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Biomedical subjects

Ming Li

Publications and source records attributed to Ming Li.

At least 325 records · Page 18Linked to original sources
PubMed2003

Isolation and culture of embryonic stem cells from porcine blastocysts.

This study was conducted to establish embryonic stem (ES) cell lines from porcine blastocysts. Blastocysts were collected from China miniature pigs at day 7-9 of pregnancy. Embryos were either directly (intact embryos) cultured on mitomysin C-inactivated murine embryonic fibroblasts (MEF) as feeder layers, or were used to isolate the inner cell masses (ICM) by enzyme digestive method and then cultured. It was found that enzyme digestive method could isolate ICMs without any damages of cells in all blastocysts (28). All ICMs attached to the feeder layers. Primary cell colonies were formed in 68% of ICM culture and 28% of intact blastocyst culture. Two ES cell lines derived from ICM passed six subcultures (passages). These cells morphologically resembled mouse ES cells and consistently expressed alkaline phosphatase activity. When the ES cells were cultured in a medium without feeder layer and leukemin inhibitory factor, they differentiated into several types of cells including neuron-like, smooth muscle-like, and epithelium-like cells. Some cells formed embryoid bodies in a suspension culture. These results indicate that porcine ES cell line can be established under the present experimental conditions and these ES cells are pluripotent.

Alkaline Phosphatase↗
PubMed2003

Assessment of RAPTOR's linear programming approach in CAFASP3.

We have developed a new algorithm based on the mathematical theory of linear programming (LP) and implemented it in our program RAPTOR. Our new approach provides an elegant formulation of the protein-threading problem, overcomes the intractability problem of protein threading, in practice, and allows us to use existing powerful linear programming software to obtain optimal protein threading solutions. CASP5 and CAFASP3 gave us the first chance to test RAPTOR in an unbiased way. RAPTOR was ranked as the top individual (automatic) server for fold recognition by the CAFASP3 organizers. In this short article, we describe RAPTOR's LP formulation, assess RAPTOR's performance in CAFASP3/CASP5, explain why it has superceded other existing automatic individual methods, and point out its strengths, limitations, extensions, and prospects for improvement.

Algorithms↗
PubMed2003

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.

A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.

Amino Acid Sequence↗
PubMed2003

Probabilistic analysis indicates discordant gene trees in chloroplast evolution.

Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny estimated for the entire genome. We present a probabilistic model that deals with heterogeneity among gene trees, implement it via the Gibbs sampler, and apply it to the plastid genome. Plastids and their genomes are transmitted as a single block without recombination, hence homogeneity among gene trees within this genome is expected. Nevertheless, previous work has revealed clear heterogeneity among plastid genes (e.g., Delwiche and Palmer 1996). Other studies, using whole plastid genomes of various algae and land plants, found little additional heterogeneity (Martin et al. 1998; Adachi et al. 2000). We augment the earlier studies by using a data set of 14 taxa: 6 land plants, 2 green algae, a diatom, 2 red algae and a cryptophyte, the cyanelle of the glaucocystophyte Cyanophora, and the blue-green alga Synechocystis as an outgroup. Contrary to the earlier analyses, we cannot find even a single, dominant consensus tree. Therefore, we formulate a probabilistic model that divides the genes into two sets: those that follow the consensus tree and those that have independent gene trees. No particular tree is supported by more than three-fourths of the genes. But the set of genes that follows a certain tree is fairly independent of data processing and the method of analysis. With one possible exception, we find no evidence for collinear or functionally related genes to follow similar trees. The phylogenetic pattern also seems independent of bias in amino acid composition. Among possible explanations for the observed phenomenon, the hypothesis that different genes have different covarion structures is difficult to assess. But gene duplication may be possible through the inverted or direct repeat regions, while horizontal gene transfer seems less likely. In contrast to green algae and land plants, inverted repeat regions in red algae and in Cyanophora show abundant differences among the copies. Thus, genes may get duplicated when they are recruited into the inverted repeat region and one of the two copies may be lost after leaving the inverted repeat region.

Chloroplasts↗
PubMed2003

MOLVIE: an interactive visualization environment for molecular structures.

A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.

Amino Acid Sequence↗
PubMed2003

Deployment of endograft in the ascending aorta to reverse type A aortic dissection.

Current surgery to treat acute type A aortic dissection involving an intimal tear in the ascending aorta consists of resection and replacement, but mortality is high. We report the case of a 46-year-old female patient with Marfan syndrome who presented with excruciating retrosternal pain and breathing distress after a bowel movement with stress. Magnetic resonance imaging and multicolour sonography showed type A aortic dissection extending from the aortic root to the right iliac artery, with intimal tears in the ascending aorta above the sinotubular junction, the distal arch beyond the left subclavian artery and the isthmic region. We adapted the endoluminal stenting technique to this case of type A aortic dissection by sealing the intimal tears in the ascending aorta using endovascular introduction of one endoluminal graft, as confirmed on angiography. The patient was discharged after 10 days. Follow-up examination by computed tomography after more than 1 year revealed no sign of dissection at any level of the aorta.

Aortic Dissection↗
PubMed2003

The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs.

Temporal control of development is an important aspect of pattern formation that awaits complete molecular analysis. We identified lin-57 as a member of the C. elegans heterochronic gene pathway, which ensures that postembryonic developmental events are appropriately timed. Loss of lin-57 function causes the hypodermis to terminally differentiate and acquire adult character prematurely. lin-57 is hbl-1, revealing a role for the worm hunchback homolog in control of developmental time. Significantly, fly hunchback (hb) temporally specifies cell fates in the nervous system. The hbl-1/lin-57 3'UTR is required for postembryonic downregulation in the hypodermis and nervous system and contains multiple putative binding sites for temporally regulated microRNAs, including let-7. Indeed, we find that hbl-1/lin-57 is regulated by let-7, at least in the nervous system. Examination of the hb 3'UTR reveals potential binding sites for known fly miRNAs. Thus, evolutionary conservation of hunchback genes may include temporal control of cell fate specification and microRNA-mediated regulation.

3' Untranslated Regions↗
PubMed2003

The heparan sulfate proteoglycan gene polymorphism: association with type 2 diabetic nephropathy in Chinese.

The objective of this study was to investigate the association between the heparan sulfate proteoglycan (HSPG) gene G/T polymorphism and diabetic nephropathy in type 2 diabetes in Chinese. The HSPG gene polymorphism (G/T) was determined using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) in 290 Chinese type 2 diabetes mellitus patients comprising 77 cases without nephropathy and 213 cases with nephropathy with either proteinuria (163) or renal insufficiency (50) and a control group of 190 non-diabetics. A significant increase in the frequencies of the T allele and TT + TG genotype was observed in subjects with diabetic renal insufficiency as compared with diabetic subjects without nephropathy and those with diabetic proteinuria (for the T allele: Fisher's two-tailed exact p was 0.015 and 0.002, respectively; for the TT + TG genotype; both p values were < 0.001). Diabetic subjects without nephropathy and those with albuminuria carrying the T allele had odds ratios for the development of renal insufficiency of 1.92 (95% CI, 1.12-3.30) and 2.09 (95% CI, 1.29-3.38), respectively, as compared to non-carriers. The T allele of the HSPG gene BamHI polymorphism located in intron 6 may be a risk factor for the development of renal insufficiency in type 2 diabetes mellitus for Chinese.

Aged↗
PubMed2003

Stability of tumor necrosis factor-alpha during ion exchange chromatography.

Denaturation of target protein by various separation and purification steps contributes significant part to the total product loss in bioseparation. The conformational change and accompanying loss of activity of tumor necrosis factor-alpha during ion exchange chromatography was reversible and was decreased by adding polyethylene glycol 200 at 2 to 5% (v/v) to the eluting solution.

Chromatography, Ion Exchange↗
PubMed2003

Refolding of a recombinant full-length non-structural (NS3) protein from hepatitis C virus by chromatographic procedures.

The non-structural protein 3 (NS3) of Hepatitis C virus (HCV) was expressed as inactive aggregates in Escherichia coli. The protein was refolded by chromatographic techniques of which ion exchange chromatography was best for crude samples and gel filtration best for partially purified samples. Immobilized metal ion affinity chromatography showed intermediate performance. Gradient procedures enhanced the recovery of active NS3 protein.

Chromatography↗
PubMed2003

Co-inheritance of specific genotypes of HSPG and ApoE gene increases risk of type 2 diabetic nephropathy.

The objective of this paper is to investigate co-inheritance of specific HSPG and ApoE genotypes in the development of Chinese type 2 diabetic nephropathy. PCR-RFLP was used to detect HSPG and ApoE genotypes in 385 Chinese subjects including 298 patients with type 2 diabetes mellitus (T2DM) and 87 non-diabetic controls (Non-DM). The T2DM group was subdivided into patients with (TDN; n = 218) and without diabetic nephropathy (Non-DN; n = 80). The latter group was further subdivided into groups of patients with microalbuminuria nephropathy (DN-1; n = 129) and severe diabetic nephropathy (DN-2; n = 89). We then compared the relative frequencies of various HSPG and ApoE genotypes and alleles among the groups, searching for predictive trends. The T allele of the HSPG gene occurred more frequently in the DN-2 group than in the Non-DN or DN-1 groups, their Fisher's exact p was 1.05 x 10(-3) and 6.58 x 10(-6); odds ratios were 2.09 (95% CI 1.32-3.30) and 2.48 (95% CI 1.64-3.74), respectively. The E2 allele of the ApoE gene occurred more frequently in the T2DM than in the Non-DM group, the Fisher's exact p was 0.0087; odds ratio was 3.45 (95% CI 1.30-9.81). Genotype analysis showed that the TT or TG of HSPG gene were paired with the E2/2 or E2/3 of ApoE gene significantly more frequently in the TDN group than in the Non-DN group, with an odds ratio of 3.03 (95% CI 1.03-8.90). There was no significant differences in other combinations of genotypes in HSPG and ApoE genes between TDN and Non-DN group. These results suggest that the HSPG T allele is a risk factor for the development of severe diabetic nephropathy in type 2 diabetic patients, and that the ApoE E2 allele is a risk factor for the occurrence of type 2 diabetes mellitus in Chinese general population. In addition, we find that co-inheritance of T/E2 confers a higher risk of type 2 diabetes mellitus progression to diabetic nephropathy in Chinese.

Aged↗
PubMed2003

Differential involvement of nucleus accumbens shell and core subregions in maternal memory in postpartum female rats.

Maternal memory refers to the long-term retention of maternal responsiveness as a consequence of animals' prior experiences with their young. This study examined the relative roles of 2 subregions of the nucleus accumbens (NA; shell and core) in maternal memory in rats. NA shell lesions either before or immediately after a short experience significantly disrupted maternal memory, but lesions after a 24-hr maternal experience had no effect. NA core lesions had no significant impact on maternal memory. Cycloheximide (a protein synthesis inhibitor) at a high dose (25 micrograms/microliter) infused in the NA shell immediately after 1 hr of maternal experience also significantly disrupted maternal memory, whereas infusions in the medial preoptic area had no effect. It was concluded that the NA shell, but not the NA core, is involved in the consolidation of maternal memory.

Animals↗
PubMed2003

Identification of a locus for dyschromatosis symmetrica hereditaria at chromosome 1q11-1q21.

Dyschromatosis symmetrica hereditaria is a rare autosomal dominant cutaneous disorder characterized by a mixture of hyperpigmented and hypopigmented macules of various sizes on the face and the dorsal aspects of the extremities. The genetic basis for this disease is unknown. We performed a genome-wide search in two large Chinese families to map the chromosome location of the responsible gene. We identified a locus at chromosome 1q11-1q21 with a cumulative maximum two-point LOD score of 8.85 at marker D1S2343 (at recombination fraction=0.00). Haplotype analyses indicated that the disease gene is located within the 11.6 cM region between markers D1S2696 and D1S2635. This is the first locus identified for dyschromatosis symmetrica hereditaria. This study provides a map location for isolation of a disease gene causing dyschromatosis symmetrica hereditaria.

China↗
PubMed2003

Pulsatilloside A and anemoside A3 protect PC12 cells from apoptosis induced by sodium cyanide and glucose deprivation.

Using sodium cyanide (NaCN) and glucose deprivation induced cell injury in PC12 as an injury model, we investigated the protective effects of pulsatilloside A and anemoside A 3 on neurons. The results showed that PC12 cells under the NaCN-injury and glucose deprivation would undergo apoptosis. Additions of pulsatilloside A and anemoside A 3, at dosages ranging from 0.1, 1 and 10 microg/ml, protected PC12 cells from apoptosis determined by MTT, LDH release analysis, and flow cytometry measurement.

Alzheimer Disease↗
PubMed2003

Polymorphisms in the CCR5 coding and noncoding regions among HIV type 1-exposed, persistently seronegative female sex-workers from Thailand.

Resistance to HIV-1 infection despite repeated exposures has been associated with one or more HIV-specific responses, enhanced nonspecific immune modifications, and/or host genetic polymorphisms in certain individuals (highly exposed, persistently seronegative, HEPS). In the present investigation, we focused on the CCR5 gene polymorphisms and the association of such mutations to resistance to HIV-1 infection among 12 HEPS women in Chiang Rai, northern Thailand, and compared our findings with data from 10 HIV-1-infected and 9 HIV-1-uninfected unexposed women from the same geographic area. Although we have previously shown that none of the Thai women carried the Delta32 mutation, further analysis of the CCR5 coding gene region revealed that none of the women had other mutations that affect coreceptor activity (C101X or FS299) or chemokine responses (C20S, A29S, L55Q, C178R). Analysis of the CCR5 promoter region revealed that the CCR5 haplogroup C (HHC; 60%) was the predominant haplogroup among these women. Comparative analysis of the frequencies of different haplogroups among the three groups did not reveal any statistically significant differences (p > 0.05). However, we did find that two individuals from the HEPS group were homozygous for HHF*2 (the CCR2b- 64I bearing haplogroup) compared to none from the HIV-1-infected and -uninfected groups. There was no detectable difference in specific CCR5 haplogroups and their ability to mediate env fusion or to mediate HIV-1 infection in vitro. These data suggest that homozygosity of the HHF*2 haplogroup may be one of the factors that mediate resistance to HIV-1 infection in this cohort of HEPS women.

Adult↗
PubMed2003

Benefits of external qigong therapy on morphine-abstinent mice and rats.

OBJECTIVE: To exclude possible psychological effects of qigong therapy in the treatment of addiction effectively, morphine-dependence models need to be established in mice and rats. METHOD: The effects of external qi on withdrawal syndrome were examined in naloxone-precipitated mice and rats in three randomized control experiments: naloxone-precipitated test in morphine-dependent mice (n = 100 in 5 groups, 20 mice each group); conditioned position preference test in morphine-abstinent mice (n = 30 for 3 groups, 10 each); and naloxone-precipitated test with paired box in morphine-dependent rats (n = 40 for 4 groups, 10 each). RESULTS: These experiments showed that morphine-dependent mice, after external qigong (EQ) therapy, had decreased incidence of jumping and lower jumping frequencies, and attenuated loss of body weight. After EQ therapy, morphine-dependent rats had reduced withdrawal scores and body weight loss was inhibited. In the conditioned place preference test, the time spent in the drug-paired box was significantly shorter for the qigong group than for the morphine group. CONCLUSION: These results suggest that qigong might have an inhibitory effect on withdrawal syndrome, and reduce the dependence potential in mice. Three different designs confirm that the impact of qigong therapy on morphine-abstinent mice and rats is reliable and substantial. Further research on the effectiveness and the mechanism of qigong therapy on addiction is warranted.

Animals↗
PubMed2003

Analysis of expression profiles of islet-associated transcription and growth factors during beta-cell neogenesis from duct cells in partially duct-ligated mice.

INTRODUCTION: Beta-cell neogenesis from pancreatic duct cells has been reported to occur in duct-ligated rat. Nevertheless, detailed process of this phenomenon has not been clarified. AIMS AND METHODOLOGY: To clarify the mechanism of beta-cell neogenesis, a partial pancreatic duct ligation mouse model was created. Proliferation of duct cells, beta-cell neogenesis, and expression of transcription factors and differentiation/growth factors were studied by immunohistochemistry, cDNA array, and RT-PCR methods. RESULTS: In the duct-ligated portion of the pancreas, newly formed islet-like cell clusters (ICCs) were observed arising from the ducts on day 7 and afterward. Transcription factors, such as pancreatic and duodenal homeobox gene-1 (PDX-1), paired box factor 6 (Pax6), islet1 and Nkx2.2-positive cells, and protein gene product 9.5 (PGP9.5) were also induced in duct lining cells. By cDNA microarray analysis, expression of insulin-like growth factor-1 (IGF-1) and transforming growth factor beta1 (TGF-beta1) were above control levels on day 5, and RT-PCR showed an increase from day 5 to day 28. IGF-1 and activin A-positive cells were detected in ducts. In addition, expression of betacellulin (BTC), heparin-binding epidermal growth factor-like growth factor (HB-EGF), and TGF-alpha were also increased from day 3 or 5. CONCLUSION: These findings suggest that beta-cell or endocrine precursors are localized among duct lining cells. Induction of several islet cell-associated transcription factors and differentiation and/or growth factors may play important roles during beta-cell neogenesis in this model.

Activins↗