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Ming D Li

Publications and source records attributed to Ming D Li.

36 records · Page 2Linked to original sources
PubMed2004

Time-dependent changes in transcriptional profiles within five rat brain regions in response to nicotine treatment.

Many years of behavioral and neurobiology studies have demonstrated broad physiological and pharmacological effects of nicotine on the central nervous system (CNS). However, the gene expression profiles associated with these effects are largely unknown. In this study, we characterized gene expression profiles in the prefrontal cortex, striatum, hypothalamus, amygdala and ventral tegmental area of the rat brain in response to subacute and chronic systemic nicotine administration using a pathway-focused microarray developed in this laboratory that contains 638 sequence-verified genes representing broad, yet targeted, biological functions. By comparing the regional effects of nicotine treatment on gene expression levels, we derived the expression profiles of targeted genes and gene families responding to the new environment created by nicotine throughout the complex connections of the CNS. While the expression of many genes was modulated by nicotine in several regions, only a few were co-modulated in multiple brain regions, suggesting region-specific transcriptional responses. Cluster analysis of significantly altered genes within each brain region over the course of nicotine treatment indicated the genes could be grouped into clusters. Subsequent ANOVA analysis demonstrated these clusters within each brain region to be significantly different at most time points. The clusters were comprised of broad functional groups, such as signaling, neurotransmission and protein modifications, demonstrating unique expression patterns within each region. Using a systematic approach to compare the different regional responses to nicotine administration will eventually provide a better understanding of how the different brain regions responding to this drug.

Amygdala↗
PubMed2004

Nicotine coregulates multiple pathways involved in protein modification/degradation in rat brain.

Previously, we used cDNA microarrays to demonstrate that the phosphatidylinositol and MAP kinase signaling pathways are regulated by nicotine in different rat brain regions. In the present report, we show that, after exposure to nicotine for 14 days, ubiquitin, ubiquitin-conjugating enzymes, 20S and 19S proteasomal subunits, and chaperonin-containing TCP-1 protein (CCT) complex members are upregulated in rat prefrontal cortex (PFC) while being downregulated in the medial basal hypothalamus (MBH). In particular, relative to saline controls, ubiquitins B and C were upregulated by 33% and 47% (P<0.01), respectively, in the PFC. The proteasome beta subunit 1 (PSMB1) and 26S ATPase 3 (PSMC3) genes were upregulated in the PFC by 95% and 119% (P<0.001), respectively. In addition to the protein degradation pathway of the ubiquitin-proteasome complexes, we observed in the PFC an increase in the expression of small, ubiquitin-related modifiers (SUMO) 1 and 2 by 80% and 33%, respectively (P<0.001), and in 3 of 6 CCT subunits by up to 150% (P<0.0001). To a lesser extent, a change in the opposite direction was obtained in the expression of the same gene families in the MBH. Quantitative real-time RT-PCR was used to validate the microarray results obtained with some representative genes involved in these pathways. Taken together, our results suggest that, in response to systemic nicotine administration, the ubiquitin-proteasome, SUMO, and chaperonin complexes provide an intricate control mechanism to maintain cellular homeostasis, possibly by regulating the composition and signaling of target neurons in a region-specific manner.

Animals↗
PubMed2004

Application of a customized pathway-focused microarray for gene expression profiling of cellular homeostasis upon exposure to nicotine in PC12 cells.

Maintenance of cellular homeostasis is integral to appropriate regulation of cellular signaling and cell growth and division. In this study, we report the development and quality assessment of a pathway-focused microarray comprising genes involved in cellular homeostasis. Since nicotine is known to have highly modulatory effects on the intracellular calcium homeostasis, we therefore tested the applicability of the homeostatic pathway-focused microarray on the gene expression in PC-12 cells treated with 1 mM nicotine for 48 h relative to the untreated control cells. We first provided a detailed description of the focused array with respect to its gene and pathway content and then assessed the array quality using a robust regression procedure that allows for the exclusion of unreliable measurements while decreasing the number of false positives. As a result, the mean correlation coefficient between duplicate measurements of the arrays used in this study (control vs. nicotine treatment, three samples each) has increased from 0.974+/-0.017 to 0.995+/-0.002. Furthermore, we found that nicotine affected various structural and signaling components of the AKT/PKB signaling pathway and protein synthesis and degradation processes in PC-12 cells. Since modulation of intracellular calcium concentrations ([Ca(2+)](i)) and phosphatidylinositol signaling are important in various biological processes such as neurotransmitter release and tissue pathogenesis including tumor formation, we expect that the homeostatic pathway-focused microarray potentially can be used for the identification of unique gene expression profiles in comparative studies of drugs of abuse and diverse environmental stimuli, such as starvation and oxidative stress.

Animals↗
PubMed2004

Microarray analysis of ethanol-treated cortical neurons reveals disruption of genes related to the ubiquitin-proteasome pathway and protein synthesis.

BACKGROUND: Chronic ethanol abuse results in deleterious behavioral responses such as tolerance, dependence, reinforcement, sensitization, and craving. The objective of this research was to identify transcripts that are differentially regulated in ethanol-treated cortical neurons compared with controls by using a pathway-focused complementary DNA microarray. METHODS: Cortical neurons were isolated from postconception day 14 C57BL/6 mouse fetuses and cultured according to a standard protocol. The cortical neuronal cells were treated with 100 mM ethanol for five consecutive days with a change of media every day. A homeostatic pathway-focused microarray consisting of 638 sequence-verified genes was used to measure transcripts differentially regulated in four ethanol-treated cortical neuron samples and four control samples. Quantitative real-time reverse transcriptase-polymerase chain reaction analysis was used to verify the mRNA expression levels of genes of interest detected from the microarray experiments. RESULTS: We identified 56 down-regulated and 10 up-regulated genes in ethanol-treated cortical neurons relative to untreated controls at a 5% false-discovery rate. The expression of many genes involved in ubiquitin-proteasome and protein synthesis was decreased by ethanol, including ubiquitin B, ubiquitin-like 3, ubiquitin-conjugating enzyme E3A, 20S proteasome alpha- and beta-subunits, and members of the ribosomal proteins. Furthermore, the mRNA expression of heat shock proteins, myristoylated alanine-rich protein kinase C substrate, phosphatase and tensin homolog deleted on chromosome 10, and FK506 binding protein rapamycin-associated protein (FKBP) (mTOR) was also decreased in ethanol-treated cortical neurons. Quantitative real-time reverse transcriptase-polymerase chain reaction analysis of genes involved in the ubiquitin-proteasome cascade revealed a down-regulation of these genes, thereby corroborating our microarray results. CONCLUSIONS: Our results indicate that chronic ethanol treatment of cortical neurons resulted in decreased mRNA expression of genes involving the ubiquitin-proteasome pathway and ribosomal proteins together with mTOR expression leading to disruption of protein degradation mechanism and impairment of protein synthesis machinery.

Animals↗
PubMed2004

Normalization of cDNA microarray data using wavelet regressions.

Normalization is an essential step in microarray data mining and analysis. For cDNA microarray data, the primary purpose of normalization is removing the intensity-dependent bias across different slides within an experimental group or between multiple groups. The locally weighted regression (lowess) procedure has been widely used for this purpose but can be comparatively time consuming when the dataset becomes relatively large. In this study, we applied wavelet regressions, a new smoothing method for recovering a regression function from data that is supposed to outperform other methods in many cases, such as spline or local polynomial fitting, to normalize two cDNA microarray datasets. Relative to the lowess procedure, we found that wavelet regressions not only produced reliable normalization results but also ran much faster. The computing speed represents one of the most important advantages over other algorithms, especially when one is interested in analyzing a large microarray experiment involving hundreds of slides.

Algorithms↗
PubMed2003

A genome-wide scan to identify loci for smoking rate in the Framingham Heart Study population.

BACKGROUND: Although many years of genetic epidemiological studies have demonstrated that genetics plays a significant role in determining smoking behavior, little information is available on genomic loci or genes affecting nicotine dependence. Several susceptibility chromosomal regions for nicotine dependence have been reported, but few have received independent confirmation. To identify susceptibility loci for nicotine dependence, 313 extended pedigrees selected from the Framingham Heart Study population were analyzed by both the GENEHUNTER and S.A.G.E. programs. RESULTS: After performing linkage analyses on the 313 extended Framingham Heart Study families, the EM Haseman-Elston method implemented in GENEHUNTER provided evidence for significant linkage of smoking rate to chromosome 11 and suggestive linkage to chromosomes 9, 14, and 17. Multipoint sib-pair regression analysis using the SIBPAL program of S.A.G.E. on 1389 sib pairs that were split from the 313 extended families identified suggestive linkage of smoking rate to chromosomes 4, 7, and 17. Of these identified positive regions for nicotine dependence, loci on chromosomes 7, 11, and 17 were identified by both GENEHUNTER and S.A.G.E. programs. CONCLUSION: Our genome-wide scan results on the Framingham Heart Study data provide evidence for significant linkage of smoking rate to chromosome 11 and suggestive linkage to chromosomes 4, 7, 9, 14, and 17. These findings suggest that some of these regions may harbor susceptibility loci for nicotine dependence, and warrant further investigation in this and other populations.

Adult↗
PubMed2003

Mapping susceptibility loci for alcohol consumption using number of grams of alcohol consumed per day as a phenotype measure.

BACKGROUND: There is substantial evidence for a significant genetic component to the risk for alcoholism. However, susceptibility loci or genes for alcohol dependence remain largely unknown. To identify susceptibility loci for alcohol dependence, we selected 329 extended families from the Framingham Heart Study population in which at least one family member reported alcohol consumption during the interview in 1970-1971, and performed genome-wide linkage analyses using various analytical methods. RESULTS: Multi-point sib-pair regression analysis using the SIBPAL program of S.A.G.E. provided strong evidence for linkage of alcohol dependence to chromosomes 9 (p-value < 0.0001) and weak evidence to chromosomes 15 and 16 (p-value < 0.005). To confirm these findings, we re-analyzed the same data set by various methods implemented in GENEHUNTER and found that only one region was significant with a LOD score > 2.0 by the variance-component method. This region is located on chromosome 9 between markers GATA21F05 and GATA81C04. CONCLUSION: Analyses of the Framingham Heart Study population provided evidence of genetic susceptibility loci for alcohol dependence on chromosomes 9, 15, and 16. The genomic region identified on chromosome 9 was particularly interesting because the region has also been previously reported to be linked to alcohol dependence in the American Indian population by another group.

Adult↗
PubMed2003

Effect of nicotine on the expression of leptin and forebrain leptin receptors in the rat.

We have previously reported that chronic nicotine administration (4.0 mg/kg/day by i.p. injection over 14 days) up-regulates orexin/hypocretin and neuropeptide Y (NPY) mRNA expression and peptide levels within the hypothalamus. Since there exists a coregulation between these neuropeptides and the protein leptin, the present study was undertaken to determine whether nicotine has a regulatory effect on leptin signaling. Under the same experimental regimen used previously, we found that nicotine down-regulates plasma leptin concentration by 48.8% (P<0.001) and leptin RNA level by 11.4% and 12.4%, respectively, in the perirenal and epididymal white adipose tissue (PWAT, EWAT) compared to the saline controls. We also measured an approximately 20% decrease in white and brown adipose tissue (BAT) by weight in nicotine-treated animals relative to saline controls (P<0.05). On the other hand, we found that chronic nicotine administration increased the expression levels of OB-Rb mRNA by 12% and OB-R mRNA by 25% in the medial basal hypothalamus compared to control rats. Subsequent radioligand binding assays indicated that nicotine also significantly increased leptin binding in ventromedial hypothalamic area (VMA), medial basal hypothalamic area (MBA), arcuate nucleus/median eminence, paraventricular nuclei and piriform cortex. Taken together, our results revealed that nicotine is involved in the regulation of leptin signaling, suggesting that leptin and its receptor play a role in the anorectic effects of nicotine on food intake and body weight in rats.

Adipose Tissue↗
PubMed2003

A meta-analysis of estimated genetic and environmental effects on smoking behavior in male and female adult twins.

BACKGROUND: Numerous twin studies on smoking behavior have shown that genetic and environmental factors play significant and approximately equal roles in the determination of smoking initiation (SI) and smoking persistence (SP). However, estimates of heritability (h2), shared (c2) and unique environmental effects (e2) from the literature display considerable variability for SI and SP, due most probably to differences in statistical analysis models, age, gender, sample size, origin of cohorts and measurement of smoking behavior. METHODS: A systematic literature search identified six studies for SI and 10 studies for SP. Data from these studies were obtained and re-analysed by meta-analytical techniques. RESULTS: For SI, our results indicate that the parameters h2, c2 and e2 are (mean +/- SEM): 0.37 +/- 0.04, 0.49 +/- 0.04 and 0.17 +/- 0.03 in male adults, and 0.55 +/- 0.04, 0.24 +/- 0.06 and 0.16 +/- 0.01 in female adults, respectively. These values were weighted by a combination of original estimates of variance from studies reporting variances plus estimated variances from studies where variances were not reported (called the combined variance method). Using the same approach for SP, we found that the parameters h2, c2 and e2 weighted by the combined variance method for the phenotype are (mean +/- SEM): 0.59 +/- 0.02, 0.08 +/- 0.04 and 0.37 +/- 0.03 in male adults, and 0.46 +/- 0.12, 0.28 +/- 0.08 and 0.24 +/- 0.07 in female adults, respectively. CONCLUSIONS: Our results indicate that genetic factors play a more significant role for SI but a less significant role for SP in female adults compared to male adults. Significant gender difference was also detected in shared environmental factors for SI and SP. However, no significant gender difference was detected for e2 for either phenotype. These findings suggest that genetic and environmental factors may contribute differently to the determination of smoking initiation and persistence in male and female smokers.

Adult↗
PubMed2003

Nonparametric disequilibrium mapping of functional sites using haplotypes of multiple tightly linked single-nucleotide polymorphism markers.

As the speed and efficiency of genotyping single-nucleotide polymorphisms (SNPs) increase, using the SNP map, it becomes possible to evaluate the extent to which a common haplotype contributes to the risk of disease. In this study we propose a new procedure for mapping functional sites or regions of a candidate gene of interest using multiple linked SNPs. Based on a case-parent trio family design, we use expectation-maximization (EM) algorithm-derived haplotype frequency estimates of multiple tightly linked SNPs from both unambiguous and ambiguous families to construct a contingency statistic S for linkage disequilibrium (LD) analysis. In the procedure, a moving-window scan for functional SNP sites or regions can cover an unlimited number of loci except for the limitation of computer storage. Within a window, all possible widths of haplotypes are utilized to find the maximum statistic S* for each site (or locus). Furthermore, this method can be applied to regional or genome-wide scanning for determining linkage disequilibrium using SNPs. The sensitivity of the proposed procedure was examined on the simulated data set from the Genetic Analysis Workshop (GAW) 12. Compared with the conventional and generalized TDT methods, our procedure is more flexible and powerful.

Algorithms↗
PubMed2003

The genetics of smoking related behavior: a brief review.

Smoking behavior is influenced by both genetic and environmental factors. Many years of twin and adoption studies have demonstrated that heritability is at least 50% for both smoking initiation and smoking persistence. Furthermore, the extent to which genetic and environmental factors contribute to smoking behavior in men is significantly different from that in women. It has been reported that polymorphisms of candidate genes, such as cytochrome P450, dopamine receptor and transporter, and serotonin transporter genes, are associated with smoking behavior. However, many of these reports have not yet received independent confirmation. Based on the results from genome-wide linkage and association analyses on different subject populations, 15 loci located on 8 chromosomes were reported to harbor susceptibility genes for nicotine and other substances of abuse. It is expected that a newly completed human genome sequence, as well as advances in genomic technologies such as genotyping and array analysis, will greatly enhance progress toward the identification of genes associated with smoking behavior.

Female↗
PubMed2003

Distinct regions of the slo subunit determine differential BKCa channel responses to ethanol.

BACKGROUND: Ethanol at clinically relevant concentrations increases BKCa channel activity in dorsal root ganglia neurons, GH3 cells, and neurohypophysial terminals, leading to decreases in cell excitability and peptide release. In contrast, ethanol inhibits BKCa channels from aortic myocytes, which likely contributes to alcohol-induced aortic constriction. The mechanisms that determine differential BKCa channel responses to ethanol are unknown. We hypothesized that nonconserved regions in the BKCa channel-forming subunit (slo) are major contributors to the differential alcohol responses of different BKCa channel phenotypes. METHODS: We constructed chimeras by interchanging the core and the tail domains of two BKCa channel-forming subunits (mslo and bslo) that, after expression, differentially respond to ethanol (activation and inhibition, respectively), and studied ethanol action on these mbslo and bmslo chimeric channels using single-channel, patch-clamp techniques. RESULTS AND CONCLUSION: Data from cell-free membranes patches demonstrate that the activity of channels that share a mslo-type core-linker (wt mslo and the mbslo chimera) is consistently and significantly potentiated by acute exposure to ethanol. Thus, a mslo tail is not necessary for ethanol potentiation of slo channels. In contrast, the activity of channels that share a bslo-type core-linker (wt bslo and the bmslo chimera) display heterogenous responses to ethanol: inhibition (in the majority of cases), refractoriness, or activation. Overall, our data indicate that the slo core-linker is a critical region likely contributing to the differential responses of BKCa channels to ethanol.

Animals↗
PubMed2003

Nicotine, body weight and potential implications in the treatment of obesity.

Obesity is an epidemic problem in the U. S. and many other industrialized nations. Historically, the drugs used for the treatment of obesity generally targeted small molecule neurotransmitters. As research grows to decipher the underlying molecular mechanisms behind energy homeostasis, it is becoming evident that the modulating effects of neuropeptides also are critical in the regulation of appetite and metabolism. The search for drugs to modify these monoaminergic and peptidergic pathways may eventually prove successful in the treatment of obesity. While tobacco smoking has long been used as one strategy to maintain a lower body weight, especially in female smokers, its adverse associations with addiction and disease overshadow its potential use as an antiobesity agent. Potential pharmacological effects of nicotine could be better understood as the intricacies of the nicotinic acetylcholine receptor are revealed. The objective of this review is threefold: first is to provide an overview of the physiological effects of nicotine on body weight while focusing on the drugs that are available as antiobesity and smoking cessation agents. Second is to provide the present status of the nicotinic acetylcholine receptor as it relates to energy homeostasis and its potential as an effective treatment modality for obesity. Third is to present the current knowledge with respect to nicotine's effects on energy homeostatic and reward related pathways at the molecular level. A better understanding of the regulatory mechanisms underlying the pharmacological effects of nicotine on body weight will provide insights in identification of potential targets for the development of appropriate medicines in the treatment of obesity.

Animals↗
PubMed2002

Molecular cloning, mapping and characterization of a novel mouse RING finger gene, Mrf1.

With a combined approach of database search, heterologous polymerase chain reaction (PCR), reverse transcription-PCR, rapid amplification of complementary DNA ends and genomic library screening, we have successfully cloned a mouse RING finger gene, mouse RING finger 1 (Mrf1). The Mrf1 gene has two exons of 63 and 2665 bp, respectively, and one intron of over 13 kb. An open reading frame was identified exclusively in exon 2, which encodes a putative protein of the RING-B box-coiled coil or the tripartite motif type of 403 amino acids. Mrf1 is moderately expressed in the spleen, brain and heart as a single 3.0 kb product and very highly expressed in the testis as two transcripts of 3.0 and 1.5 kb, respectively. The Mrf1 gene was mapped to mouse chromosome 3, between markers D3Mit70 and D3Mit277. Western blotting analysis indicated that an expected protein of approximately 44 kD was detected in the brain extracts of mouse, rat and human. The possible functions of Mrf1 are discussed in the contexts of protein-protein interactions, oncogenesis and ubiquitination.

Amino Acid Sequence↗
PubMed2002

Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents.

Gene expression is regulated by a highly coordinated network of events whose efficiency may constrain the level of expression. Among other factors, natural selection for increased translational efficiency and/or fidelity may shape nucleotide composition and, hence, codon usage during evolution. Previous studies have shown that highly expressed genes in Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster have relatively higher codon usage biases. However, in the case of mammals, results have been equivocal. In this study, we assessed the correlation between nucleotide composition and mRNA expression levels of rodent genes measured by cDNA microarray and serial analysis of gene expression (SAGE) techniques. We found that mRNA expression levels were correlated with the third nucleotide position GC (GC3) content for both Rattus norvegicus (r = 0.246, p = 0.01; N = 110) and Mus musculus (r = 0.21, p = 0.0026; N = 203) genes. However, no significant correlation was evident between mRNA expression level and GC contents of 5'- and 3'-untranslated regions (UTRs) for either species. This suggests that, in rodents, nucleotide composition of coding sequences and UTRs might evolve differentially when considered along an expression gradient. Accordingly, it is possible that higher GC levels may present the rodent genes with a selective advantage for translational efficiency. However, the increase in GC3 content seems to level off above an expressional threshold (e.g., >or=threefold the median expression for R. norvegicus), suggesting that conflicting demands posed by different aspects of transcriptional and translational machineries (e.g., efficiency versus fidelity) may set an upper limit for GC3.

Animals↗
PubMed2002

Analysis of heterosis by a direct method using the concept of heritability.

The presence of heterosis has been observed in many species at both phenotypic and gene levels. Strangely, the genetic basis of heterosis was and still is largely unknown. In this study, we extended and simplified some formulas that we reported previously. The foundation of our model was based on partitioning the F1 phenotypic variance of the cross between two pure lines into additive, dominance and epistasis components, which lead to the estimation of effective factors, crossheritability in the broad and narrow sense and heterotic power. In the model, we assume that all polygenes controlling a quantitative trait have an equal genetic effect and are independent of each other. By extension of the heritability to a cross population, new features appear. The word 'crossheritability' acquires the status of a new genetic parameter that suffices to deal with the problem of crossbreeding and clarifies the picture of heterosis. Lastly, an example of employing the proposed method in analyzing the crossing data from Drosophila melanogaster is given to illustrate its application.

Animals↗
PubMed2002

Microarray technology and its application on nicotine research.

Since its development, microarray technique has revolutionized almost all fields of biomedical research by enabling high-throughput gene expression profiling. Using cDNA microarrays, thousands of genes from various organisms have been examined with respect to differentiation/development, disease diagnosis, and drug discovery Nevertheless, research on nicotine using cDNA microarrays has been rather limited. Therefore, it is our intention in this article to report the findings of our cDNA microarray study on nicotine. We first present an overview of the microarray technology, particularly focusing on the factors related to microarray design and analysis. Second, we provide a detailed description of several newly identified biological pathways in our laboratory, such as phosphatidylinositol signaling and calcium homeostasis, which are involved in response to chronic nicotine administration. Additionally, we illustrate how comparisons between microarray studies help identify candidate genes that potentially may explain the observed inverse association between smoking and schizophrenia. Lastly, given the early stage of microarray research on nicotine, we elaborate on the need for an efficient analysis of genetic networks to further enhance our understanding of the mechanisms involved in nicotine abuse and addiction.

Animals↗