Biomedical subjects

Miao Sun

Publications and source records attributed to Miao Sun.

29 records · Page 2Linked to original sources

PubMed2004

Over 20% of human transcripts might form sense-antisense pairs.

The major challenge to identifying natural sense- antisense (SA) transcripts from public databases is how to determine the correct orientation for an expressed sequence, especially an expressed sequence tag sequence. In this study, we established a set of very stringent criteria to identify the correct orientation of each human transcript. We used these orientation-reliable transcripts to create 26 741 transcription clusters in the human genome. Our analysis shows that 22% (5880) of the human transcription clusters form SA pairs, higher than any previous estimates. Our orientation-specific RT-PCR results along with the comparison of experimental data from previous studies confirm that our SA data set is reliable. This study not only demonstrates that our criteria for the prediction of SA transcripts are efficient, but also provides additional convincing data to support the view that antisense transcription is quite pervasive in the human genome. In-depth analyses show that SA transcripts have some significant differences compared with other types of transcripts, with regard to chromosomal distribution and Gene Ontology-annotated categories of physiological roles, functions and spatial localizations of gene products.

Base Pairing↗

PubMed2004

[A de nono I462S mutation in the KRT6A gene is associated with pachyonychia congenita type I].

OBJECTIVE: To analyze the KRT6A gene mutation and mutating patterns in a sporadic Chinese patient with Pachyonychia congenita (PC)-1 so as to provide a basis for gene diagnosis and genetic counseling of this disorder. METHODS: Genomic DNA was extracted from whole blood by standard methods from a female patient with PC-1 and her parents, and from 50 normal, unrelated individuals. Primers for specific amplification of the structural KRT6A gene without co amplification of homologous genes were designed and synthesized. All exons of the gene and their flanking intronic sequences were amplified using polymerase chain reaction (PCR) and subjected to automatic DNA sequencing. The mutation was confirmed by Mbo I restriction digestion of the KRT6A-specific PCR products. RESULTS: Direct sequencing of the PCR products revealed a novel heterozygous missense mutation, I462S in the KRT6A gene, which resulted from T to G transversion at nucleotide 1385 (1385T > G) in exon 7 was detected in the patient. This mutation would result in the substitution of Isoleucine by Serine at codon 462 (I462S) located in the end 2B domain of keratin 6A. No such mutation was found in the patient's parents by sequencing of PCR products and this mutation was confirmed in the patient and excluded from both parents and 50 normal, unrelated controls by restriction analysis of PCR fragments using Mbo I enzyme. CONCLUSIONS: A de novo missense mutation in the KRT6A gene, I462S, has been found in a sporadic PC-1 patient. The identification of this novel mutation in the KRT6A gene provides further evidence that mutation in the KRT6A gene causes PC-1 phenotype.

Base Sequence↗

PubMed2004

Dissecting the binding energy epitope of a high-affinity variant of human growth hormone: cooperative and additive effects from combining mutations from independently selected phage display mutagenesis libraries.

Phage display mutagenesis is a widely used approach to engineering novel protein properties and is especially powerful in probing structure-function relationships in molecular recognition processes. The relative contributions of additive and cooperative binding forces and the influence of conformational diversity in producing a novel protein-protein interface is investigated using as a model an ultra-high-affinity receptor binding variant of human growth hormone (hGHv) that has been previously affinity matured. The modular aspect of how the mutations were grouped in the phage display libraries and combined allowed for a systematic probing of the inherent functional cross-talk between the different secondary structure elements that make up the remodeled hGHv binding surface. We performed an alanine scanning analyses of 35 hGHv residues and determined the kinetics of each variant by surface plasmon resonance (SPR). This analysis showed that there is a significant difference between the additive and cooperative binding forces existing among the selected residues in each library module, and the binding advantage of these residues is maximized over the original wild-type residue when in the context of the other mutations in the library. The degree to which residues in a particular mutagenesis library display binding cooperativity characteristics is generally correlated with the conformational plasticity of the polypeptide chain. Additionally, these cooperativity effects change when the mutations from one library are combined with the mutations from one or several of the other separate libraries. This supports the idea that significant functional cross-talk exists between the combined library modules that can affect the binding energetics of individual residues over a large distance.

Epitopes↗

PubMed2004

SAGE is far more sensitive than EST for detecting low-abundance transcripts.

BACKGROUND: Isolation of low-abundance transcripts expressed in a genome remains a serious challenge in transcriptome studies. The sensitivity of the methods used for analysis has a direct impact on the efficiency of the detection. We compared the EST method and the SAGE method to determine which one is more sensitive and to what extent the sensitivity is great for the detection of low-abundance transcripts. RESULTS: Using the same low-abundance transcripts detected by both methods as the targeted sequences, we observed that the SAGE method is 26 times more sensitive than the EST method for the detection of low-abundance transcripts. CONCLUSIONS: The SAGE method is more efficient than the EST method in detecting the low-abundance transcripts.

3' Untranslated Regions↗

PubMed2004

Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase.

Although the GSK3/SHAGGY-like kinase is a highly conserved serine/threonine kinase implicated in many signaling pathways in eukaryotes, the lack of knowledge of its three-dimensional (3D) structure has hindered efforts to understand the binding specificities of substrate and catalytic mechanism. To understand the structure-activity relationships, the protein 3D structure was built by using homology modeling based on the known X-ray diffraction structure of Glycogen synthase kinase-3beta (Gsk3beta) and the model structure was further refined using unrestrained molecular dynamics simulations. The research indicates that the general 3D organization of the GSK3/SHAGGY-like kinase is a typical kinase family and comprises an N-terminal domain of beta-sheet and a larger C-terminal domain mainly constituted by alpha-helix. In order to understand the molecular interactions between the natural substrate-ATP and GSK3/SHAGGY-like kinase, a 3D model of the complex ATP-GSK3/SHAGGY-like kinase is developed by molecular docking program, which is helpful to guide the experimental realization and the new mutant designs as well. One important finding is that the identification of the key binding-site residue of Lys69 which plays an important role in the catalysis of GSK3/SHAGGY-like kinase and this is in consistent with experimental observation.

Adenosine Triphosphate↗

PubMed2004

Novel mutations of the RNA-specific adenosine deaminase gene (DSRAD) in Chinese families with dyschromatosis symmetrica hereditaria.

Dyschromatosis symmetrica hereditaria (DSH) is an autosomal dominant skin disorder. It is also called "reticulate acropigmentation of Dohi" or "symmetric dyschromatosis of the extremities". The DSH locus has recently been mapped to chromosome 1q21 and pathogenic mutations were identified in the DSRAD gene encoding double-stranded RNA-specific adenosine deaminase in Japanese patients with DSH. We report here two novel point mutations, Q513X(1537C>T) and R916W(2746C>T) in the DSRAD gene identified in two Chinese families, respectively. These data suggest that mutations in DSRAD were also associated with DSH in Chinese. This is the first report on DSRAD as the causative gene of DSH in the Chinese population.

Adenosine Deaminase↗

PubMed2004

[Identification of a recurrent mutation in the ROR2 gene in a Chinese family with brachydactyly type B].

OBJECTIVE: To identify the disease-causing mutation in a Chinese family with brachydactyly type B (BDB). METHODS: Genomic DNA was extracted from peripheral blood samples of family members. Exons 8 and 9 of the ROR2 gene were amplified by polymerase chain reaction (PCR) and sequenced directly. Furthermore, the PCR products showing mutation were cloned into pMD18T vector and the insert fragments were sequenced. RESULTS: A 1398-1399 insA heterozygous mutation was detected in the patient. This mutation had been found in German families with BDB. CONCLUSION: To the authors' knowledge, it is the first report on identification of the ROR2 pathogenic mutation in Chinese patients with BDB.

Amino Acid Sequence↗

PubMed2003

Determination of the energetics governing the regulatory step in growth hormone-induced receptor homodimerization.

Signaling in the human growth hormone (hGH)-human GH receptor system is initiated by a controlled sequential two-step hormone-induced dimerization of two hGH receptors via their extracellular domains (ECDs). Little is currently known about the energetics governing the important regulatory step in receptor signaling (step 2) because of previously existing experimental barriers in characterizing the binding of the second receptor (ECD2). A further complication is that ECD2 binds through contacts from two spatially distinct sites: through its N-terminal domain to hGH, and to ECD1 through its C-terminal domain, which forms a pseudo-2-fold symmetrical interaction between the stems of the two receptors. We report here a detailed evaluation of the energetics of step 2 binding using a modified surface plasmon resonance method that is able to measure accurately the kinetics of the trimolecular binding process and separate the effects of the two binding sites. The binding kinetics of 23 single and 126 ECD1-ECD2 pair-wise alanine mutations was measured. Although both of the ECD2 binding interfaces were found to be important, the ECD1-ECD2 stem-stem contact is the stronger of the two. It was determined that most residues in the binding interfaces act in additive fashion, and that the six residues common in both ECDs contribute very differently to homodimerization depending on which ECD they reside in. This interface is characterized by a binding "hot-spot" consisting of a core of three residues in ECD1 and two in ECD2. There is no similar hot-spot in the N-terminal domain of ECD2 binding to Site2 of hGH. This study suggests ways to engineer ECD molecules that will bind specifically to either Site1 or Site2 of hGH, providing novel reagents for biophysical and biological studies.

Alanine↗

PubMed2003

[Analysis on genetic polymorphism of 14 short tandem repeat loci on chromosome 7p14-15 and 12q13 in Chinese north Hans].

OBJECTIVE: To analyze the genetic polymorphism of 6 short tandem repeat (STR) loci on chromosome 7p14-15 and 8 STR loci on chromosome 12q13 in Chinese north Hans. METHODS: Fluorescence-labeling polymerase chain reaction and capillary electrophoresis were used to analyze the genetic polymorphism of 100 randomly selected individuals from Chinese north Han nationality at 6 STR loci (D7S1808, D7S2250, D7S2251, D7S683, D7S656 and D7S528) on chromosome 7p14-15 and 8 STR loci(D12S1056, D12S1293, D12S83, D12S1655, D12S1662, D12S334, D12S137 and D12S102) on chromosome 12q13. RESULTS: In the Chinese north Han population, 7 alleles and 24 genotypes, 8 alleles and 27 genotypes, 7 alleles and 22 genotypes, 4 alleles and 10 genotypes, 6 alleles and 17 genotypes, 5 alleles and 13 genotypes were observed at D7S1808, D7S2250, D7S2251, D7S683, D7S656 and D7S528. The heterozygosities at the above 6 STR loci were 86%, 88%, 83%, 79%, 85% and 80%, respectively. Five alleles and 15 genotypes, 5 alleles and 15 genotypes, 8 alleles and 29 genotypes, 6 alleles and 17 genotypes, 6 alleles and 17 genotypes, 6 alleles and 19 genotypes, 5 alleles and 13 genotypes, 7 alleles and 24 genotypes were observed at D12S1056, D12S1293, D12S83, D12S1655, D12S1662, D12S334, D12S137 and D12S102. The heterozygosities at the above 8 STR loci were 86%, 84%, 87%, 82%, 84%, 85%, 81% and 89%, respectively. CONCLUSION: The distributions of allele frequencies of 6 STR loci on chromosome 7p14-15 and of 8 STR loci on chromosome 12q13 were consistent with the Hardy-Weinberg equilibrium. The highly genetic polymorphism was observed in Chinese north Han population.

Asian People↗

PubMed2002

Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags.

The number of genes in the human genome is still a controversial issue. Whereas most of the genes in the human genome are said to have been physically or computationally identified, many short cDNA sequences identified as tags by use of serial analysis of gene expression (SAGE) do not match these genes. By performing experimental verification of more than 1,000 SAGE tags and analyzing 4,285,923 SAGE tags of human origin in the current SAGE database, we examined the nature of the unmatched SAGE tags. Our study shows that most of the unmatched SAGE tags are truly novel SAGE tags that originated from novel transcripts not yet identified in the human genome, including alternatively spliced transcripts from known genes and potential novel genes. Our study indicates that by using novel SAGE tags as probes, we should be able to identify efficiently many novel transcripts/novel genes in the human genome that are difficult to identify by conventional methods.

Base Pair Mismatch↗

PubMed1999

Construction and Expression of hTNFalpha-hTGF3 Fused Gene.

Human tumor necrosis factor was fused with hTGF3, the third loop region of hTGFalpha specifically binding to EGF receptor, through a flexible linker by recombinant DNA techniques. The constructed plasmid containing hTNFalpha-hTGF3 fused gene, pSB92-TLT, was expressed under the control of P(L) promoter and after the induction at 42 degrees it gave a high level of expression of the fused gene, ranging in 50%-60% of total bacterial protein. 95% of the expressed product was inclusion body, and only 5% was soluble. When the fused gene was constructed into the constitutive plasmid pLC, a new plasmid controlled by P(L) promoter but without cIts857, and expressed at 30 degrees, the expression yield reached 50% and a high proportion of soluble protein, 35% of total bacterial protein, was obtained. Western blot analysis indicated that the fusion protein could specifically bind to anti-hTNFalpha antibody. Comparing to original hTNFalpha, the fused hTNFalpha derivative showed about equal cytotoxicity to L929 cell line and higher cytotoxicity to some human tumor cell lines. This shows that the fusion protein TLT may be promising in application.

Journal Article↗