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Biomedical subjects

Li Liu

Publications and source records attributed to Li Liu.

At least 271 records · Page 15Linked to original sources
PubMed2003

Robust singular value decomposition analysis of microarray data.

In microarray data there are a number of biological samples, each assessed for the level of gene expression for a typically large number of genes. There is a need to examine these data with statistical techniques to help discern possible patterns in the data. Our technique applies a combination of mathematical and statistical methods to progressively take the data set apart so that different aspects can be examined for both general patterns and very specific effects. Unfortunately, these data tables are often corrupted with extreme values (outliers), missing values, and non-normal distributions that preclude standard analysis. We develop a robust analysis method to address these problems. The benefits of this robust analysis will be both the understanding of large-scale shifts in gene effects and the isolation of particular sample-by-gene effects that might be either unusual interactions or the result of experimental flaws. Our method requires a single pass and does not resort to complex "cleaning" or imputation of the data table before analysis. We illustrate the method with a commercial data set.

Cluster Analysis↗
PubMed2003

hSef inhibits PC-12 cell differentiation by interfering with Ras-mitogen-activated protein kinase MAPK signaling.

Growth factor signaling by receptor tyrosine kinases regulates several cell fates, such as proliferation and differentiation. Sef was genetically identified as a negative regulator of fibroblast growth factor (FGF) signaling. Using bioinformatic methods and rapid amplification of cDNA ends-PCR, we isolated both the mouse and the human Sef genes, which encoded the Sef protein and Sef-S isoform that was generated through alternative splicing. We provide evidence that the Sef gene products were located mainly on the cell membrane. Co-immunoprecipitation and immunostaining experiments indicate that hSef interacts with FGFR1 and FGFR2 but not FGFR3. Our results demonstrated that stably expressed hSef strongly inhibits FGF2- or nerve growth factor-induced PC-12 cell differentiation. The intracellular domain of hSef is necessary for the inhibitory effect on FGF2-induced PC-12 cell differentiation. Furthermore, our data suggested Sef exerted the negative effect on FGF2-induced PC-12 cell differentiation through the prevention of Ras-mitogen-activated protein kinase signaling, possibly functioning upstream of the Ras molecule. These findings suggest that Sef may play an important role in the regulation of PC-12 cell differentiation.

Alternative Splicing↗
PubMed2003

Cyclooxygenase-2 expression in squamous dysplasia and squamous cell carcinoma of the esophagus.

Cyclooxygenase-2 (cox-2) overexpression has been observed in several types of human cancers and has been implicated in carcinogenesis. To elucidate the role of cox-2 in esophageal carcinogenesis, we evaluated the expression of cox-2 in normal squamous epithelium squamous epithelial dysplasia (n=47), and squamous cell carcinoma of the esophagus (n=86) by immunohistochemistry, reverse transcription-PCR assay, and western blotting. A significant overexpression of cox-2 was observed in esophageal squamous dysplasia and squamous cell carcinoma compared with normal squamous epithelium. The immunoreactive score of cox-2 expression, an index determined by intensity and positivity of cox-2 staining, was 0.71 +/- 0.46 (mean +/- SD) in normal squamous esophagus, 2.19 +/- 1.79 in squamous epithelial dysplasia, and 2.67 +/- 1.77 in squamous cell carcinoma. The results of immunohistochemistry were confirmed by a reverse transcription-PCR assay and western blotting analysis. Cox-2 expression level was correlated with proliferation activity assessed by proliferating cell nuclear antigen (PCNA) index and MIB-1 index in dysplastic lesion (r=0.55, P<0.01 with PCNA and r=0.72, P<0.01 with MIB-1) and carcinoma (r=0.56, P<0.01 with PCNA and r=0.72, P<0.01 with MIB-1). Elevated cox-2 expression was associated with high p53 expression (p<0.001) but not with clinicopathological features including age, sex, tumor size, histological grade, lymph node metastasis, and TNM stage. The results indicated that cox-2 may be involved in an early stage of squamous carcinogenesis of the esophagus, and that cox-2 overexpression was related to cell proliferation in esophageal squamous dysplasia and squamous cell carcinoma.

Analysis of Variance↗
PubMed2003

A global view of the selectivity of zinc deprivation and excess on genes expressed in human THP-1 mononuclear cells.

Among the micronutrients required by humans, zinc has particularly divergent modes of action. cDNA microarray and quantitative PCR technologies were used to investigate the zinc responsiveness of known genes that influence zinc homeostasis and to identify, through global screening, genes that may relate to phenotypic outcomes of altered dietary zinc intake. Human monocytic/macrophage THP-1 cells were either acutely zinc depleted, using a cell-permeable zinc-specific chelator, or were supplemented with zinc to alter intracellular zinc concentrations. Initially, genes associated with zinc homeostasis were evaluated by quantitative PCR to establish ranges for fold changes in transcript abundance that might be expected with global screening. Zinc transporter-1 and zinc transporter-7 expression increased when cellular zinc increased, whereas Zip-2 expression, the most zinc-responsive gene examined, was markedly increased by zinc depletion. Microarrays composed of approximately 22,000 elements were used to identify those genes responsive to either zinc depletion, zinc supplementation, or both conditions. Hierarchal clustering and ANOVA revealed that approximately 5% or 1,045 genes were zinc responsive. Further sorting based on this pattern of the zinc responsiveness of these genes into seven groups revealed that 104 genes were linearly zinc responsive in a positive mode (i.e., increased expression as cellular zinc increases) and 86 genes that were linearly zinc responsive in a negative mode (i.e., decreased expression as cellular zinc increases). Expression of some genes was responsive to only zinc depletion or supplementation. Categorization by function revealed numerous genes needed for host defense were among those identified as zinc responsive, including cytokine receptors and genes associated with amplification of the Th1 immune response.

Cell Line↗
PubMed2003

Requirement of the p130CAS-Crk coupling for metastasis suppressor KAI1/CD82-mediated inhibition of cell migration.

KAI1/CD82 protein is a member of the tetraspanin superfamily and has been rediscovered as a cancer metastasis suppressor. The mechanism of KAI1/CD82-mediated suppression of cancer metastasis remains to be established. In this study, we found that migration of the metastatic prostate cancer cell line Du145 was substantially inhibited when KAI1/CD82 was expressed. The expression of focal adhesion kinase (FAK) and Lyn, a Src family tyrosine kinase and substrate of FAK, was up-regulated at both RNA and protein levels upon KAI1/CD82 expression. The activation of FAK and Lyn, however, remained unchanged in Du145-KAI1/CD82 cells. As a downstream target of FAK-Lyn signaling, the p130CAS (Crk-associated substrate) protein was decreased upon the expression of KAI1/CD82. Consequently, less p130CAS-CrkII complex, which functions as a "molecular switch" in cell motility, was formed in Du145-KAI1/CD82 cells. To confirm that the p130CAS-CrkII complex is indeed important for the motility inhibition by KAI1/CD82, overexpression of p130CAS in Du145-KAI1/CD82 cells increased the formation of p130CAS-CrkII complex and largely reversed the KAI1/CD82-mediated inhibition of cell motility. Taken together, our studies indicate the following: 1) signaling of FAK-Lyn-p130CAS-CrkII pathway is altered in KAI1/CD82-expressing cells, and 2) p130CAS-CrkII coupling is required for KAI1/CD82-mediated suppression of cell motility.

Antigens, CD↗
PubMed2003

The trypanosomatid signal recognition particle consists of two RNA molecules, a 7SL RNA homologue and a novel tRNA-like molecule.

Trypanosomatids are ancient eukaryotic parasites affecting humans and livestock. Here we report that the trypanosomatid signal recognition particle (SRP), unlike all other known SRPs in nature, contains, in addition to the 7SL RNA homologue, a short RNA molecule, termed sRNA-85. Using conventional chromatography, we discovered a small RNA molecule of 85 nucleotides co-migrating with the Leptomonas collosoma 7SL RNA. This RNA molecule was isolated, sequenced, and used to clone the corresponding gene. sRNA-85 was identified as a tRNA-like molecule that deviates from the canonical tRNA structure. The co-existence of these RNAs in a single complex was confirmed by affinity selection using an antisense oligonucleotide to sRNA-85. The two RNA molecules exist in a particle of approximately 14 S that binds transiently to ribosomes. Mutations were introduced in sRNA-85 that disrupted its putative potential to interact with 7SL RNA by base pairing; such mutants were unable to bind to 7SL RNA and to ribosomes and were aberrantly distributed within the cell. We postulate that sRNA-85 may functionally replace the truncated Alu domain of 7SL RNA. The discovery of sRNA-85 raises the intriguing possibility that sRNA-85 functional homologues may exist in other lower eukaryotes and eubacteria that lack the Alu domain.

Animals↗
PubMed2003

Deoligomerization: a new route to lactams from unsaturated amides via radical oligomerization.

[reaction: see text] Triethylborane-initiated atom transfer radical oligomerization of N-allyl or N-(3-butenyl)iodoacetamides followed by treatment with hydrochloric acid and subsequent neutralization with K(2)CO(3) led to the formation of the corresponding 5-hydroxyl-substituted delta-lactams or caprolactams, respectively. This oligomerization-deoligomerization sequence serves as an alternative to the corresponding intramolecular cyclization reactions.

Amides↗
PubMed2003

Abeta levels in serum, CSF and brain, and cognitive deficits in APP + PS1 transgenic mice.

We compared beta-amyloid peptide (Abeta) levels in the serum, CSF and brain (hippocampus) and correlated these with spatial learning in APP+PS1 transgenic mice. Compared with non-transgenic littermates, male 14-month-old APP + PS1 mice were impaired in spatial learning in the water maze. Among the APP + PS1 mice, only the hippocampal insoluble Abeta42 level correlated with spatial memory (r = -0.44). The levels of insoluble Abeta40 and Abeta42 were highly correlated (r = 0.92), and also correlated with soluble hippocampal Abeta42 (r = 0.64/0.69), which further correlated with the CSF Abeta42 (r = 0.52). None of these parameters correlated with serum Abeta40 levels. These findings support the role of insoluble Abeta42 in memory dysfunction and suggest a model with several pools (insoluble, extracellular soluble, CSF) of Abeta being in partial equilibrium with each other.

Alzheimer Disease↗
PubMed2003

Identification of a novel protein, PDIP38, that interacts with the p50 subunit of DNA polymerase delta and proliferating cell nuclear antigen.

The yeast two-hybrid screening method was used to identify novel proteins that associate with human DNA polymerase delta (pol delta). Two baits were used in this study. These were the large (p125) and small (p50) subunits of the core pol delta heterodimer. p50 was the only positive isolated with p125 as the bait. Two novel protein partners, named PDIP38 and PDIP46, were identified from the p50 screen. In this study, the interaction of PDIP38 with pol delta was further characterized. PDIP38 encodes a protein of 368 amino acids whose C terminus is conserved with the bacterial APAG protein and with the F box A protein. It was found that PDIP38 also interacts with proliferating cell nuclear antigen (PCNA). The ability of PDIP38 to interact with both the p50 subunit of pol delta and with PCNA was confirmed by pull-down assays using glutathione S-transferase (GST)-PDIP38 fusion proteins. The PCNA-PDIP38 interaction was also demonstrated by PCNA overlay experiments. The association of PDIP38 with pol delta was shown to occur in calf thymus tissue and mammalian cell extracts by GST-PDIP38 pull-down and coimmunoprecipitation experiments. PDIP38 was associated with pol delta isolated by immunoaffinity chromatography. The association of PDIP38 with pol delta could also be demonstrated by native gel electrophoresis.

Amino Acid Sequence↗
PubMed2003

Similar gene structure of two Sox9a genes and their expression patterns during gonadal differentiation in a teleost fish, rice field eel (Monopterus albus).

The Sox9 gene encodes a transcription factor that is critical for testis determination and chondrogenesis in vertebrates. Mutations in human SOX9 cause campomelic dysplasia, a dominant skeletal dysmorphology syndrome often associated with male to female sex reversal. Here we show that the Sox9a gene was duplicated during evolution of the rice field eel, Monopterus albus, a freshwater fish which undergoes natural sex reversal from female to male during its life, and has a haploid genome size (0.6-0.8 pg) that is among the smallest of the vertebrates. The duplicated copies of the gene (named Sox9al and Sox9a2) fit within the Sox9 clade of vertebrates, especially in the Sox9a subfamily, not in the Sox9b subfamily. They have similar structures as revealed by both genomic and cDNA analysis. Furthermore, both Sox9al and Sox9a2 are expressed in testis, ovary, and ovotestis; and specifically in the outer layer (mainly gonocytes) of gonadal epithelium with bipotential capacity to form testis or ovary, suggesting that they have similar roles in gonadal differentiation during sex reversal in this species. The closely related gene structure and expression patterns of the two sox9a genes in the rice field eel also suggest that they arose in recent gene duplication events during evolution of this fish lineage.

Amino Acid Sequence↗
PubMed2003

Experimental study of relationship between intracoronary alcohol injection and the size of resultant myocardial infarct.

BACKGROUND: Hypertrophic obstructive cardiomyopathy (HOCM) is a complex disease with unique pathophysiologic characteristics and a great diversity of morphologic,functional and clinical features. Percutaneous transluminal septal myocardial ablation (PTSMA) using alcohol injection via a catheter into the septal branch of the left anterior descending coronary artery has been recently introduced as a promising nonsurgical therapy for HOCM. However, the relationship between the volume and velocity of intracoronary injection of absolute alcohol and the size of the resultant myocardial infarct has not been investigated. We therefore studied such a relationship in piglets. OBJECTIVES: To investigate the relationship between the volume and velocity of selective intracoronary alcohol injection by means of a catheter and the size of the resultant myocardial infarction. METHODS: Twenty piglets were equally divided at random into four groups (n=5 in each) according to the volume and the velocity of intracoronary absolute alcohol injection and the coronary arteries injected. Group I: the volume and velocity of injection of alcohol into the left circumflex coronary artery (LCX) were 0.5 ml and 0.2 ml/s, respectively. Group II: the volume and velocity of injection into LCX were 2.0 ml and 0.2 ml/s, respectively. Group III: the volume and velocity of injection of alcohol into the left anterior descending coronary artery (LAD) were 1.2 ml and 0.06 ml/s, respectively. Group IV: the volume and velocity of injection into the LAD were 1.2 ml and 1.2 ml/s, respectively. The resultant myocardial infarcts were then quantitatively measured 6 h after myocardial ablation. RESULTS: The myocardial infarct size for group I was 4.26+/-2.71(%), for group II was 10.12+/-4.55(%), for group III was 5.84+/-1.21(%) and for group IV was 7.11+/-1.63(%). There were significant differences in myocardial infarct size with different volumes of intracoronary absolute alcohol injection (0.02<P<0.05). but there were no apparent differences found in myocardial infarct size with different velocities of intracoronary alcohol injection (0.05<P<0.2). CONCLUSIONS: The myocardial infarct size is directly related to the volume of intracoronary absolute alcohol injection during myocardial ablation by a catheter, but has no relation to the injection velocity.

Animals↗
PubMed2003

The development and regulation of gene repair.

A technique that can direct the repair of a genetic mutation in a human chromosome using the DNA repair machinery of the cell is under development. Although this approach is not as mature as other forms of gene therapy and fundamental problems continue to arise, it promises to be the ultimate therapy for many inherited disorders. There is a continuing effort to understand the potential and the limitations of this controversial approach.

Animals↗
PubMed2003

Apoptosis in cerebellar granule neurons is associated with reduced interaction between CREB-binding protein and NF-kappaB.

Cerebellar granule neurons undergo apoptosis when switched from medium containing depolarizing levels of potassium (high K+ medium, HK) to medium containing low K+ (LK). NF-kappaB, a ubiquitously expressed transcription factor, is involved in the survival-promoting effects of HK. However, neither the expression nor the intracellular localization of the five NF-kappaB proteins, or of IkappaB-alpha and IkappaB-beta, are altered in neurons primed to undergo apoptosis by LK, suggesting that uncommon mechanisms regulate NF-kappaB activity in granule neurons. In this study, we show that p65 interacts with the transcriptional co-activator, CREB-binding protein (CBP), in healthy neurons. The decrease in NF-kappaB transcriptional activity caused by LK treatment is accompanied by a reduction in the interaction between p65 and CBP, an alteration that is accompanied by hyperphosporylation of CBP. LK-induced CBP hyperphosphorylation can be mimicked by inhibitors of protein phosphatase (PP) 2A and PP2A-like phosphatases such as okadaic acid and cantharidin, which also causes a reduction in p65-CBP association. In addition, treatment with these inhibitors induces cell death. Treatment with high concentrations of the broad-spectrum kinase inhibitor staurosporine prevents LK-mediated CBP hyperphosphorylation and inhibits cell death. In vitro kinase assays using glutathione-S-transferase (GST)-CBP fusion proteins map the LK-regulated site of phosphorylation to a region spanning residues 1662-1840 of CBP. Our results are consistent with possibility that LK-induced apoptosis is triggered by CBP hyperphosphorylation, an alteration that causes the dissociation of CBP and NF-kappaB.

Animals↗
PubMed2003

Telomerase reconstitution immortalizes human fetal hepatocytes without disrupting their differentiation potential.

BACKGROUND & AIMS: The availability of in vitro expandable human hepatocytes would greatly advance liver-directed cell therapies. Therefore, we examined whether human fetal hepatocytes are amenable to telomerase-mediated immortalization without inducing a transformed phenotype and disrupting their differentiation potential. Telomerase is a ribonucleoprotein that plays a pivotal role in maintaining telomere length and chromosome stability. Human somatic cells, including hepatocytes, exhibit no telomerase activity. Consequently, their telomeres progressively shorten with each cell cycle until critically short telomeres trigger replicative senescence. METHODS: The catalytic subunit, telomerase reverse transcriptase, was expressed in human fetal hepatocytes. Transduced cells were characterized for telomerase activity, telomere length, proliferative capacity, hepatocellular functions, oncogenicity, and their in vivo maturation potential. RESULTS: The expression of human telomerase reverse transcriptase restored telomerase activity in human fetal hepatocytes. Telomerase-reconstituted cells were capable of preserving elongated telomeres, propagated in culture beyond replicative senescence for more than 300 cell doublings (to date), and maintained their liver-specific nature, as analyzed by a panel of hepatic growth factors, growth factor receptors, and transcription factors as well as albumin, glucose-6-phosphatase, glycogen synthesis, cytochrome P450 (CYP) expression profiles, and urea production. Moreover, the immortalized cells exhibited no oncogenicity, and no up-regulation of c-Myc was detected. The cells engrafted and survived in the liver of immunodeficient mice with hepatocellular gene expression. CONCLUSIONS: Reconstitution of telomerase activity induces indefinite replication in human fetal hepatocytes and offers unique opportunities for examining basic biologic mechanisms and for considering development of stable cell lines for liver-directed therapies.

Animals↗
PubMed2003

Weight gain among women in the late reproductive years.

BACKGROUND: Given the impact of obesity on mortality and morbidity in women, we evaluated correlates of weight gain in women ages 35-47 years. METHODS: Three hundred and thirty-six African American and Caucasian American women, randomly selected from among urban residents aged 35-47 years and pre-menopausal at baseline, were included in the prospective cohort study. Participants were followed over a 4-year period. Baseline measures included anthropometric variables, socio-demographic factors, measures of anxiety, depressed mood, quality of life, and self-reported measures of diet, vigorous physical activity, alcohol consumption and cigarette smoking. Hormone measurements were obtained during the follicular phase of the menstrual cycle. Weight gain was assessed by comparing the baseline weight with weight measured at the end of the 4-year period. RESULTS: Over 25% of the cohort gained > or =10 lb during follow-up. Five of the 14 women (36%) who were considered menopausal gained weight. Women aged 45-47 were 61% less likely to gain > or =10 lb compared with women aged 35-39 [odds ratio (OR) = 0.39, 95% confidence interval (CI) 0.18-0.87]. Depressed mood was a major correlate of weight gain (OR = 1.9, 95% CI 1.09-3.31). Other psychological measures, including anxiety and quality of life, were similarly correlated with weight gain. No association was detected for levels of sex hormones or self-reported measures of physical activity. Most recalled dietary factors were not predictive of subsequent weight gain in our population. CONCLUSIONS: In this population-based sample of women aged 35-47 years, psychological factors were the major predictors of gaining > or =10 lb during a 4-year follow-up period. Few of the other measures, including baseline hormone values, were correlated with subsequent weight gain. These findings suggest that screening for depression and anxiety may be important clinical assessments to identify women at increased risk of substantial weight gain.

Adult↗
PubMed2003

Identification of a novel, embryonal carcinoma cell-associated molecule, nucling, that is up-regulated during cardiac muscle differentiation.

EC cells are characterized by their potent capacity to differentiate into several cell types, such as mesoderm-like cells, endoderm-like cells, or ectoderm-like cells. By subtracting the mRNAs expressed by one EC cell clone, F9 cells, with the mRNAs expressed by another EC cell clone, P19 cells, we identified six novel genes that are expressed selectively by F9 cells. One of these genes (Nucling) encodes a polypeptide of 1411 amino acids containing an ankyrin repeat, aspartyl protease motif, a leucine zipper motif, and two t-SNARE coiled-coil domains. Northern blot analyses revealed the Nucling mRNA to be detected predominantly in heart, liver, kidney and testis, but not in brain or spleen. Immunostaining analyses revealed a unique feature of Nucling that the transiently expressed protein forms aggregates exclusively around nuclear membranes. Moreover, the expression level of the Nucling gene transcript increases progressively during the early developmental stages in mice, and specifically at cardiomuscular differentiation in vitro and in vivo. These results suggest that Nucling may play some role in the gene regulation of cell differentiation during embryonal development.

Amino Acid Sequence↗
PubMed2003

Nuclease activity of Saccharomyces cerevisiae Mre11 functions in targeted nucleotide alteration.

Oligonucleotides can be used to direct site-specific changes in genomic DNA through a process in which mismatched base pairs in the oligonucleotide and the target DNA are created. The mechanism by which these complexes are developed and resolved is being studied by using Saccharomyces cerevisiae as a model system. Genetic analyses have revealed that in all likelihood the reaction occurs in two phases: DNA pairing and DNA repair. While the former phase involves strand assimilation, the latter phase likely involves an endonucleolytic processing step that leads to joint resolution. In this study, we established the importance of a functioning MRE11 gene in the overall reaction, as yeast strains deficient in MRE11 exhibited severely reduced activity. The activity could be rescued by complementation with wild-type MRE11 genes but not with MRE11 alleles lacking the nuclease function. Taken together, the data suggest that Mre11 provides nuclease activity for targeted nucleotide exchange, a process that could be used to reengineer yeast genes.

Base Sequence↗