Objective To explore the distribution on-511C/T,-31T/C single nucleotide polymorphism of IL-1β gene among Uygur population in Xinjiang,and to analyze the correlation between IL-1β gene polymorphism and depressive disorders.Methods A total of 100 patients with depressive disorders and 120 control subjects were selected.Polymerase chain reaction and restriction fragment length polymorphism (RFLP-PCR),enzyme digestion and sequence reaction were used to detect the common-511C/T,-31T/C polymorphism of the IL-1β gene.The relationship between the polymorphism in the IL-1β gene and the severity of depressive disorders was analyzed.Results The frequencies of CC,CT,TT in-511 were 19.0％,58.0％ and 23.0％ in patient group,while those were 19.2％,55.0％,25.8％ in the control group,which did not show statistically significant differences (x2=0.266,P=0.875).The frequencies of CC,CT,TT in-31 were 24.0％,58.0％ and 18.0％ in the patient group,while those were 24.2％,58.3％,17.5％ in the control group,which did not show statistically significant differences (x2=0.0093,P=0.995).The frequencies of CC,CT,TT genotypes of the IL-1β gene polymorphism (-511 C/T,-31 T/C) were not statistically different between depressive patients and healthy controls.Conclusion The findings suggest no significant association between-511C/T,-31T/C polymorphism and depressive disorders in Uygur population of Xinjiang.

Objective To investigate the action of interlukin-2(IL-2),interlukin-6(IL-6) and its soluble receptors (sIL-2R,sIL-6R) in the first episode of depression in the patients of Uyghur nationality and the differences in IL-2,IL-6 and sIL-2R,sIL-6R levels between the responsive depressed patients and the refractory depressed patients treated with venlafaxine.Methods A case-control study design was conducted.57 first-episode patients with depression (patient group) and 55 healthy people matched with gender and age (control group) were recruited in the study.An intervention with sustained-releasing venlafaxine tablets at fixed dose of 150 mg/d was performed in the patient group.The severity of the illness was evaluated by using the Hamilton's depression scale (HAMD-17) before and after the therapy.And by calculating the reduction rate of HAMD-17 (≥ 50％ or ＜50％),the patients were divided into the responsive or refractory groups.The serum levels of IL-2,IL-6,sIL-2R and sIL-6R in patients and controls were tested by ELISA,and a re-test was done with the patients after treatment.Results There were statistical significant differences of the levels of serum IL-2,IL-6 and sIL-2R,sIL-6R between the patients and the control group (P ＜ 0.01).After treatment,the levels of serum IL-2,IL-6,sIL-2R and sIL-6R in responsive patients were significantly decreased when compared with those before the treatment(P＜ 0.01).The four indexes of refractory patients didn' t alter after venlafaxine treatment (P ＞ 0.05).There were positive correlations between HAMD,serum IL-2 (r =0.677 ; P =0.000) and IL-6 (r =0.197 ; P =0.033) before treatment in all patients.Conclusion Serum IL-2 and IL-6 may play a role in the onset of the depression.The efficacy of venlafaxine is negatively correlated with the levels of serum IL-2 and IL-6.Regulating the imbalanced inflammatory cytokines and the immune system may be one of the mechanisms of drug therapy of depression.

AIM To construct a non-normalized cDNA library from Agkistrodon acutus venom gland as an imtial step to develop new and more effective venom by genetic engineering technique for screening and expressing target genes. METHODS The total RNA was extracted from fresh venom gland using Trizol. mRNA was reversely transcripted to cDNA using superscriptⅡ reverse transcriptase. Second-strand synthesis was performed using DNA polymeraseⅠ. After adding EcoRⅠ adaptor, phosphorylating the end and digesting with XhoⅠ, the cDNA was collected in five fractions (<0.25 kb, 0.25-0.5 kb, 0.5-1 kb, 1-2 kb and >2 kb) using the QIAquick Gel Extraction kit and ligated to pBluescriptⅡ vectors. The five libraries obtained were plated by infecting E.coli DH10B, constructing a cDNA library of Agkistrodon acutus venom gland. Sequencing clones at random, 8696 high quality 5′ end expressed sequenced tags (ESTs) were obtained and analyzed. The initial sequences were assembled into 2855 clusters. Among which, one of the clusters (Agkihagin) consisting of 74 ESTs was identified as a novel metalloprtoteinase based on RT-PCR and sequence analysis. RESULTSThe titers of library were 2.048×106. The novel metalloproteinase belonged to PⅢ type metalloproteinase. Its open reading frame was composed of 1827 nucleotides and coded a pre-zymogen of 608 amino acid with zinc-binding domain for metalloproteinase and Asp-Glu-Cys-Asp(DECD) domain for disintegrin. CONCLUSION The capacity of cDNA library of venom gland is above the general level of cDNA library. It would be a helpful platform to construct a catalog for transcripts in the venom gland of the Agkistrodon acutus. The sequence analysis indicates that the deduced amino acid sequence of the identified gene for metalloproteinase share the highest 87% identity with the metalloproteinase genes of other snakes in the GenBank. It lays a good foundation for the study of structure-function relationships of snake venom metalloproteinases.

To obtain an initial overview of gene diversity and expression pattern in porcine thymus, 11,712 ESTs (Expressed Sequence Tags) from 100-day-old porcine thymus (FTY) were sequenced and 7,071 cleaned ESTs were used for gene expression analysis. Clustered by the PHRAP program, 959 contigs and 3,074 singlets were obtained. Blast search showed that 806 contigs and 1,669 singlets (totally 5,442 ESTs) had homologues in GenBank and 1,629 ESTs were novel. According to the Gene Ontology classification, 36.99% ESTs were cataloged into the gene expression group, indicating that although the functional gene (18.78% in defense group) of thymus is expressed in a certain degree, the 100-day-old porcine thymus still exists in a developmental stage. Comparative analysis showed that the gene expression pattern of the 100-day-old porcine thymus is similar to that of the human infant thymus.
Animals ; Computational Biology ; Expressed Sequence Tags ; Fetus ; metabolism ; Gene Expression Profiling ; Genetic Variation ; Sequence Analysis, DNA ; Sus scrofa ; genetics ; metabolism ; Thymus Gland ; metabolism

DNA barcoding is a powerful approach for characterizing species of organisms, especially those with almost identical morphological features, thereby helping to to establish phylogenetic relationships and reveal evolutionary histories. In this study, we chose a 648-bp segment of the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), as a standard barcode region to establish phylogenetic relationships among brine shrimp (Artemia) species from major habitats around the world and further focused on the biodiversity of Artemia species in China, especially in the Tibetan Plateau. Samples from five major salt lakes of the Tibetan Plateau located at altitudes over 4,000 m showed clear differences from other Artemia populations in China. We also observed two consistent amino acid changes, 153A/V and 183L/F, in the COI gene between the high and low altitude species in China. Moreover, indels in the COI sequence were identified in cyst and adult samples unique to the Co Qen population from the Tibetan Plateau, demonstrating the need for additional investigations of the mitochondrial genome among Tibetan Artemia populations.
Animals ; Artemia ; classification ; genetics ; Base Sequence ; China ; DNA, Mitochondrial ; chemistry ; genetics ; Electron Transport Complex IV ; genetics ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Tibet

China has entered a period of high incidence of colorectal cancer. The year of 2015 is the start of precision medicine. Colorectal cancer "precision medicine" is based on the analysis of the cancer genome sequencing and information analysis, interprets the mechanism of the occurrence, development, invasion, metastasis and recurrence of colorectal cancer, and helps to implement targeted individual treatment. The experts of the world's Colorectal Cancer Subtyping Consortium, integrated the past genetic testing based on the classification of colorectal cancer subtypes, refered to the indices of gene mutation, copy number, methylation, microRNA and proteomics, and coalesce the types of colorectal cancer into four consensus molecular subtypes(CMSs) with distinguishing features. CMSs may be the most powerful classification system of colorectal cancer because of its clear biological interpretation, and is expected to provide a reference basis for the establishment of clinical precision treatment system.
China ; Colorectal Neoplasms ; Humans ; Mutation ; Precision Medicine ; Proteomics ; Recurrence

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression patterns in different tissues, developmental stages, and in a conditional sterile mutant, after checking the libraries are comparable by means of sequence coverage. We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development.
Arabidopsis ; genetics ; DNA, Complementary ; metabolism ; Databases as Topic ; Expressed Sequence Tags ; Gene Library ; Genome, Plant ; Genomics ; methods ; Multigene Family ; Open Reading Frames ; Oryza ; genetics ; Quality Control ; Software

OBJECTIVETo study the severe acute respiratory syndrome (SARS)-associated coronavirus genotype and its characteristics.

METHODSA SARS-associated coronavirus isolate named ZJ01 was obtained from throat swab samples taken from a patient in Hangzhou, Zhejing province. The complete genome sequence of ZJ01 consisted of 29,715 bp (GenBank accession: AY297028, version: gi: 30910859). Seventeen SARS-associated coronavirus genome sequences in GenBank were compared to analyze the common sequence variations and the probability of co-occurrence of multiple polymorphisms or mutations. Phylogenetic analysis of those sequences was done.

RESULTSBy bioinformatics processing and analysis, the 5 loci nucleotides at ZJ01 genome were found being T, T, G, T and T, respectively. Compared with other SARS-associated coronavirus genomes in the GenBank database, an A/G mutation was detected besides the other 4 mutation loci (C:G:C:C/T:T:T:T) involved in this genetic signature. Therefore a new definition was put forward according to the 5 mutation loci. SARS-associated coronavirus strains would be grouped into two genotypes (C:G:A:C:C/T:T:G:T:T), and abbreviated as SARS coronavirus C genotype and T genotype. On the basis of this new definition, the ZJ01 isolate belongs to SARS-associated coronavirus T genotype, first discovered and reported in mainland China. Phylogenetic analysis of the spike protein gene fragments of these SARS-associated coronavirus strains showed that the GZ01 isolate was phylogenetically distinct from other isolates, and compared with groups F1 and F2 of the T genotype, the isolates of BJ01 and CUHK-W1 were more closely related to the GZ01 isolate. It was interesting to find that two (A/G and C/T) of the five mutation loci occurred in the spike protein gene, which caused changes of Asp to Gly and Thr to Ile in the protein, respectively.

CONCLUSIONAttention should be paid to whether these genotype and mutation patterns are related to the virus's biological activities,epidemic characteristics and host clinical symptoms.

Objective To explore the correlation between exon region polymorphism of PPP1R3A gene and schizophrenia in Uygur Chinese population. Methods PPP1R3A gene exon region DNA amplification was performed using multiple PCR targeted capture next-generation sequencing method in 528 patients with schizophrenia and 576 healthy controls of Uyghur descent, Illumina HiSeq X Ten was used for sequencing, the symptoms of schizophrenia were assessed by positive and negative symptoms scale (PANSS). Results The allelic and genotypic distributions in rs1800000 of PPP1R3A gene between patients with schizophrenia and healthy controls had significant difference (P＜0.05), rs1799999 in genotype frequency between the female case and control groups showed significant difference (P＜0.05). Furthermore, the allelic distributions of rs8192686 between male cases and controls had significant difference (P＜0.05). Conclusion PPP1R3A gene rs1800000 may be associated with the development of schizophrenia in Uygur Chinese population; rs1799999 may be a risk factor for susceptibility of female Uygur Chinese schizophrenia; The C allele at rs8192686 may be associated with male Uygur Chinese schizophrenia.

Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future.
Crops, Agricultural ; genetics ; Genome, Plant ; genetics ; Genomics ; High-Throughput Nucleotide Sequencing ; Oryza ; genetics ; growth & development ; Phenotype