Computational identification of new potential transcriptional partners of ERRα in breast cancer cells: specific partners for specific targets.

Estrogen related receptors are orphan members of the nuclear receptor superfamily acting as transcription factors (TFs). In contrast to classical nuclear receptors, the activities of the ERRs are not controlled by a natural ligand. Regulation of their activities thus relies on availability of transcriptional co-regulators.

[Evaluating the current protocol of influenza A (H1N1) based on the epidemic situations of Zhengzhou,a middle-sized city in China].

Objective: From May 2009-January 2010, a total of 3768 biosamples were tested for influenza A (H1N1) infection at Zhengzhou center for disease control and prevention, China. 1452 cases were laboratory confirmed H1N1 infection and 2316 were considered suspected victims. To evaluate the current protocol of influenza A (H1N1) based on the epidemic situations of Zhengzhou, relationships among features were explored and whether additional clinical characteristics should be part of H1N1 diagnosis protocols were determined.

[Variation feature of receptor binding sites of H1N1 influenza hemagglutinin in different hosts].

Recent outbreak of H1N1 virus worldwide has caused 16 226 deaths in over 213 countries and districts. Binding between the virus and the receptor on the host cell surface is the key initial event for the infection, which results in the fusion of viral host cell membrane. Hemagglutinin (HA) is the viral protein that mediates the receptor binding and membrane fusion.

Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana.

Chloroplast is a typical plant cell organelle where photosynthesis takes place. In this study, a total of 1,808 chloroplast core proteins in Arabidopsis thaliana were reliably identified by combining the results of previously published studies and our own predictions. We then constructed a chloroplast protein interaction network primarily based on these core protein interactions.

Gene expression profiling-based in silico approach to identify potential vaccine candidates and drug targets against B. pertussis and B. parapertussis.

Whooping cough (pertussis) caused by B. pertussis (B.p) is still serious public health threat.

[Polymorphism of DYS287 on Y chromosome in 28 ethnic populations of China].

Objective: To investigate the polymorphism of DYS287 among 28 ethnic populations in 9 provinces of China.

Method: YAP element was detected by Touchdown PCR amplification and 2% agarose gel electrophoresis.

Results: YAP+ frequencies in these ethnic populations were as follows: Zang 36.

Computational methods for protein-protein interaction and their application.

Protein-protein interactions play a central role in numerous processes in cell and are one of the main research fields in current functional proteomics. The increase of finished genomic sequences has greatly stimulated the progress for detecting the functions of the genes and their encoded proteins. As complementary ways to the high through-put experimental methods, various methods of bioinformatics have been developed for the study of the protein-protein interaction.

Synthetic peptides derived from SARS coronavirus S protein with diagnostic and therapeutic potential.

The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) is an important viral structural protein. Based on bioinformatics analysis, 10 antigenic peptides derived from the S protein sequence were selected and synthesized. The antigenicity and immunoreactivity of all the peptides were tested in vivo and in vitro.

Association between alcohol, smoking and HLA-DQA1*0201 genotype in psoriasis.

Psoriasis is a chronic skin disease triggered by genetic, environment or other risk factors such as infection, drugs, stress, moisture, alcohol, and smoking. A major psoriasis susceptibility locus at 6p21.3 has been identified.

Development of genome-wide DNA polymorphism database for map-based cloning of rice genes.

DNA polymorphism is the basis to develop molecular markers that are widely used in genetic mapping today. A genome-wide rice (Oryza sativa) DNA polymorphism database has been constructed in this work using the genomes of Nipponbare, a cultivar of japonica, and 93-11, a cultivar of indica. This database contains 1,703,176 single nucleotide polymorphisms (SNPs) and 479,406 Insertion/Deletions (InDels), approximately one SNP every 268 bp and one InDel every 953 bp in rice genome.

mRNA expression profiling reveals a role of Helicobacter pylori vacuolating toxin in escaping host defense.

Aim: To study the immune response of host to Helicobacter pylori VacA.

Methods: The monocyte/macrophage-like U937 cells were infected with Helicobacter pylori vacA-positive strain NCTC 11638 or isogenic vacA-negative mutant. Differentially expressed genes were identified at 2, 6, 10, and 24 h post-infection by cDNA microarray.

Identification of an epitope of SARS-coronavirus nucleocapsid protein.

The nucleocapsid (N) protein of severe acute respiratory syndrome-coronavirus (SARS-CoV) is a major virion structural protein. In this study, two epitopes (N1 and N2) of the N protein of SARS-CoV were predicted by bioinformatics analysis. After immunization with two peptides, the peptides-specific antibodies were isolated from the immunized rabbits.

Small envelope protein E of SARS: cloning, expression, purification, CD determination, and bioinformatics analysis.

Aim: To obtain the pure sample of SARS small envelope E protein (SARS E protein), study its properties and analyze its possible functions.

Methods: The plasmid of SARS E protein was constructed by the polymerase chain reaction (PCR), and the protein was expressed in the E coli strain. The secondary structure feature of the protein was determined by circular dichroism (CD) technique.

A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening.

Aim: To constructed a three-dimensional (3D) model for the 3C like (3CL) proteinase of SARS coronavirus (SARS-CoV), and to design inhibitors of the 3CL proteinase based on the 3D model.

Methods: Bioinformatics analyses were performed to search the homologous proteins of the SARS-CoV 3CL proteinase from the GenBank and PDB database. A 3D model of the proteinase was constructed by using homology modeling technique.

Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.

Aim: To predict the probable genomic packaging signal of SARS-CoV by bioinformatics analysis. The derived packaging signal may be used to design antisense RNA and RNA interfere (RNAi) drugs treating SARS.

Methods: Based on the studies about the genomic packaging signals of MHV and BCoV, especially the information about primary and secondary structures, the putative genomic packaging signal of SARS-CoV were analyzed by using bioinformatic tools.

Putative hAPN receptor binding sites in SARS_CoV spike protein.

Aim: To obtain the information of ligand-receptor binding between the S protein of SARS-CoV and CD13, identify the possible interacting domains or motifs related to binding sites, and provide clues for studying the functions of SARS proteins and designing anti-SARS drugs and vaccines.

Methods: On the basis of comparative genomics, the homology search, phylogenetic analyses, and multi-sequence alignment were used to predict CD13 related interacting domains and binding sites in the S protein of SARS-CoV. Molecular modeling and docking simulation methods were employed to address the interaction feature between CD13 and S protein of SARS-CoV in validating the bioinformatics predictions.

Isolates of Microbotryum violaceum from North American host species are phylogenetically distinct from their European host-derived counterparts.

Microbotryum violaceum is a basidiomycete that infects the anthers of its Caryophyllaceae host species. Individual fungal isolates are host limited, though they are not morphologically distinct. This study used variable regions of the highly conserved gamma-tubulin, beta-tubulin, and ribosomal RNA-encoding genes to determine the relationships among M.