PubMed Health⌕ Search

Biomedical subjects

Lei Bao

Publications and source records attributed to Lei Bao.

At least 19 recordsLinked to original sources
PubMed2006

PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits.

Polymorphism in microRNA Target Site (PolymiRTS) database is a collection of naturally occurring DNA variations in putative microRNA target sites. PolymiRTSs may affect gene expression and cause variations in complex phenotypes. The database integrates sequence polymorphism, phenotype and expression microarray data, and characterizes PolymiRTSs as potential candidates responsible for the quantitative trait locus (QTL) effects. It is a resource for studying PolymiRTSs and their implications in phenotypic variations. PolymiRTS database can be accessed at http://compbio.utmem.edu/miRSNP/.

Animals↗
PubMed2006

The role of interleukin-11 in pregnancy involves up-regulation of alpha2-macroglobulin gene through janus kinase 2-signal transducer and activator of transcription 3 pathway in the decidua.

IL-11 expressed by endometrial stromal cells is crucial for normal pregnancy. IL-11 receptor alpha (IL-11Ralpha) null mice are infertile due to abnormal development of the placenta. In these mice, the mesometrial decidual tissue, which is the site of trophoblast invasion, thins and disappears at mid-pregnancy. Degeneration of the decidua is accompanied by uncontrolled trophoblast invasion. In this report, we show, using IL-11Ralpha null mice, that a defect in IL-11 signaling in the decidua leads to severe down-regulation of alpha(2)-macroglobulin (alpha(2)-MG), a metalloproteinase inhibitor crucial for limiting trophoblast invasion. We also present evidence, using uterine stromal cells that decidualize in culture, that IL-11 robustly stimulates the endogenous alpha(2)-MG expression and enhances alpha(2)-MG promoter activity. Serial 5' deletion and internal deletion of the promoter reveal two important signal transducer and activator of transcription (Stat) binding sites. Mutation of either one of these motifs decreases IL-11 stimulation, whereas double mutation prevents IL-11 action. We also found that IL-11 activates Janus kinase 2 (Jak2) and induces rapid phosphorylation, nuclear translocation, and promoter binding activity of Stat3 in decidual cells, whereas Jak1, Tyk2, and Stat5 activities are not affected. In addition, Jak2 inhibitor totally prevents alpha(2)-MG expression in decidual cells. Taken together, results of this investigation provide, at least in part, an explanation for the overinvasiveness of the trophoblast in IL-11Ralpha null mice and reveal, for the first time, that IL-11 signals through the Jak2/Stat3 pathway in decidual cells to stimulate the expression of alpha(2)-MG, a protease inhibitor essential for normal placentation in pregnancy.

Animals↗
PubMed2006

Dietary ascorbic acid may be necessary for enhancing the immune response in Siberian sturgeon (Acipenser baerii), a species capable of ascorbic acid biosynthesis.

Siberian sturgeon (Acipenser baerii Brandt) is one of few fish species capable of synthesizing ascorbic acid (AA); however, it is unknown whether dietary AA is still necessary for this species to generate an optimal non-specific immune response, as is found in most teleostean species that do not synthesize AA. Sturgeon fed either 0 or 500 mg AA (AA polyphosphate) equivalent kg(-1) diets for 2 weeks were then either sham or experimentally injected with Aeromonas hydrophila lipopolysaccharide (LPS) to mimic infection and therefore instigate a non-specific immune response. No significant differences were found in growth and survival throughout the duration of the experiment between sham and LPS groups and between both diets. Two and eight days after injection, serum lysozyme levels were elevated in both LPS and non-LPS groups. Respiratory burst was not affected by dietary AA and significantly higher in LPS groups over non-LPS groups; however, dietary AA may have enhanced the effects seen in the LPS injected fish fed the AA supplemented diet. There were no significant differences in renal l-gulono-1, 4-lactone oxidase (GLO) activity between dietary and LPS treatments, but fish exposed to LPS without dietary AA demonstrated an inter-organ transfer of AA from posterior kidney to liver. Our results indicate that dietary AA may be conditionally necessary for Siberian sturgeon to achieve optimal immune response, particularly in early developmental stages, information imperative to developing successful aquaculture programs for sturgeon species.

Animals↗
PubMed2006

Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships.

Gene expression QTL (eQTL) mapping can suggest candidate regulatory relationships between genes. Recent advances in mammalian phenotype annotation such as mammalian phenotype ontology (MPO) enable systematic analysis of the phenotypic spectrum subserved by many genes. In this study we combined eQTL mapping and phenotypic spectrum analysis to predict gene regulatory relationships. Five pairs of genes with similar phenotypic effects and potential regulatory relationships suggested by eQTL mapping were identified. Lines of evidence supporting some of the predicted regulatory relationships were obtained from biological literature. A particularly notable example is that promoter sequence analysis and real-time PCR assays support the predicted regulation of protein kinase C epsilon (Prkce) by cAMP responsive element binding protein 1 (Creb1). Our results show that the combination of gene eQTL mapping and phenotypic spectrum analysis may provide a valuable approach to uncovering gene regulatory relations underlying mammalian phenotypes.

Animals↗
PubMed2006

Functional impacts of non-synonymous single nucleotide polymorphisms: selective constraint and structural environments.

In this work, we studied the correlations between selective constraint, structural environments and functional impacts of non-synonymous single nucleotide polymorphisms (nsSNPs). We found that the relation between solvent accessibility and functional impacts of nsSNPs is not as simple as generally thought. Finer structural classifications need to be taken into account to reveal the complex relations between the characteristics of a structure environment and its influence on the functional impacts of nsSNPs. We introduced two parameters for each structural environment, consensus residue percentage and residue distribution distance, to characterize the selective constraint imposed by the environment. Both parameters significantly correlate with the functional bias of nsSNPs across the structural environments. This result shows that selective constraint underlies the bias of a structural environment towards a certain type of nsSNPs (disease-associated or benign).

Genetic Diseases, Inborn↗
PubMed2005

Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits.

Genetic loci that regulate inherited traits are routinely identified using quantitative trait locus (QTL) mapping methods. However, the genotype-phenotype associations do not provide information on the gene expression program through which the genetic loci regulate the traits. Transcription modules are 'self-consistent regulatory units' and are closely related to the modular components of gene regulatory network [Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet., 31, 370-377; Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176]. We used genome-wide genotype and gene expression data of a genetic reference population that consists of mice of 32 recombinant inbred strains to identify the transcription modules and the genetic loci regulating them. Twenty-nine transcription modules defined by genetic variations were identified. Statistically significant associations between the transcription modules and 18 classical physiological and behavioral traits were found. Genome-wide interval mapping showed that major QTLs regulating the transcription modules are often co-localized with the QTLs regulating the associated classical traits. The association and the possible co-regulation of the classical trait and transcription module indicate that the transcription module may be involved in the gene pathways connecting the QTL and the classical trait. Our results show that a transcription module may associate with multiple seemingly unrelated classical traits and a classical trait may associate with different modules. Literature mining results provided strong independent evidences for the relations among genes of the transcription modules, genes in the regions of the QTLs regulating the transcription modules and the keywords representing the classical traits.

Animals↗
PubMed2005

Stable gene transfer and expression in human primary T cells by the Sleeping Beauty transposon system.

The Sleeping Beauty (SB) transposon system is a nonviral DNA delivery system in which a transposase directs integration of an SB transposon into TA-dinucleotide sites in the genome. To determine whether the SB transposon system can mediate stable gene expression in human T cells, primary peripheral blood lymphocytes (PBLs) were nucleofected with SB vectors carrying a DsRed reporter gene. Plasmids containing the SB transposase on the same molecule as (cis) or on a molecule separate from (trans) the SB transposon mediated long-term and stable reporter gene expression in human primary T cells. Sequencing of transposon:chromosome junctions confirmed that stable gene expression was due to SB-mediated transposition. In other studies, PBLs were successfully transfected using the SB transposon system and shown to stably express a fusion protein consisting of (1) a surface receptor useful for positive T-cell selection and (2) a "suicide" gene useful for elimination of transfected T cells after chemotherapy. This study is the first report demonstrating that the SB transposon system can mediate stable gene transfer in human primary PBLs, which may be advantageous for T-cell-based gene therapies.

Animals↗
PubMed2005

Decreased IgG production but increased MIP-1beta expression in collagen-induced arthritis in C-C chemokine receptor 5-deficient mice.

Collagen-induced arthritis (CIA) is a widely used model of human rheumatoid arthritis (RA) characterized by chronic inflammation of the synovial joints. The pathogenesis of RA and CIA has not been completely defined, but both involve the recruitment of leukocytes and lymphocytes to the joints and Th1-type cell mediated autoimmune responses. The C-C chemokine receptor 5 (CCR5) is preferentially expressed on Th1 cells and has been strongly implicated in inflammatory process through trafficking of leukocytes and lymphocytes into the sites of inflammation. We investigated the role of the CCR5 in CIA using CCR5 knockout mice (CCR5-/-) in which we analyzed the consequences of CCR5 deficiency for the immune response and inflammation. We found that CCR5-/- mice showed a significant reduction in the incidence of CIA after collagen II (CII)-immunization as compared to wild-type (CCR5+/+) mice. The reduced incidence seen in CCR5-/- mice was associated with these animals having significantly lower IgG levels, especially IgG2a and IgG2b antibodies against CII, as well as an obviously augmented IL-10 production in splenocytes. Overproduction of MIP-1beta in CCR5-deficient mice after CII-immunization may contribute partially to the occurrence of arthritis.

Animals↗
PubMed2005

nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

Nonsynonymous single nucleotide polymorphisms (nsSNPs) are prevalent in genomes and are closely associated with inherited diseases. To facilitate identifying disease-associated nsSNPs from a large number of neutral nsSNPs, it is important to develop computational tools to predict the nsSNP's phenotypic effect (disease-associated versus neutral). nsSNPAnalyzer, a web-based software developed for this purpose, extracts structural and evolutionary information from a query nsSNP and uses a machine learning method called Random Forest to predict the nsSNP's phenotypic effect. nsSNPAnalyzer server is available at http://snpanalyzer.utmem.edu/.

Algorithms↗
PubMed2005

Inferring gene transcriptional modulatory relations: a genetical genomics approach.

Bayesian network modeling is a promising approach to define and evaluate gene expression circuits in diverse tissues and cell types under different experimental conditions. The power and practicality of this approach can be improved by restricting the number of potential interactions among genes and by defining causal relations before evaluating posterior probabilities for billions of networks. A newly developed genetical genomics method that combines transcriptome profiling with complex trait analysis now provides strong constraints on network architecture. This method detects those chromosomal intervals responsible for differences in mRNA expression using quantitative trait locus (QTL) mapping. We have developed an efficient Bayesian approach that exploits the genetical genomics method to focus computational effort on the most plausible gene modulatory networks. We exploit a dense marker map for a genetic reference population (GRP) that consists of 32 BXD strains of mice made by intercrossing two progenitor strains--C57BL/6J and DBA/2J. These progenitors differ at approximately 1.3 million known single nucleotide polymorphisms (SNPs), all of which can be exploited to estimate the probability that a gene contains functional polymorphisms that segregate within the GRP. We constructed 66 candidate networks that include all the candidate modulator genes located in the 209 statistically significant trans-acting QTL regions. SNPs that distinguish between the two progenitor strains were used to further winnow the list of candidate modulators. Bayesian network was then used to identify the genetic modulatory relations that best explain the microarray data.

Algorithms↗
PubMed2005

Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information.

MOTIVATION: There has been great expectation that the knowledge of an individual's genotype will provide a basis for assessing susceptibility to diseases and designing individualized therapy. Non-synonymous single nucleotide polymorphisms (nsSNPs) that lead to an amino acid change in the protein product are of particular interest because they account for nearly half of the known genetic variations related to human inherited diseases. To facilitate the identification of disease-associated nsSNPs from a large number of neutral nsSNPs, it is important to develop computational tools to predict the phenotypic effects of nsSNPs. RESULTS: We prepared a training set based on the variant phenotypic annotation of the Swiss-Prot database and focused our analysis on nsSNPs having homologous 3D structures. Structural environment parameters derived from the 3D homologous structure as well as evolutionary information derived from the multiple sequence alignment were used as predictors. Two machine learning methods, support vector machine and random forest, were trained and evaluated. We compared the performance of our method with that of the SIFT algorithm, which is one of the best predictive methods to date. An unbiased evaluation study shows that for nsSNPs with sufficient evolutionary information (with not <10 homologous sequences), the performance of our method is comparable with the SIFT algorithm, while for nsSNPs with insufficient evolutionary information (<10 homologous sequences), our method outperforms the SIFT algorithm significantly. These findings indicate that incorporating structural information is critical to achieving good prediction accuracy when sufficient evolutionary information is not available. AVAILABILITY: The codes and curated dataset are available at http://compbio.utmem.edu/snp/dataset/

Algorithms↗
PubMed2005

Identifying genes related to chemosensitivity using support vector machine.

In an effort to identify genes involved in chemosensitivity and to evaluate the functional relationships between genes and anticancer drugs acting by the same mechanism, a supervised machine learning approach called support vector machine (SVM) is used to associate genes with any of five predefined anticancer drug mechanistic categories. The drug activity profiles are used as training examples to train the SVM and then the gene expression profiles are used as test examples to predict their associated mechanistic categories. This method of correlating drugs and genes provides a strategy for finding novel biologically significant relationships for molecular pharmacology.

Algorithms↗
PubMed2005

Changes in epidemiology and clinical characteristics of cervical cancer over the past 50 years.

OBJECTIVE: To evaluate the changes in the epidemiology and clinical characteristics of cervical cancer over the past 50 years, and explore appropriate treatment corresponding to these changes. METHODS: The clinical and pathological data of 1557 patients with invasive cervical cancer treated between January, 1955 and December, 2004 were retrospectively analyzed. RESULTS AND CONCLUSIONS: The average age of cervical cancer onset gradually decreased over the past 50 years, from 56.27+/-8.45 in 1955-1964 to 43.81+/-8.9 years in 1995-2004, whereas the ratio of young (< or =35 years old) patients rose from 3.42% to 24.91%. The ratio of early clinical stage (stages I-II) and non-squamous cancer also steadily increased (P<0.05, respectively). The tumor stage, pathological type and rate of lymph node metastasis were all significantly different among different age groups (P<0.05). In particular, the young (< or =35 years old) group had evidently higher ratios of non-squamous and advanced stage (III-IV) cancers with a higher rate of lymphatic metastasis in comparison with other age groups (P<0.01, respectively). Because of the changes in epidemiology and clinical characteristics of cervical cancer, it is necessary to modify the conventional treatment regimens and explore reasonable therapy corresponding to these changes. Preservation of reproductive endocrine function ought to be fully considered in cervical cancer treatment in women at childbearing age. Neoadjuvant intraarterial chemotherapy is an useful method for cervical cancer treatment at present.

Adenocarcinoma↗
PubMed2004

CCR5 deficiency does not prevent P0 peptide 180-199 immunized mice from experimental autoimmune neuritis.

Experimental autoimmune neuritis (EAN) is an inflammatory autoimmune demyelinating disease of peripheral nervous system (PNS) and represents an animal model of Guillain-Barré syndrome (GBS) in man. The inflammatory cell infiltrating into the PNS is a prerequisite for developing EAN. To explore the role of CC chemokine receptor 5 (CCR5) in the inflammatory process of EAN, we induced EAN in CCR5-deficient (CCR5(-/-)) mice with P0 protein peptide 180-199. We found that CCR5(-/-) mice showed a similar EAN clinical course and severity as well as profile of infiltrating macrophages and T cells in cauda equina (CE) of EAN and the same levels of spleen mononuclear cell (MNC) response to antigen and mitogen when compared with CCR5(+/+) control mice. However, increased IP-10 and MIP-1beta production in sciatic nerves were seen in CCR5(-/-) mice. These results suggest that CCR5 deficiency does not prevent P0 peptide 180-199-immunized mice from EAN. Increased MIP-1beta and IP-10 in sciatic nerves may compensate the CCR5 deficiency and contribute to inflammatory cells infiltrating to the PNS.

Animals↗
PubMed2004

Increased susceptibility to experimental autoimmune neuritis after upregulation of the autoreactive T cell response to peripheral myelin antigen in apolipoprotein E-deficient mice.

Experimental autoimmune neuritis (EAN), an acute demyelinating inflammatory disease of the peripheral nervous system (PNS), is a good model for the human counterpart, Guillain-Barré syndrome. Apolipoprotein E (ApoE), a 34 kDa glycosylated protein with multiple biological properties, has been linked both with the innate immune response of mice and with neurological disease. The present study investigated the previously unexplored role of ApoE in autoimmune-mediated demyelination. ApoE-deficient (apoE -/-) mice exhibited a greater susceptibility to EAN induced by the PNS myelin P0 protein peptide 180-199, as compared to wild type (apoE +/+) mice. The augmented susceptibility seen in apoE -/- mice was associated with increased inflammatory cell infiltrates in the PNS during the effector phase. Although the 2 groups of mice exhibited no quantitative or proportional differences in splenic lymphocyte populations, the apoE -/- mice showed enhanced antigen-specific proliferation of T cells of spleen, which is related to modified macrophage function, upregulation of Th1 and downregulation of Th2-autoreactive responses to P0 peptide. These effects were shown as increased numbers of IFN-gamma expressing cells in the spleen and of IFN-gamma, IL-12 and TNF-alpha expressing cells in the PNS, as well as a decreased IL-10 production by splenic cells in apoE -/- mice. In addition, apoE -/- mice had enhanced antigen-specific antibody responses, which might have contributed to their aggravated EAN. These data provide strong evidence that apoE acts as an inhibitor of this inflammatory and demyelinating disease by upregulating IL-10, as well as by inhibiting Th1 responses and antigen-specific antibody formation. These data may aid the development of new and more effective therapeutic strategies for inflammatory and demyelinating diseases such as Guillain-Barré syndrome.

Analysis of Variance↗
PubMed2003

Exogenous soluble tumor necrosis factor receptor type I ameliorates murine experimental autoimmune neuritis.

Tumor necrosis factor (TNF) and its receptor (TNFR) have been strongly implicated in the pathogenesis of autoimmune disease. Soluble cytokine receptors may be shed naturally from cell membranes to inhibit cytokine activity. Experimental autoimmune neuritis (EAN) is a CD4 Th1 cell-mediated animal model of Guillain-Barré syndrome (GBS) in humans. In the present study, we investigated the effects of soluble TNFR type I (sTNFR I) in EAN induced in mice by P0 peptide 180-199 and Freund's complete adjuvant. Our data from two different therapeutic regimens indicate that the administration of sTNFR I effectively ameliorated the clinical and pathological signs of EAN, i.e., decreased its severity, shortened its duration, and reduced inflammatory cell infiltration into the peripheral nervous system. The suppression of clinical EAN was accompanied in vitro by a marked reduction in antigen-specific T-cell proliferation and IFN-gamma synthesis by spleen cells from sTNFR I-treated mice, compared to control mice treated with PBS. These data directly demonstrate a pivotal role for TNF in the development of EAN and also suggest that sTNFR I may have therapeutic potential for alleviating GBS in humans.

Animals↗
PubMed2003

Low content of protein S29 in ribosomes of human lung cancer cell line a549: detected by two-dimensional electrophoresis.

This study revealed that the content of protein S29 in ribosomes of cancer cell line A549 was distinctly low (equivalent to about 30% of that of 2BS). The conclusion was acquired based on the ratios of spot volume of ribosomal protein S29 to that of several other ribosomal proteins (S29/L37a, S29/L38, S29/S27 and S29/S28) in the same gel plate. The possible biological roles of ribosomal protein S29 in malignant transformation and translation regulation are briefly discussed.

Blotting, Northern↗