanobacterial genomes where no sphR gene is encoded, our results show that there is virtually no functional SphR binding site, suggesting that transcription regulators probably play an important role in retaining their binding sites.The Pho regulons in cyanobacteria are highly diversified to accommodate to their respective living environments. The phosphorus assimilation pathways in cyanobacteria are probably tightly coupled to a number of other important biological processes. The loss of a regulator may lead to the rapid loss of its binding sites in a genome.Cyanobacteria are among the oldest life form on Earth. These organisms inhabit a broad range of ecological environments from fresh water, soil to diverse open oceanographic areas [1]. It is estimated that several cyanobacteria living in the open oceans contribute a significant fraction of Earth's primary production [2]. These bacteria also play important roles in the global cycling of nitrogen and phosphorus [3,4]. Therefore their activities have significant impacts on global environmental changes.Phosphorus is one of the essential elements for all li
Computational analysis of LexA regulons in Cyanobacteria
Shan Li, Minli Xu, Zhengchang Su
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-527
Abstract: Our analysis indicates that six of 33 sequenced cyanobacterial genomes do not harbor a lexA gene although they all encode the key SOS response genes, suggesting that LexA is not an indispensable transcription factor in these cyanobacteria, and that their SOS responses might be regulated by different mechanisms. Our phylogenetic analysis suggests that lexA was lost during the course of evolution in these six cyanobacterial genomes. For the 26 cyanobacterial genomes that encode a lexA gene, we have predicted their LexA-binding sites and regulons using an efficient binding site/regulon prediction algorithm that we developed previously. Our results show that LexA in most of these 26 genomes might still function as the transcriptional regulator of the SOS response genes as seen in E. coli and other organisms. Interestingly, putative LexA-binding sites were also found in some genomes for some key genes involved in a variety of other biological processes including photosynthesis, drug resistance, etc., suggesting that there is crosstalk between the SOS response and these biological processes. In particular, LexA in both Synechocystis sp. PCC6803 and Gloeobacter violaceus PCC7421 has largely diverged from those in other cyanobacteria in the sequence level. It is likely that LexA is no longer a regulator of the SOS response in Synechocystis sp. PCC6803.In most cyanobacterial genomes that we analyzed, LexA appears to function as the transcriptional regulator of the key SOS response genes. There are possible couplings between the SOS response and other biological processes. In some cyanobacteria, LexA has adapted distinct functions, and might no longer be a regulator of the SOS response system. In some other cyanobacteria, lexA appears to have been lost during the course of evolution. The loss of lexA in these genomes might lead to the degradation of its binding sites.The LexA protein was first characterized as the transcriptional regulator of the SOS response in Escherichia c
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes
Shaoqiang Zhang, Shan Li, Phuc T Pham, Zhengchang Su
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-397
Abstract: Here, we designed a new algorithm based on GLECLUBS called extended GLECLUBS (eGLECLUBS) for simultaneous prediction of TFBSs in a group of related prokaryotic genomes. When tested on a group of γ-proteobacterial genomes including E. coli K12, a group of firmicutes genomes including B. subtilis and a group of cyanobacterial genomes using the same parameter settings, eGLECLUBS predicts more than 82% of known TFBSs in extracted inter-operonic sequences in both E. coli K12 and B. subtilis. Because each genome in a group is equally treated, it is highly likely that similar prediction accuracy has been achieved for each genome in the group.We have developed a new algorithm for genome-wide de novo prediction of TFBSs in a group of related prokaryotic genomes. The algorithm has achieved the same level of accuracy and robustness as its predecessor GLECLUBS, but can work on dozens of genomes at the same time.With the continuous decline in the cost of genome sequencing due to the development of new technologies [1,2], numerous prokaryotic genomes are being sequenced, and this number will soon approach a few thousand. Since the biological functions of an organism are encoded in its genome, knowing its genome sequence can greatly facilitate the understanding of its biological functions. However, due to the expensive nature of experimental characterization of biological functions of an organism, ideally, these functions should be largely deduced computationally from its genome sequence. Nevertheless, understanding the function of even a relatively simple prokaryotic cell from its genome sequence remains one of the most daunting challenges in the post-genomic era. In particular, we know very little about the cis-regulatory elements or transcription factor (TF) binding sites (TFBSs) in the vast majority of sequenced prokaryotic genomes because of the lack of an accurate and efficient computational method for predicting TFBSs in sequenced genomes.The difficulty of computational pre
MotifClick: prediction of cis-regulatory binding sites via merging cliques
Shaoqiang Zhang, Shan Li, Meng Niu, Phuc T Pham, Zhengchang Su
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-238
Abstract: Here, we present a graph-based polynomial-time algorithm, MotifClick, for the prediction of cis-regulatory binding sites, in particular, those that have a similar nucleotide distribution to that of their background sequences. To find binding sites with length k, we construct a graph using some 2(k-1)-mers in the input sequences as the vertices, and connect two vertices by an edge if the maximum number of matches of the local gapless alignments between the two 2(k-1)-mers is greater than a cutoff value. We identify a motif as a set of similar k-mers from a merged group of maximum cliques associated with some vertices.When evaluated on both synthetic and real datasets of prokaryotes and eukaryotes, MotifClick outperforms existing leading motif-finding tools for prediction accuracy and balancing the prediction sensitivity and specificity in general. In particular, when the distribution of nucleotides of binding sites is similar to that of their background sequences, MotifClick is more likely to identify the binding sites than the other tools.Deciphering complex genetic regulatory networks encoded in a genome is a challenging problem in the post-genomic era [1]. Identifying cis-regulatory binding sites recognized by transcription factors (TF) in a genome is the first step towards this goal [2]. Since any segment of genomic sequence can be potentially a cis-regulatory binding site, a binding site motif (In this paper, we call a set of similar cis-regulatory binding sites recognized by the same TF a motif) can only be predicted by comparing multiple sequences that potentially contain the cis-regulatory binding sites sought after, based on the assumption that cis-regulatory binding sites are usually more conserved than their flanking non-functional sequences [3]. Therefore, the motif-finding problem is usually formulated to identify overrepresented segments of sequences from a set of input intergenic sequences that can be obtained by using a group of co-regulated genes in
Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets
Lan Ye,Xianmin Su,Zhengchang Wu,Xianrui Zheng,Jin Wang,Chen Zi,Guoqiang Zhu,Shenglong Wu,Wenbin Bao
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0043741
Abstract: Small RNA duodenal libraries were constructed for Escherichia coli F18-sensitive and -resistant weaned piglets in full-sib pair groups and sequenced using Illumina Solexa high-throughput sequencing technology. The identification of differentially expressed miRNAs provides the basis for improved database information on pig miRNAs, understanding the genetic basics of differences in resistance to E. coli F18 between local Chinese and exotic pig breeds, and finding new resistance markers for E. coli F18 infection. The duodenum of all individuals contained more than 90% of known swine miRNAs. A total of 58 differentially expressing miRNAs were identified, of which 46 were increased and 12 were decreased in E. coli F18-sensitive pigs. Of miRNAs with increased expression, ssc-miR-143 was most highly expressed, followed by ssc-let-7f, ssc-miR-192, and ssc-miR-21. We identified a total of 2036 intersection target genes by comparing TargetScan data and previous gene expression profile results. Gene ontology and pathway analysis of intersection genes showed that differentially expressed miRNAs were mainly involved in the immune response and transcriptional regulation. Combining information on differential miRNA expression and their regulatory relationships with transcription factors, identified 12 candidate miRNA disease markers, including 11 miRNAs with increased expression, ssc-miR-143, ssc-let-7f, ssc-miR-30e, ssc-miR-148a, ssc-miR-148b, ssc-miR-181a, ssc-miR-192, ssc-miR-27b, ssc-miR-15b, ssc-miR-21, and ssc-miR-215, and one with decreased expression, ssc-miR-152. Quantitative real-time PCR analysis of candidate miRNA expression in a larger cohort of E coli F18-sensitive and -resistant animals confirmed the high-throughput sequencing results.
Adenosine Triphosphate (ATP) Is a Candidate Signaling Molecule in the Mitochondria-to-Nucleus Retrograde Response Pathway
Feng Zhang,Tammy Pracheil,Janet Thornton,Zhengchang Liu
Genes , 2013, DOI: 10.3390/genes4010086
Abstract: Intracellular communication from the mitochondria to the nucleus is achieved via the retrograde response. In budding yeast, the retrograde response, also known as the RTG pathway, is regulated positively by Rtg1, Rtg2, Rtg3 and Grr1 and negatively by Mks1, Lst8 and two 14-3-3 proteins, Bmh1/2. Activation of retrograde signaling leads to activation of Rtg1/3, two basic helix-loop-helix leucine zipper transcription factors. Rtg1/3 activation requires Rtg2, a cytoplasmic protein with an N-terminal adenosine triphosphate (ATP) binding domain belonging to the actin/Hsp70/sugar kinase superfamily. The critical regulatory step of the retrograde response is the interaction between Rtg2 and Mks1. Rtg2 binds to and inactivates Mks1, allowing for activation of Rtg1/3 and the RTG pathway. When the pathway is inactive, Mks1 has dissociated from Rtg2 and bound to Bmh1/2, preventing activation of Rtg1/3. What signals association or disassociation of Mks1 and Rtg2 is unknown. Here, we show that ATP at physiological concentrations dissociates Mks1 from Rtg2 in a highly cooperative fashion. We report that ATP-mediated dissociation of Mks1 from Rtg2 is conserved in two other fungal species, K. lactis and K. waltii. Activation of Rtg1/3 upregulates expression of genes encoding enzymes catalyzing the first three reactions of the Krebs cycle, which is coupled to ATP synthesis through oxidative phosphorylation. Therefore, we propose that the retrograde response is an ATP homeostasis pathway coupling ATP production with ATP-mediated repression of the retrograde response by releasing Mks1 from Rtg2.

Zhu Zhengchang,Xu Keqin,Liu Xuejun,

环境科学学报 , 1985,
Abstract: The TLC-EI technique was selected to analyze the smoke residue from combustion of an insecticides mixture consisting of organophos-phorus and carbamate. The sensitivity of the technique could usually reach ng grade.Under the designed experimental conditions, three insecticides in the smoke residue could be separated and the color spots of these insecticides would stay for a relatively long time. The Rf values for these insecticides are 0.71,0.875 and 0.538 respectively.By using the procedure, the residual concentrations in pine needles within threehours after insecticide application were 102.715,19.3315 and 6.701 ppm respectively.
Transcriptional Activity of the FUT1 Gene Promoter Region in Pigs
Chen Zi,Zhengchang Wu,Jing Wang,Yongjiu Huo,Guoqiang Zhu,Shenglong Wu,Wenbin Bao
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms141224126
Abstract: This study aims to provide a theoretical basis on the regulatory mechanism of the α-l,2-fucosyltransferase ( FUT1) gene in pigs by analyzing the transcriptional activity of its promoter region. On the basis of the previously obtained promoter sequence, primers upstream and downstream of the gene were designed using the restriction endonucleases KpnI and HindIII respectively, and the recombinant plasmids of the pGL3-promoter were constructed by inserting promoter sequences with partially missing regions. The resultant mutants were observed by transient transfection assay into HEK293 cells, and the transcriptional activity of the promoter region was determined by luciferase activity. The 5'-flanking region of the FUT1 gene (?1150 to +50 bp) exhibited promoter activity. The ?1150-bp to ?849-bp region showed negative regulation of the gene. The recombinant plasmid pGL3-898 showed the strongest luciferase activity, and the activity showed a decreasing trend when the deleted region was increased. Recombinant plasmids were successfully constructed, verified, and the positive and negative regulation areas and core promoter region were detected, providing a deeper insight into the transcriptional regulatory mechanism of the FUT1 gene.
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