Biomedical subjects

Zhi-Feng Li

Publications and source records attributed to Zhi-Feng Li.

4 recordsLinked to original sources

PubMed2006

Evolutionary diversity of ketoacyl synthases in cellulolytic myxobacterium Sorangium.

The diversity of type I polyketide synthases (PKSs) in cellulolytic myxobacterium Sorangium was explored by assaying the ketoacyl synthases (KSs) in 10 Sorangium strains with two degenerate primer sets and 64 different KS fragments were obtained. For their deduced amino acid sequences, eight were identical to three known KSs from Sorangium and Magnetospirillum, while the others showed 54-83% identities to the modular KS domains reported from various microorganisms. Parts of the Sorangium KSs tightly share the clade with Actinobacteria excluding any other analyzed myxobacterial KSs, or with Cyanobacteria /Myxobacteria. Parts are widely located in the three functional groups - "Loading", "NRPS/PKS" and "Trans-AT". Sorangium KSs in the Actinobacteria, Cyanobacteria/Myxobacteria, or "Loading" clade further evolved independently on its own genus. Notably, the modular KSs from other Myxobacteria genera, i.e. Myxococcus, Stigmatella, Melittangium, Cystobacter and Angiococcus are often distributed crosswise and form non-Sorangium blend subgroups. "NRPS/PKS" and "Trans-AT" are two rather diverse groups and the Sorangium KSs in these clades evolved crosswise with other taxa lineages. The results presented in this paper suggest that the inherent genetic strategies, together with frequent gene importing from many organisms (HGT) have contributed to the evolution of modular PKSs in Sorangium. These findings reinforce that Sorangium strains are really excellent creators for novel and diverse polyketides.

Evolution, Molecular↗

PubMed2006

Expression of vascular endothelial growth factors A and C in human pancreatic cancer.

AIM: To study the expression of vascular endothelial growth factor A (VEGF-A) and VEGF-C and to determine whether the presence of VEGF-A and VEGF-C was associated with the clinicopathologic characteristics of pancreatic cancer. METHODS: VEGF-A and VEGF-C mRNA transcripts were examined by Northern blot in 6 human pancreatic cancer cell lines and 8 normal pancreatic tissues and 8 pancreatic carcinoma specimens. The expression of VEGF-A and VEGF-C proteins was examined by Western blot in the tested cell lines and by immunohistochemical stain in 50 pancreatic carcinoma samples. RESULTS: VEGF-A and VEGF-C mRNA transcripts were present in all the 6 human pancreatic cancer cell lines. Immunoblotting revealed the presence of VEGF-A and VEGF-C proteins in all the cell lines. Northern blot analysis of total RNA revealed 3.0-fold and 3.6-fold increase in VEGF-A and VEGF-C mRNA transcript in the cancer samples, respectively. Immunohistochemical analysis confirmed the expression of VEGF-A and VEGF-C in cancer cells within the tumor mass. Immunohistochemical analysis of 50 pancreatic cancer tissue samples revealed the presence of VEGF-A and VEGF-C immunoreactivity in 50% and 80% of the cancer tissue samples, respectively. The presence of VEGF-A in these cells was associated with larger tumor size and enhanced local spread (c2 = 6.690, P = 0.035<0.05) but was not associated with decreased patient survival. However, the presence of VEGF-C in the cancer cells was associated with increased lymph node metastasis (c2 = 5.710, P = 0.017 < 0.05), but was not associated with decreased patient survival. There was no correlation between the expression of VEGF-A and VEGF-C in the same cancer cells. CONCLUSION: VEGF-A and VEGF-C are commonly overexpressed in human pancreatic cancer and may contribute to tumor growth and lymph node metastasis. There is no relationship between the expression of VEGF-A and VEGF-C in pancreatic cancer.

Adult↗

PubMed2006

[Construction of standard human transcript dataset based on RefSeq and human genome sequence database].

The NCBI Reference Sequence (RefSeq) database aimed to provide a biologically non-redundant collection of DNA, RNA, and protein sequences and to promote the research on genes and proteins of human beings and other species. However, because of widely distributed polymorphisms and different quality control of experiments in individual laboratories, there are potential problems need to be identified in the RefSeq database. Regarding which, we herein define the concept, standard transcript, based on the Central Dogmas of Biology that each standard transcript should be perfectly mapped to the standard genomic DNA sequence at the exon level. A large scale analysis for mapping all of the RefSeq records of human being (2005-4-18) to the officially released human genome sequence database (2005-4-20) was further performed using BLAT, Sim4 and a homemade program, EIparser, which was especially designed for this purpose. The standard transcripts based on the RefSeq database were obtained according to the alignment with standard human genome database. There are 9,771 RefSeq records of human being labeled with "NM_" and "NR_" could be perfectly mapped to human genome sequences, while other 10,943 records could be considered as standard transcripts after reasonable revision by comparing with the genome sequences according to all of the three methods. Moreover, the left 203 unrevisable records and 2,676 inconsistent records reported by the above programs could not be considered as standard transcripts and should be checked critically before using because of potential errors in them. Our study has thus provided a reference standard dataset of human beings with high quality for further bioinformatic and experimental analysis such as polymorphism and mutation of human genes. The reference standard dataset based on above criteria could be retrieved from http://biocompute.bmi.ac.cn/transcriptome/index.htm.

Databases, Genetic↗

PubMed2003

[The PKS/NRPS hetero-gene cluster of epothilones].

Novel macrolides epothilones, produced by cellulolytic myxobacterium Sorangium cellulosum, have the activity to promote microtubule assembly, and are considered to be a potential successor to the famous antitumor drug taxol. The biosynthetic genes leading to the epothilones are clustered into a large operon. The multi-enzyme complex is a hetero-gene cluster of polyketide synthase (PKS) and non-ribosomal peptide synthetases (NRPS) and contains several functional modules, i.e. a loading module, one NRPS module, eight PKS modules, and a P450 epoxidase. The former ten modules biosynthesize desoxyepothilone (epothilones C and D), which is then epoxidized at C12 and C13 and converted into epothilones (epothilones A and B) by the P450 epoxidase. The NRPS module is responsible for the formation of the thiazole side chain from cysteine. The biosynthesis procedure of epothilones can be divided into 5 stages, i.e. formation of holo-ACP/PCP, chain initiation and thiazole ring formation, chain elongation, termination and epoxidation, and post-modification. The analysis of the gene cluster and the biosynthetic pathway reveals that novel epothilone analogs could not only be produced by chemical synthesis/modification, tranditional microbial technologies, but also can be genetically manipulated through combinatiorial biosynthesis approaches.

Bacterial Proteins↗