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Biomedical subjects

Yumin Mao

Publications and source records attributed to Yumin Mao.

At least 55 records · Page 3Linked to original sources
PubMed2004

Comparison of hybridization behavior between double and single strands of targets and the application of asymmetric PCR targets in cDNA microarray.

Double stranded targets on the cDNA microarray contain representatives of both the coding and noncoding strands, which will introduce hybridization competition with probes. Here, the effect of double and single strands of targets on the signal intensity and the ratios of Cy5/Cy3 within the same slide were compared. The results show that single stranded targets can increase the hybridization efficiency without changing the Cy5/Cy3 ratio. Based on these results, a new strategy was established by generating cDNA targets with asymmetric PCR, instead of conventional PCR, to increase the sensitivity of the cDNA microarray. Furthermore, the feasibility of this approach was validated. The results indicate that the cDNA microarray system based on asymmetric PCR is more sensitive, with no decrease in the reliability and reproducibility as compared with that based on conventional symmetric PCR.

Carbocyanines↗
PubMed2004

Systematic comparison of the fidelity of aRNA, mRNA and T-RNA on gene expression profiling using cDNA microarray.

In cDNA microarray technology, there are three main reverse transcription based RNA labeling methods, using total RNA (T-RNA), mRNA, and amplified antisense RNA (aRNA), respectively. However, despite the common use of the three types of RNAs, limited data are available regarding their differences and concordances. In this report, we compared the three methods through two sets of self-comparison experiments using the same RNA sample in all cases. Within each method, duplicate hybridizations are highly reproducible with low biases, which are randomly produced. When combining different RNAs within a single array, correlation coefficients between the two channels are rather low, while the discrepancies are persistent. Furthermore, the fidelity of aRNA and mRNA microarrays in the expression profile study shows no significant difference with standard T-RNA based labeling methods. These results suggest that some RNA abundance are selectively changed during aRNA amplification/mRNA purification processes, but it will not affect the gene expression ratio of the two samples if the same type RNA are used. Therefore all three types of RNAs can be used in expression profiling analysis as long as the test and reference samples are generated by identical method within single study.

Carcinoma, Hepatocellular↗
PubMed2004

Molecular cloning and characterization of a novel dual-specificity phosphatase 23 gene from human fetal brain.

Most of dual-specificity protein phosphatases (DSPs) play an important role in the regulation of mitogenic signal transduction and controlling the cell cycle in response to extracellular stimuli. In this study, a novel human dual-specificity protein phosphatases gene named dual-specificity phosphatase 23 (DUSP23) was isolated by large-scale sequencing analysis of a human fetal brain cDNA library. Its cDNA was 726 bp in length, encoding a 150-amino acid polypeptide which contained a dual-specificity phosphatase catalytic (DSPc) domain but not a CDC25 homology (CH2) domain. Reverse transcription-PCR (RT-PCR) revealed that the DUSP23 was expressed in most fetal tissues and two adult tissues: testis and colon. Transient transfection experiment suggested that DUSP23 was localized in the cytoplasm of HEK293 cells. DUSP23 showed distinctive phosphatase activity toward p-nitrophenyl phosphate (pNPP), as well as oligopeptides containing phospho-tyrosine and phospho-threonine residues. Furthermore, DUSP23 could dephosphorylate p44ERK1 but not p38 and p54SAPKbeta in vitro. All the results indicated that DUSP23 was a novel protein phosphatase with dual substrate specificity.

Adult↗
PubMed2004

Cloning and characterization of a novel human TGF-beta activated kinase-like gene.

TGF-beta activated kinase (TAK1) plays a critical role in the TGF-beta signaling transduction pathway. By screening a human 18-week fetal brain library, we isolated a novel human TAK1-like (TAKL) gene. The gene encoded a putative protein of 242 amino acids, which shared a homology with human, mouse, and Xenopus TAK1. The TAKL gene was located in chromosome 21q21. Northern blot analysis revealed that the TAKL mRNA was expressed predominantly in peripheral blood leukocytes and ubiquitously in human adult and fetal tissues. TAKL was also expressed strongly in breast carcinoma GI-101, colon adenocarcinoma GI-112, and prostatic adenocarcinoma PC3.

Adenocarcinoma↗
PubMed2004

A novel human gene (WDR25) encoding a 7-WD40-containing protein maps on 14q32.

Members of the large family of WD-repeat proteins are involved in diverse functions such as RNA-procession, signal transduction, vesicular trafficking, cytoskeletal assembly, and cell cycle control. By large-scale-sequencing analysis of a human fetal brain cDNA library, we isolated a novel human cDNA encoding a 7-WD40-repeat protein. This cDNA is 2004 bp in length and it codes for a 544-amino-acid protein. We term it human WD40-repeat-containing gene 25 (WDR25) and this gene shows significant similarity with human pre-mRNA splicing factor 17. The WDR25 gene is mapped to chromosome 14q32 and contains seven exons. RT-PCR analysis shows that the WDR25 gene is widely expressed in human tissues and the expression levers in heart, muscle, testis, ovary, uterus, and prostate are relatively high.

Amino Acid Motifs↗
PubMed2004

cDNA cloning and expression analysis of a novel human F-box domain containing gene.

F-box proteins are a large family of eukaryotic proteins that are characterized by an approximately 40 amino acid motif. Some F-box proteins are critical for the controlled degradation of cellular regulatory proteins. Here we report that a novel member of F-box proteins, FBXO35 gene, was cloned and identified during the large-scale sequencing analysis from a human fetal brain cDNA library. FBXO35 gene shares amino acid similarity with several putative mouse genes not only in F-box domain but also in the rest of the sequence, which indicates that FBXO35 might also contain some other unknown conserved domain. RT-PCR analysis indicated that FBXO35 gene had a ubiquitously low expression pattern in most human adult tissues. According to bioinformatics analysis, the FBXO35 gene was found located in chromosome 3p21.

Amino Acid Sequence↗
PubMed2004

Characterization of a human Sec14-like protein cDNA SEC14L3 highly homologous to human SPF/TAP.

Supernatant protein factor (SPF) and alpha-tocopherol-associated protein (TAP) both belong to a widespread lipid-binding Sec 14-like protein family. All the members of the family have the lipid-binding motif called CRAL_TRIO. SPF is showed to stimulate the conversion of squalene to lanosterol and enhance cholesterol biosynthesis. TAP is identified to be involved in the intracellular distribution of alpha-tocopherol. Recently TAP is identified as SPF though they have very different functions. Here we report a human SPF/TAP homology SEC14L3 with 2082 base pairs in length and contains an open reading frame encoding a 400 amino acids protein. Analysis shows that SEC14L3 is mapped to 22q12 and expresses only in the liver among the used sixteen tissues in the test.

ATP-Binding Cassette Transporters↗
PubMed2004

Characterization of a cDNA encoding a protein with limited similarity to beta1, 3-N-acetylglucosaminyltransferase.

Glycosyltransferases constitute a large group of enzymes that are involved in a wide range of functions in all living organisms. By large-scale sequencing analysis of a human fetal brain cDNA library, we isolated a novel human putative glycosyltransferase gene named beta3GnTL1. Its cDNA is 1372 base pair in length, encoding a predicted protein with 361 amino acid residues. The human beta3GnTL1 is located to chromosome 17q25.3 by comparison of its cDNA with human gemome database. RT-PCR result shows the beta3GnTL1 is expressed at various levels in most of tissues examined.

Amino Acid Sequence↗
PubMed2004

Cloning and characterization of a human cDNA ACAD10 mapped to chromosome 12q24.1.

Mitochondrial fatty acid beta-oxidation is an important energy resource for many mammal tissues. Acyl-CoA dehydrogenases (ACADs) are a family of flavoproteins that are involved in the beta-oxidation of the fatty acyl-CoA derivatives. Deficiency of these ACADs can cause metabolic disorders including muscle fatigue, hypoglycaemia, hepatic lipidosis and so on. By large scale sequencing, we identified a cDNA sequence of 3960 base pairs with a typical acyl-CoA dehydrogenase function domain. RT-PCR result shows that it is widely expressed in human tissues, especially high in liver, kidney, pancreas and spleen. It is hypothesized that this is a novel member of ACADs family.

Acyl-CoA Dehydrogenase↗
PubMed2004

Molecular cloning and characterization of a novel human protein phosphatase 2C cDNA (PP2C epsilon*).

We have isolated a novel cDNA from the human fetal brain cDNA library with homology to the Mg2+ -dependent serine/threonine protein phosphatase 2C (PP2C) family. The cDNA is 3055 bp in length, and the predicted coding region encodes a 360-amino-acid protein, which shows 99% identity to the PP2C epsilon from rat and mouse. Then we term it human PP2C epsilon gene. The gene is mapped to chromosome 3q26.1 and contains 4 exons. RT-PCR analysis shows that the PP2C epsilon is widely expressed in human tissues and the expression levels in heart, placenta, lung, liver, kidney, and pancreas are relatively high.

Amino Acid Sequence↗
PubMed2004

Cloning and identification of a novel human gene PDLIM5, a homolog of AD-associated neuronal thread protein (AD7c-NTP).

A novel human gene cDNA was successfully cloned from the human fetal brain cDNA library constructed by our lab, and this gene was termed PDLIM5 after acquiring the agreement of HUGO. BLASTX searching revealed that the hypothetical protein is a homolog of AD-associated neuronal thread protein (AD7c-NTP), which is over-expressed in Alzheimer disease (AD) beginning early in the course of disease, and over-expression of the AD7c-NTP gene would cause neuritic sprouting and cell death. SMART analysis showed that both our predicted protein and AD7c-NTP comprise BCL domain (only contains BH1 and BH2 regions). RT-PCR experiment revealed that the expression level of PDLIM5 in brain, skeletal muscle, prostate, colon and leukocyte is obviously higher than that in other tissues.

Amino Acid Sequence↗
PubMed2004

Molecular cloning and characterization of SGT1.2, a novel splice variant of Homo sapiens SGT1.

SGT1.2, a novel splice variant of Homo sapiens SGT1 was isolated from a human fetal brain cDNA library. This cDNA is 1404 bp and contains an open reading frame from 68 to 1165 encoding a putative protein of 365 amino acids (SGT1.2) that share 90% identities to Homo sapiens SGT1, suppressor of G2 allele of SKP1 at protein level. RPS-BLAST searching revealed that SGT1.2 have a TPR domain, a p23 domain, a SGS domain and a CS domain. According to the search of the human genome database, SGT1.2 was mapped to human chromosome 13q14.13. Reversed transcription-polymerase chain reaction analysis indicated that it widely expressed in human adult tissues.

Alternative Splicing↗
PubMed2004

Cloning and analysis of human Apg16L.

Autophagy is an intracellular bulk degradation system, which delivers cytoplasmic components to the lysosome/vacuole. In yeast and mammalian cells, the Apg12-Apg5 conjugate, together with Apg16, form a multimeric complex, which plays an essential role in autopihageosome formation. By large-scale sequencing analysis of a human fetal brain cDNA library, we isolated a cDNA encoding a putative protein with 607 amino acid residues, which shows 90% identity and 93% similarity to mouse Apg16L. This protein, designated human Apg16L, contains a coiled-coil domain and a motif with seven WD repeats, which are also shared by mouse Apg16L. Database searching revealed that Apg16L is mapped to chromosome 2q37.1 and there exist at least four splice variants.

Alternative Splicing↗
PubMed2004

Cloning and characterization of a splice variant of human Bardet-Biedl syndrome 4 gene (BBS4).

Bardet-Biedl syndrome (BBS) is a heterogeneous multisystemic disorder characterized primarily by five cardinal features of retinal degeneration, obesity, polydactyly, hypogenitalism and mental retardation. To date, six distinct BBS loci that have been identified on different chromosomes. BBS4 gene is mapped to 15q22.2-23, which when mutated can cause BBS4. Its protein shows strong homology to O-linked N-acetylglucosamine (O-GlcNAc) transferase. Here we report a splice variant of BBS4, which is 2556 bp in length and has an open reading frame coding a predicted 527 amino-acids protein. RT-PCR shows that the cDNA is widely expressed while it has higher expression levels in pancreas, liver and prostate.

Alternative Splicing↗
PubMed2004

Asiaticoside induction for cell-cycle progression, proliferation and collagen synthesis in human dermal fibroblasts.

Asiaticoside, isolated from Centella asiatica, promotes fibroblast proliferation and extracullar matrix synthesis in wound healing. The precise mechanism, however, in molecular and gene expression levels still remains partially understood. Using cDNA microarray technology, the alternation of genes expression profiles was determined in a human dermal fibroblast in vitro in the presence of asiaticoside (30 microg/ml). Fifty-four genes, with known functions for cell proliferation, cell-cycle progression and synthesis of the extracellular matrix, were significantly up-regulated in our "whole-genes nest" expression profile at various timepoints. Furthermore, mRNA levels and protein productions of certain genes responsible for extracellular matrix (ECM) synthesis (e.g. encoding type I and type III collagen proteins) were evaluated by Northern blot and radioimmunoassay, respectively. As a result, there is a close correlation among the gene profile, mRNA and protein production in the cells response to asiaticoside stimulation. This information could be used for exploring the target genes in response to asiaticoside in fibroblasts.

Cell Cycle↗
PubMed2004

Cloning, characterization and expression of CDK5RAP1_v3 and CDK5RAP1_v4, two novel splice variants of human CDK5RAP1.

Two novel splice variants of CDK5RAP1, named CDK5RAP1_v3 and CDK5RAP1_v4, were isolated through the large-scale sequencing analysis of a human fetal brain cDNA library. The CDK5RAP1_v3 and CDK5RAP1_v4 cDNAs are 1923bp and 1792bp in length, respectively. Sequence analysis revealed that CDK5RAP1_v4 lacked 1 exon, which was present in CDK5RAP1_v3, with the result that these cDNAs encoded different putative proteins. The deduced proteins were 574 amino acids (designated as CDK5RAP1_v3) and 426 amino acids (CDK5RAP1_v4) in length, and shared the 420 N-terminal amino acids. RT-PCR analysis showed that human CDK5RAP1_v3 was widely expressed in human tissues. The expression level of CDK5RAP1_v3 was relatively high in placenta and lung, whereas low levels of expression were detected in heart, brain, liver, skeletal muscle, pancreas, spleen, thymus, small intestine and peripheral blood leukocytes. In contrast, human CDK5RAP1_v4 was mainly expressed in brain, placenta and testis.

Alternative Splicing↗
PubMed2004

Molecular cloning and characterization of a novel human BTBD8 gene containing double BTB/POZ domains.

BTB/POZ domain is an evolutionarily conserved protein-protein interaction domain often found in developmentally regulated transcription factors. Previous studies have shown that many additional conserved motifs have been found in association with BTB/POZ domain, including kelch repeats, zinc finger domains, FYVE fingers and ankyrin repeats. Here we report a novel human gene containing double BTB/POZ domains, named BTBD8 in agreement with the HUGO Nomenclature Committee. The cDNA sequence contains an open reading frame of 918 bp encoding a putative protein of 305 amino acid residues with a predicted molecular mass of 34.6 kDa. Protein pattern analysis shows that it contains double BTB/POZ domains. Weak expression was detected in adult brain and prostate of the 16 adult tissues examined, while it had a more abundant expression pattern in human fetal brain. The expression pattern of BTBD8 shows it may have a function related to brain development.

Amino Acid Sequence↗