OBJECTIVEScreening for special genes of matrix proteins of dentin and enamel of mouse dental germ.

METHODSA cDNA library of dental germ of mouse was screened by differential display. The interesting clones were sequenced.

RESULTSSix positive clones were isolated from the cDNA library. The sequence of one of the six positive clones was homologous with the ameloblastin sequence of rat. There are 497 homologous base pairs between the 526 base pairs sequenced by pTriplEX 3' primer of this clone and the 32-580 sequence of the rat ameloblastin gene; and there are 533 homologous base pairs between the 567 base pairs sequenced by pTriplEX 5' primer of this clone and the 1285-1854 sequence of the rat ameloblastin gene.

CONCLUSIONSThe full length cDNA sequence of the mouse ameloblastin was cloned.

Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Complementary ; Gene Library ; Mice ; Molecular Sequence Data

OBJECTIVETo identify a novel human leukocyte antigen (HLA) A allele.

METHODSA new HLA-A allele was found during routine HLA genotyping by polymerase chain reaction-sequence specific oligonucleotide probes (PCR-SSOP) and sequencing-based typing (SBT).

RESULTSThe novel HLA-A*30 allele was identical to A*300101 except that a nucleotide C at position 294 of exon 2 is substituted by A, resulting in codon 98 changed from GAC (D) to GAA (E).

CONCLUSIONA new HLA allele, HLA-A*3020, was identified, and was named officially by the WHO Nomenclature Committee.

Alleles ; Base Sequence ; HLA-A Antigens ; chemistry ; genetics ; Humans ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA

Gene mutation (e.g. substitution, insertion and deletion) and related phenotype information are important biomedical knowledge. Many biomedical databases (e.g. OMIM) incorporate such data. However, few studies have examined the quality of this data. In the current study, we examined the quality of protein single-point mutations in the OMIM and identified whether the corresponding reference sequences align with the mutation positions. Our results show that close to 20% of mutation data cannot be mapped to a single reference sequence. The failed mappings are caused by position conflict, site shifting (peptide, N-terminal methionine) and other types of data error. We propose a preliminary model to resolve such inconsistency in the OMIM database.
Amino Acid Sequence ; Consensus Sequence ; Databases, Genetic ; Molecular Sequence Data ; Point Mutation ; Sequence Alignment

Proteinase inhibitors are widely distributed in many living organisms and play crucial roles in many biological processes, particularly in regulating the proteinase activity spatially and temporally. However, The Kazal family of serine protease inhibitors is one of the most important and extensively studied protease inhibitor families. This type of protease inhibitor normally consists of one or several domains. Every domain has a highly conserved sequence structure and molecular conformation. It is found that contact residues are hyper variable, which are responsible for the interaction of inhibitors and proteinases. Most of them are in the solvent exposed loop. But P1 residue is the key active site of the interaction between inhibitor and enzyme. The types of the amino acid at P1 site likely play an important role in causing different inhibitory activity. The substitutions at the contact residues cause significant effects on the association constant. By using the Laskowski algorithm, the Ki values of a Kazal domain against six serine proteinases can be predicted from the domain' s sequence alone. At present there are many Kazal proteinase inhibitors found in the organisms, which show important biological functions. This article gives a comprehensive review of the newer developments in the characters and the interaction of the Kazal-type inhibitors.
Amino Acid Sequence ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Serine Proteinase Inhibitors ; chemistry ; physiology

Molecular Sequence Data ; Ribotyping ; Streptococcus suis ; classification ; genetics

The matK genes of 10 samples in Paris from Hunan, Yunnan and Jilin provinces were sequenced and compared. The phylogenetic tree was constructed based on the matK gene sequences and the ten pairs samples were divided into four groups. The results did not support the reality of four taxa named P. polyphylla var. pseudothibetica, P. polyphylla var. yunnanensis, P. polyphylla var. appendiculata and P. polyphylla var. chinenis. They are supposed to be treated as different forms of P. polyphylla var. polyphylla.
Genes, Plant ; genetics ; Liliaceae ; classification ; genetics ; Molecular Sequence Data ; Phylogeny

OBJECTIVETo study the types of subspecies of Francisella tularensis from China and to investigate the genetic relationships between F. tularensis strains from China and from other countries.

METHODSTen strains of F. tularensis isolated from China were amplified by using typing primers C1/C4 and RD1. On the basis of the lengths of the polymerase chain reaction (PCR) products, it was concluded that these strains of F. tularensis belonged to the same subspecies. At the same time, the fopA, tul4, and 16S rRNA genes of the 10 strains were amplified, and a three-gene based phylogenetic analysis was performed using the Molecular Evolutionary Genetics Analysis software version 4.0.

RESULTSThe 10 strains of F. tularensis from China were all identified as belonging to subspecies holarctica (type B). We found no direct relationship between the genotypes of F. tularensis subsp. holarctica and the geographical area from where they were isolated.

CONCLUSIONThe F. tularensis strains isolated from North China mainly belong to subspecies holarctica (type B). The strains of F. tularensis subsp. holarctica from China may have evolved earlier than those from Europe and North America.

China ; Francisella tularensis ; classification ; genetics ; Molecular Sequence Data ; Phylogeny

OBJECTIVETo investigate the genome structure variation (SV) related with keloid using the whole-gene resequencing technology.

METHODSWe studied a keloid pedigree containing 4 generation of 27 people. 5 people (4 cases of keloid patients, and 1 case of normal) were selected to extract the genomic DNA. Then the whole-gene resequencing technique was used to check the variations.

RESULTSThrough database comparison and variation annotation analysis, we obtained 2 SVs associated with keloid formation. We used DAVID software to do the gene ontology and pathway analysis. We found a 168 bp inversion in gene tetraspanin 8 (TSPAN8) in all keloid patients, which contained the forth exon of TSPAN8.

CONCLUSIONSThere was no report about SVs related to keloid. In this study, we found 2 SVs associated with keloid, especially TSPAN8. The tumor cells express the TSPAN8 can up-regulate the vascular endothelial growth factor and its receptors, promote the adjacent fibroblasts secrete matrix metalloproteinases and uridylyl phosphate adenosine. So we hypothesis that the inversion of the forth exon in TSPAN8 may lead to the signal transduction disorder in the keloid patients. This study was a preliminary research. It needs a further study containing large sample to confirm.

Base Sequence ; Female ; Humans ; Keloid ; genetics ; Male ; Molecular Sequence Data ; Pedigree ; Sequence Analysis ; methods ; Tetraspanins ; genetics

OBJECTIVETo identify a novel HLA allele in Chinese population.

METHODSA new HLA-B allele was initially detected by an usual PCR-SSP and PCR-SSOP in routine typing HLA allele. Sequence-based typing (SBT) was used to identify and analysis the difference between the new allele and HLA-B 4409 allele.

RESULTSThe HLA-B exon 3 nucleotide sequence of the novel allele was different from all other known alleles. The allele had 3 nucleotides replaced of the closest matching B 4409 allele at nt538(G>C), nt539(A>T) and nt540 (C>G) in exon 3, resulting in an amino acid change from D(GAC) to L(CTG) at codon 180.

CONCLUSIONA novel HLA allele was confirmed by the SBT and it was officially designated as HLA-B 4446 by WHO Nomenclature Committee for Factors of the HLA System in September,2005.

Alleles ; Base Sequence ; HLA-B Antigens ; classification ; genetics ; Humans ; Male ; Molecular Sequence Data ; Sequence Analysis, DNA

This paper is to show a way of acqusition of the variable region gene of rabbit osteoprotegerin (OPG) and to analyse series. Total RNA was extracted from rabbit tibia, transcripted reversely into cDNA with random primers. The variable region of the OPG gene ampliflied using 5'RACE. Sequencing was confirmed by agarose gel electrophoresis and sequencing analysis. Full length of OPG gene was 1540bp that encoding 400 amino acids. It shared 89% identity with human OPG in whole amino acid sequence and about 85% with rattus norvegicus and other mammal. The OPG sequence of rabbit was obtained by 5'RACE, which could provide a good basis for OPG functional study.
Animals ; Base Sequence ; Molecular Sequence Data ; Osteoprotegerin ; genetics ; Rabbits ; Sequence Homology, Amino Acid