Jing-Jing Zhang | PubMed Health

PubMed2006

[A novel method of the genome-wide prediction for the target genes and its application].

Based on the protein databases of several model species, this study developed a new method of the Genome-wide prediction for the target genes, using Hidden Markov model by Perl programming. The advantages of this method are high throughput, high quality and easy prediction, especially in the case of multi-domains proteins families. By this method, we predicted the PPR and TPR proteins families in whole genome of several model species. There were 536 PPR proteins and 199 TPR proteins in Oryza sativa ssp. japonica, 519 PPR proteins and 177 TPR proteins in Oryza sativa L. ssp. indica, 735 PPR proteins and 292 TPR proteins in Arabidopsis thaliana, 6 PPR proteins and 32 TPR proteins in Cyanidioschyzon merolae. Synechococcus and Thermophilic archaebacterium did not have PPR proteins. By contrast, 10 TPR proteins were found in Synechococcus and 4 TPR proteins were found in Thermophilic archaebacterium. Moreover, of these results, some further bioinformatics analyses were conducted.

Bacterial Proteins↗

PubMed2004

[Relationship between podocyte molecule's distribution and expression, foot process morphology and proteinuria].

OBJECTIVE: To investigate the association between nephrin, podocin and alpha-actinin of the glomerular podocyte molecules, the morphometric change of podocyte foot process and the development of proteinuria. METHODS: Puromycin aminonucleoside (PAN) nephrosis was established. Immunofluorescence staining, image analysis and real time quantitative PCR were employed to study the distribution and quantitation of glomerular expression of nephrin, podocin and alpha-actinin. Morphometric methods were applied to evaluate the morphology change of podocyte foot processes under electron microscopy. RESULTS: (1) Before the onset of proteinuria, 2 days after PAN injection, the podocyte foot process became swollen nephrin and podocin staining were changed into discontinuous pattern accompanied by the decrease of podocin staining intensity. The foot process became more swollen on day 5,and podocin intensity continued to decrease. Meanwhile, nephrin decreased significantly both in protein intensity and at mRNA level. (2) When heavy proteinuria [(130.8+/-30.7) mg/d, P=0.02] occurred, complete effacement of podocyte foot processes was revealed; both podocin and nephrin staining intensity decreased dramatically(P<0.01), and no linear staining could be observed; nephrin and podocin mRNA gained back. (3) During the recovery of proteinuria, the foot process morphology recovered stepwise; both the intensity of nephrin and podocin increased. When proteinuria disappeared, the podocyte foot process reappeared; podocin immunofluorescence intensity recovered whereas nephrin did not; the intensity of alpha-actinin increased significantly and the distribution changed too. (4) Podocyte foot process volume density correlated negatively with nephrin(r(nephrin)=-0.78, P=0.000 1) and podocin immunofluorescence intensity(r(podocin)=-0.76, P=0.000 1), respectively. CONCLUSION: Before the onset of proteinuria, the first response of podocyte is the swollen foot process, the distribution change of nephrin and podocin and the decreased podocin intensity. There was close relationship between nephrin, podocin protein level and distribution pattern with the development of proteinuria and podocyte foot process effacement, whereas no major role was found for mRNA of nephrin and podocin. Our results suggest that proteinuria might occur after series of events of nephrin and podocin distribution change, their protein and mRNA expression level decrease, and morphology change of podocyte foot process.

Actinin↗