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

BACKGROUNDTo study differences among Paragonimus skrjabini (P. skrjabini) populations from five provinces in China (Guangdong, Fujian, Yunnan, Hubei, and Sichuan) and Paragonimus szechuanensis.

METHODSDNA sequences were obtained from the ITS2 and CO1 genes and phylogenetic trees were constructed from the results. Sequences were also obtained from several other species of Paragonimus for comparative purposes.

RESULTSAlthough differences existed in the DNA sequence among P. skrjabini populations from five provinces, the differences were very small. There was also some resemblance between P. miyazakii from Japan and Fujian strains of P. skrjabini.

CONCLUSIONAll studied populations can be regarded as different strains of P. skrjabini; P. szechuanensis is not a separate species but may be a geographical strain of P. skrjabini. We also found that P. miyazakii may be synonymous with P. skrjabini.

Animals ; Base Sequence ; genetics ; China ; Paragonimus ; genetics ; Philology

TIR (Translation Initiation Region) efficiency is very important in prokaryotic expression. The TIR's efficiency is highly dependent on SD (Shine-Dalgarno) sequence, distance between SD sequence and start codon, DB (Downstream Box) sequence, TIR's second structure, codon adaptation and so on. In this paper, we designed and implemented the software to optimize DB sequence and 5' rare codons. It generated some optimization sequences by analyzing the target sequence and comparing it with 16S RNA. And the optimization sequences is sorting by number of base pairing, location of base pairing and codon adaptation. We drew up the algorithm and the core of code in this paper.
Base Sequence ; Codon ; genetics ; Programming Languages ; Protein Biosynthesis ; genetics ; Software

Streptomyces aureofaciens DM-1 is a high-yielding 6-demethylchlortetracycline producer. The genome sequencing of DM-1 reveals a linear chromosome containing 6 824 334 bps nucleotides with GC content of 72.6%. In this genome, a total of 6 431 open reading frames were predicted by using glimmer 3.02, Genemark and Z-Curve softwares. Twenty-eight secondary metabolite biosynthetic gene clusters were uncovered by using AntiSMASH gene prediction software, including the complete 6-demethylchlortetracycline biosynthetic gene cluster. A frame-shift mutation in methyltransferase coding region was detected, which may result in the demethylation of chlortetracycline. The complete genome sequence of S. aureofaciens DM-1 provides basic information for functional genomics studies and selection of high-yielding strains for 6-demethylchlortetracycline.
Base Sequence ; Chlortetracycline ; Demeclocycline ; Multigene Family/genetics* ; Streptomyces aureofaciens/genetics*

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

Vitamin E (Tocopherols) is lipid-soluble antioxidants and essential for human health. Gamma-tocopherol methyltransferase (delta-TMT), one of the key enzymes in tocopherol biosynthetic pathway in plants, converts delta,sigma-tocopherols into alpha,beta-tocopherols. In this study, we isolated the 1552 bp promoter of Arabidopsis TMT gene. The promoter was fused with GUS reporter gene and this expression cassette was introduced into wild Arabidopsis thaliana by Agrobacterium-mediated transformation. GUS staining shows that GUS gene is expressed in leaves, stems and flowers, with the highest expression in young leaves, stamens and stem apices, while not observable in roots, seeds and siliques. The data indicate that gamma-TMT gene promoter is likely to be expressed preferentially in some of the tissues of Arabidopsis.
Arabidopsis ; genetics ; Base Sequence ; Genes, Reporter ; Immunohistochemistry ; Methyltransferases ; genetics ; Molecular Sequence Data ; Promoter Regions, Genetic ; genetics

OBJECTIVE: To explore the genetic basis for a pedigree affected with hereditary spastic paraplegia type 4 (HSP4). METHODS: Peripheral venous blood samples were taken from members of the four-generation pedigree and 50 healthy controls for the extraction of genomic DNA. Genes associated with peripheral neuropathy and hereditary spastic paraplegia were captured and subjected to targeted capture and next-generation sequencing. The results were confirmed by Sanger sequencing. RESULTS: DNA sequencing suggested that the proband has carried a heterozygous c.1196C>G variant in exon 9 of the SPAST gene, which can cause substitution of serine by threonine at position 399 (p.Ser399Trp) and lead to change in the protein function. The same variant was also detected in other patients from the pedigree but not among unaffected individuals or the 50 healthy controls. Based on the ACMG 2015 guidelines, the variant was predicted to be possibly pathogenic. CONCLUSION The c.1196C>G variant of the SPAST gene probably underlay the HSP4 in this pedigree.
Base Sequence ; Humans ; Mutation ; Paraplegia/genetics* ; Pedigree ; Sequence Analysis, DNA ; Spastic Paraplegia, Hereditary/genetics* ; Spastin/genetics*

OBJECTIVETo identify and confirm a novel HLA allele.

METHODSA new human leukocyte antigen class I 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-B*52 allele was identical to B*52:01:01 with an exception of one base substitution at position 583 of exon 3 where a C was changed to T resulting in codon 195 changed from CAC(H) to TAC(Y).

CONCLUSIONA new HLA class I allele, B*52:11, is identified, and is named officially by the WHO Nomenclature Committee.

Alleles ; Amino Acid Sequence ; Base Sequence ; Genotype ; HLA-B Antigens ; genetics ; Humans ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA

Prediction of RNA secondary structures including pseudoknots is a difficult topic in RNA field. Current predicting methods usually have relatively low accuracy and high complexity. Considering that the stacking of adjacent base pairs is a common feature of RNA secondary structure, here we present a method for predicting pseudoknots based on covariance with stacking and minimum free energy. A new score scheme, which combined stacked covariance with free energy, was used to assess the evaluation of base pair in our method. Based on this score scheme, we utilized an iterative procedure to compute the optimized RNA secondary structure with minimum score approximately. In each interaction, helix of high covariance and low free energy was selected until the sequences didn't form helix, so two crossing helixes which were selected from different iterations could form a pseudoknot. We test our method on data sets of ClustalW alignments and structural alignments downloaded from RNA databases. Experimental results show that our method can correctly predict the major portion of pseudoknots. Our method has both higher average sensitivity and specificity than the reference algorithms, and performs much better for structural alignments than for ClustalW alignments. Finally, we discuss the influence on the performance by the factor of covariance weight, and conclude that the best performance is achieved when lambda1 : lambda2 = 5 : 1.
Algorithms ; Base Pairing ; Base Sequence ; Computational Biology ; methods ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA ; chemistry ; genetics ; Sequence Analysis, RNA

OBJECTIVETo identify a novel human leukocyte antigen (HLA) B allele and explore its family heritage.

METHODSA novel HLA allele was suspected upon routine HLA typing using a polymerase chain reaction-sequence specific oligonucleotide probe (PCR-SSOP) assay. The sequence was confirmed with DNA sequencing and compared with its closest matching allele, B*55:02. The family was also investigated.

RESULTSAn unusual reaction pattern was detected during routine HLA typing. The sequence was confirmed to be a novel HLA-B allele, which differed from the closest matching allele, B*55:02 in 7 nt positions in exon 2. Among the 7 mutations from 6 codons, there were two amino acids changes including 69Glu→Met and 70Glu→Ala.

CONCLUSIONA novel HLA-B allele has been identified and officially named as B*55:35 by the WHO Nomenclature Committee for Factors of the HLA System (GenBank accession number FJ898284).

Alleles ; Base Sequence ; HLA-B Antigens ; genetics ; Histocompatibility Testing ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA