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Jia Jia

Publications and source records attributed to Jia Jia.

9 recordsLinked to original sources
PubMed2006

EHPred: an SVM-based method for epoxide hydrolases recognition and classification.

A two-layer method based on support vector machines (SVMs) has been developed to distinguish epoxide hydrolases (EHs) from other enzymes and to classify its subfamilies using its primary protein sequences. SVM classifiers were built using three different feature vectors extracted from the primary sequence of EHs: the amino acid composition (AAC), the dipeptide composition (DPC), and the pseudo-amino acid composition (PAAC). Validated by 5-fold cross tests, the first layer SVM classifier can differentiate EHs and non-EHs with an accuracy of 94.2% and has a Matthew's correlation coefficient (MCC) of 0.84. Using 2-fold cross validation, PAAC-based second layer SVM can further classify EH subfamilies with an overall accuracy of 90.7% and MCC of 0.87 as compared to AAC (80.0%) and DPC (84.9%). A program called EHPred has also been developed to assist readers to recognize EHs and to classify their subfamilies using primary protein sequences with greater accuracy.

Algorithms↗
PubMed2006

Downregulation of the constitutively expressed Hsc70 in diabetic myocardium is mediated by insulin deficiency.

The 70 kDa heat shock protein family plays important cardiac protective roles against myocardial injuries. Reduced myocardial protection is a common feature of diabetic myocardium. This study was carried out to define the changes in the 70 kDa heat shock protein family in the myocardium in the of streptozotocin-diabetes rats, and to explore the mechanisms through which diabetes alters the abundance of Hsp70/Hsc70 in cardiac muscle. In the diabetic myocardium, the abundance of Hsc70 was significantly reduced. The abundance of Hsp70 was low in cardiac muscle and was not induced in the diabetic myocardium. Unlike Hsp60, Hsp70 and Hsc70 did not augment insulin-like growth factor-I receptor signaling in cardiac muscle cells. In cultured cardiomyocytes, insulin directly increased the abundance of Hsc70, whereas insulin could not modulate Hsp70. Treating diabetic rats with insulin restored myocardial Hsc70 level, but phlorizin treatment failed to restore myocardial Hsc70. These in vivo and in vitro studies showed that downregulation of Hsc70 in diabetic myocardium was secondary to insulin deficiency. Thus, insulin played a major role in maintaining adequate expression of Hsc70 in cardiac muscle.

Adenoviridae↗
PubMed2005

[Genomic analysis of serine carboxypeptidase-like protein family of Arabidopsis thaliana].

Based on hidden Markov models (HMM), the paper utilized reported SCP (Serine Carboxypeptidases) protein sequences as datasets to build HMM profile. To search Arabidopsis thaliana whole proteome,and identified 54 SCPL (Serine Carboxypeptidase-Like) proteins coding genes. The intron-exon structure, the chromosome mapping and the characteristic of coded protein sequences of those 54 putative genes were analyzed in details, revealing seven gene clusters probably resulted from recent gene duplication. This implied that a remarkable number of Arabidopsis thaliana SCPL genes are harboring alternative splice sites. Phylogenetics evolution analysis suggested 88.9% proteins encoded by Arabidopsis genes belong to two string subfamily of carboxypeptidase, I or II, while only 11.1% proteins fall into single string carboxypeptidase III subfamily. Our results indicated besides the facts that all enzymes of this family contained a central catalytic domain of unique topology and three dimensional structure designated as "alpha/beta hydrolase fold", the DNA and their encoded protein sequences also gave clues to phylogentics studies.

Amino Acid Sequence↗
PubMed2004

Superresolution laser beam shaping.

The superresolution technique is well known for its ability to compress the central diffractive spot that is smaller than the Airy diffractive spot. In this paper, we extend the superresolution technique for different laser beam shaping. A complete set of superresolution diffractive elements is developed for the flat-top beam shaping, the single-circle beam shaping, and the novel circular Dammann grating. Five phase plates, corresponding to each of its applications, have been made by use of micro-optics technology. Experiments that are presented are in good agreement with the theoretical results. The superresolution technique presented in this paper should be highly interesting for the wide applications of laser beam shaping.

Journal Article↗
PubMed2003

Circular Dammann grating.

A circular Dammann grating that can produce circular equal intensities at various orders in the far field is described. A set of parameters such as order, circular number, uniformity, and diffraction efficiency has been defined to describe the novel diffractive phase elements. Numerical solutions of binary-phase (0, pi) circular Dammann gratings are given. The results of experiments with a four-order circular Dammann grating made by a lithographic technique are presented. This novel diffractive optical element should be highly interesting in a wide variety of practical applications.

Journal Article↗
PubMed2003

Using DNA microarray to identify Sp1 as a transcriptional regulatory element of insulin-like growth factor 1 in cardiac muscle cells.

High throughput gene expression profiling with DNA microarray provides an opportunity to analyze transcriptional regulation of hundreds or thousands of similarly regulated genes. Transcriptional regulation of gene expression plays an important role in myocardial remodeling. We have studied cardiac muscle gene expression with DNA microarray and used a computational strategy to identify common promoter motifs that respond to insulin-like growth factor 1 (IGF-1) stimulation in cardiac muscle cells. The analysis showed that the Sp1 binding site is a likely target of IGF-1 action. Further experiments with gel shift assay indicated that IGF-1 regulated the Sp1 site in cardiomyocytes, by increasing the abundance of Sp1 and Sp3 proteins. Using firefly luciferase as reporter gene, additional experiments showed that IGF-1 activated the promoter of cyclin D3 and Glut1. Both promoters contain one Sp1 site. The effect of IGF-1 on these two promoters was abolished with siRNA for Sp1. Thus, the transcriptional activation of these two promoters by IGF-1 requires the induction of Sp1 protein. These experiments suggest that the global transcriptional regulatory actions of IGF-1 involve activation of the Sp1 site in cardiac muscle. The computational model we have developed is a prototypical method that may be further developed to identify unique cis- and trans-acting elements in response to hormonal stimulation during cardiac muscle growth, repair, and remodeling in normal and abnormal cardiac muscle.

Animals↗
PubMed2003

Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing.

Leptospirosis is a widely spread disease of global concern. Infection causes flu-like episodes with frequent severe renal and hepatic damage, such as haemorrhage and jaundice. In more severe cases, massive pulmonary haemorrhages, including fatal sudden haemoptysis, can occur. Here we report the complete genomic sequence of a representative virulent serovar type strain (Lai) of Leptospira interrogans serogroup Icterohaemorrhagiae consisting of a 4.33-megabase large chromosome and a 359-kilobase small chromosome, with a total of 4,768 predicted genes. In terms of the genetic determinants of physiological characteristics, the facultatively parasitic L. interrogans differs extensively from two other strictly parasitic pathogenic spirochaetes, Treponema pallidum and Borrelia burgdorferi, although similarities exist in the genes that govern their unique morphological features. A comprehensive analysis of the L. interrogans genes for chemotaxis/motility and lipopolysaccharide synthesis provides a basis for in-depth studies of virulence and pathogenesis. The discovery of a series of genes possibly related to adhesion, invasion and the haematological changes that characterize leptospirosis has provided clues about how an environmental organism might evolve into an important human pathogen.

Bacterial Adhesion↗
PubMed2002

Sequence and analysis of rice chromosome 4.

Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.

Arabidopsis↗