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Simplification of Protein Sequence and Alignment?-free Sequence Analysis

Progress in Biochemistry and Biophysics.2006;0(12):-.

Alignment-free comparison is a recently developed method for sequence alignment, which has high computational efficiency and suitable to the low identical sequences. Alignment-free comparison was successfully applied in the DNA analysis. However, the accuracy of analysis is not high when it was applied in protein analysis because the complexity of protein is larger than DNA by consisting of 20 types of residues. Thus, residues are clustered into a few groups based on their similarity of physicochemical features. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. Therefore, the accuracy of alignment-free comparison is improved.

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Cloning, Expression and Characterization of The Cold Active Lipase (Lip3) From Metagenomic DNA of an Antarctic Deep Sea Sediment

Jinwei ZHANG ; Runying ZENG

Progress in Biochemistry and Biophysics.2006;0(12):-.

The metagenomic DNA was extracted from the deep sea sediment with the depth of 900m of Prydz Bay, Antarctic. A lipase gene (lip3) with the size of 948bp was cloned from the metagenomic DNA by PCR with the primers designed. The deduced Lip3 protein was composed of 315 amino acids (AA) with a molecular mass of 34.577 ku. The motifs GFGNS(GXGXS)and G-N-S-M-G(GXSXG)in the AA sequences of Lip3 were found to be conserved in other lipase. They were most conserved sequence among the serine hydrolase and were necessary for the activity. A 35 ku of Lip3 was purified by Ni-NTA chelating sepharose column from the extract of recombinant E.coli Top 10F′ cell harboring a pLLP-OmpA plasmid inserted with lip3. The purified Lip3 was most active at 25℃ and kept 22% of activity at 0℃. Only 10% of activity was retained after it was incubated at 35℃ for 60 min. The optimal pH value for the Lip3 activity was 8.0. The Km value of the enzyme towards p-nitrophenyl palmitate increased with the increasing of assayed temperature. These results indicated that Lip3 was a typical alkaline cold active enzyme.

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Study of The Effect on Islets Cultured In vitro and STZ-induced Diabetic Rats In vivo of EGF-like Domain of Betacellulin

Hong LI ; Weibin ZHOU ; Fengying LI ; Yanyun GU ; Jingyan TIAN ; Lei QIAN ; Di ZHANG ; Wenzhong ZHOU ; Guoting WU ; Tianhong LUO ; Guo LI ; Min LUO

Progress in Biochemistry and Biophysics.2006;0(12):-.

Betacellulin (BTC) is one of "islets regeneration factors" which received more and more attention these years. BTCe is the C-terminal 50-residue region of mature BTC protein and can bind with erbB-1?erbB-4 receptor. It has the same mitogenic activity on cells as the whole section. BTC and BTCe can improve the level of glucose-stimulated insulin secretion (GSIS) during islets culture in vitro though they had no effect on the acute insulin secretion. BTCe also effectively ameliorated the hyperglycemia of STZ-induced diabetic rats by a single plasmid injection into muscle of rats. It is supposed that BTCe promote the proliferation of PDX-1 positive cells or repair some signal transduction pathway. Perhaps the latter is more important.

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Advances in The Research of Diseases Related to Notch Signaling Pathway

Mei ZHAO ; Wei HAN

Progress in Biochemistry and Biophysics.2006;0(12):-.

Notch signaling pathway plays a vital role in cell fate decisions. Notch signals are transferred among adjacent cells through Notch receptors and their ligands, which can regulate differentiation, proliferation and apoptosis of many cell types including stem cells. They can also influence organ formation and morphopoiesis. Genetic mutations in the Notch signaling pathway are related to the emergence and development of many diseases. Notch signaling pathway is increasingly becoming important drug targets for cancer, hereditary disease such as CADASIL and other related diseases. It is also used to develop stem cell therapeutics to treat age or trauma related degenerative diseases such as Alzheimer's disease, Parkinson disease and diabetes.

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Gadd45a Function in Suppressing Cell Transformation and Tumor Malignancy

Junfang JI ; Min WU ; Qimin ZHAN

Progress in Biochemistry and Biophysics.2006;0(12):-.

Gadd45a, a p53 and BRCA1-regulated growth arrest and DNA damage gene, plays important roles in suppressing cell transformation and tumor malignancy. Gadd45a maintains the genomic stability through inhibiting the cell growth and promoting the DNA repair etc, by which it suppresses the tumor development. Additionally, Gadd45a is involved in some important signaling pathway, contributing to its function in tumor suppressing.

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Recent Advance on Cellular Signal Transduction in Response to Virus Infections

Kai YANG ; Chen WANG

Progress in Biochemistry and Biophysics.2006;0(12):-.

How the hosts recognize and clear invading viruses is one of the key issues in molecular immunology. Previous studies uncovered that many early antiviral proteins, such as Type Ⅰ interferons and PKR, are strongly induced upon virus infection. These proteins not only limit virus replication and spread or cause infected cells to undergo apoptosis, but also induce consequently expression of cytokines and chemokines to initiate acquired immunity. However, the immediate-early signaling events among host and virus interaction were largely unknown. In the past few years, there are great breakthroughs in this rapidly evolving field. TLR3 and RIG-I/MDA5 signaling pathways were shown to play a crucial regulatory role in antiviral processes. These pathways are essential for the vertebrate immune system to recognize and clear RNA virus with different strategies, which are integral parts of innate immune response and directly affect later-stage acquired immunity. The recent know-how on TLR3 and RIG-I/MDA5 signal transduction pathways and their roles in antiviral immunity were summarized.

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Screening of EGFR-regulated Secreted Proteins in Human NPC Cell Line CNE2

Ke LIANG ; Zhuchu CHEN ; Hong YI ; Jianling LI ; Pengfei ZHANG ; Maoyu LI ; Cui LI ; Xueping FENG ; Fang PENG ; Zhiqiang XIAO

Progress in Biochemistry and Biophysics.2006;0(01):-.

In order to screen EGFR-regulated secreted proteins in human nasopharyngeal carcinoma(NPC), and to reveal the role and mechanism of epidermal growth factor receptor(EGFR) in the pathogenesis of NPC. NPC cell line CNE2 cells were cultured in serum-free medium and stimulated by transforming growth factor-? (TGF-?) for 24 h in experimental group. Control CNE2 cells were cultured at the same condition but without TGF-? stimulation. The culture medium of control and experimental cells was desalted and concentrated through ultrafiltration to prepared the total secreted proteins. Two-dimensional gel electrophoresis (2-DE) was used to separate the secreted proteins of control and experimental cells, PDQuest software was applied to analyze 2-DE images, and the differential protein spots between the control and experimental cells were identified by desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The 2-DE patterns of the secreted proteins of TGF-? stimulated and un-stimulated CNE2 cells were established, 22 differential proteins spots between the two groups of cells were found, and 8 non-redundant proteins were identified with MALDI-TOF-MS, the functions of which were involved in invasion, metastasis, apoptosis and proliferation of cancer cells. The data will be valuable for further to study the role and mechanism of EGFR in the pathogenesis of NPC.

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Study on The Expression of Coagulation Factor Mediated by Recombinant AAV Serotype 8

Zuowu CAO ; Guangui LI ; Yuqiang LIANG ; Dongmei HE

Progress in Biochemistry and Biophysics.2006;0(01):-.

Recombinant AAV serotype 8 (rAAV8) vector is new and promising for gene delivery,which transduces muscular and hepatic cells highly efficiently. The transduction varies with the administration routes. It was observed that the rAAV8 virus injected intraperitoneally had been delivered to many different tissues through the blood circulation and resulted in extensive and prolonged gene expression. The interest gene (human coagulation factor Ⅸ) has been highly expressed via the rAAV8 vector injected intraperitoneally into mice at the dose of 5?1010 gc/ mouse. Considerable expression was detected in mouse plasma at two weeks after the administration. Expression peak up to 1 000% level compared to the UCRP occurred between 1~2 months after administration, and then the expression declined gradually but obvious expression persisted at 4 months post administration. APTT test proved the clotting activity of the recombinant hFⅨ in mouse plasma. Immunohistochemical assay showed that the human coagulation factor has been expressed significantly in several organs including liver, kidney, heart and muscles (abdominal and hindleg). These suggest that the rAAV8 virus injected intraperitoneally has been delivered via blood circulation and transduced different cells of multi-organs, and the product of the gene mediated by the rAAV8 vector is biologically active.

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Comparative Proteomics Analysis of Normal Colonic Epithelium in Young and Old People

Jie ZHENG ; Guo ZHU ; Zhuchu CHEN ; Ming LI ; Ailan CHENG ; Lin RUAN ; Yingfu LIU ; Weijian YUAN ; Pengfei ZHANG ; Zhiqiang XIAO

Progress in Biochemistry and Biophysics.2006;0(01):-.

The aging process of human colonic epithelium involves a slow decline in physiological vigor and an increasing susceptibility to age-related diseases, especially, colon cancer, but the molecular mechanisms of the aging and susceptibility of aged colonic epithelium to carcinogenesis is still unclear. Identification of aging related proteins in colonic epithelium will help to reveal the molecular mechanisms of colonic epithelial aging and age-related colonic diseases. Therefore, the total proteins of human normal colonic epithelial tissues from 10 young and 10 old men were separated by two-dimensional gel electrophoresis(2-DE), respectively. PDQuest software was applied to analyze 2-DE images, the differentially expressed protein spots of colonic epithelium between young and old groups were identified by matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF-MS), and the expression levels of partial identified proteins were determined by real-time quantitative PCR and immunohistochemistry. Well-resolved, reproducible 2-DE maps of human colonic epithelial tissues from young and old men were established, 17 aging related proteins were identified by MALDI-TOF-MS, and the differential expression levels of partial identified proteins were confirmed by real-time quantitative PCR and immunohistochemistry. The results indicate that injury of mitochondrial function and decline of antioxidant capability are important reasons for the aging of human colonic epithelium, and four differential proteins (guanine nucleotide-binding protein beta subunit-like protein, stress-70 protein, 40 S ribosomal protein SA and chloride intracellular channel protein1) may be involved in susceptibility of aged colonic epithelium to carcinogenesis.

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Fusing ZAP to HIV RNA Binding Proteins to Inhibit HIV

Zhiqiang LI ; Lixin LIU ; Fengxiang LU ; Jing MA ; Guangxia GAO

Progress in Biochemistry and Biophysics.2006;0(01):-.

The zinc finger antiviral protein (ZAP) specifically inhibits the replication of Moloney murine leukemia virus (MLV) and Sindbis virus (SIN), but has very modest inhibitory effect on HIV. Previous studies suggest that ZAP directly binds to the viral RNA and recruit the RNA degradation machinery to degrade the target RNA. The HIV-1 Tat and Rev are regulatory proteins which bind to HIV RNA. Tat and Rev were fused with ZAP in various manners. Two fusion proteins, ZAP-Tat and ZAP-Rev were found to be able to inhibit the expression HIV-1 vector.

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