PubMed Health⌕ Search

Biomedical subjects

Lin Tao

Publications and source records attributed to Lin Tao.

At least 19 recordsLinked to original sources
PubMed2007

Overlapping substrate specificity for sucrose and maltose of two binding protein-dependent sugar uptake systems in Streptococcus mutans.

Sugar metabolism by Streptococcus mutans is associated with tooth decay. The most abundant sugars in the human diet are sucrose and maltose, a derivative of starch. Previously, we reported a binding protein-dependent transport system (msm) in S. mutans that transports sucrose and maltose, but its associated enzymes do not metabolize maltose. By searching the S. mutans genomic sequence for a maltose system (mal), we found a gene cluster encoding proteins with homology to those of msm and the Escherichia coli maltose system. Mutants were constructed by deleting msm or mal, or both, and tested for sugar utilization. Deletion of the mal system diminished the ability of S. mutans to ferment maltose, but deletion of only the mal transporter genes or msm showed reduced utilization of chromogenic maltosides. Maltose, sucrose, glucose, fructose, mannose, and N-acetyl glucosamine inhibited utilization of chromogenic maltosides by the wild-type strain and mutants. In conclusion, the two binding protein-dependent systems in S. mutans appear to transport collaboratively their common substrate sugars, notably sucrose and maltose.

Bacterial Proteins↗
PubMed2006

Photocatalytic degradation of gaseous benzene over TiO2/Sr2CeO4: preparation and photocatalytic behavior of TiO2/Sr2CeO4.

The paper demonstrates that the photocatalytic activity of TiO(2) towards the decomposition of gaseous benzene in a batch reactor can be greatly improved by loading TiO(2) on the surface of Sr(2)CeO(4). The research investigates the optimum loading amount of TiO(2) on Sr(2)CeO(4) in enhancing the photocatalytic activity of TiO(2). The prepared photocatalyst was characterized by XRD, UV-vis diffuse reflectance and XPS analyses. TiO(2) is loaded on Sr(2)CeO(4) at 773K. TiO(2)/Sr(2)CeO(4) absorbs much more visible light than TiO(2). The XPS spectrum shows that there are Ti, O, C, Sr elements on the surface of the TiO(2)/Sr(2)CeO(4), and that the binding energy value of Ti2p transfers to a lower value. TiO(2)/Sr(2)CeO(4) demonstrates 2.0 times the photocatalytic activity of pure TiO(2). Based upon these observations, the mechanistic role of Sr(2)CeO(4) in the photocatalytic oxidation reaction has been suggested.

Benzene↗
PubMed2006

Photocatalytic degradation of gaseous benzene over TiO2/Sr2CeO4: kinetic model and degradation mechanisms.

Photocatalytic oxidation of benzene in air was carried out over TiO2/Sr2CeO4 catalysts. The prepared photocatalyst was characterized by SBET, UV-vis diffuse reflectance and XPS. TiO2/Sr2CeO4 absorbs much more visible light than TiO2 in the visible light region. The XPS spectrum shows that the binding energy value of Ti 2p3/2 transfers to a lower value. The main purpose was to investigate the kinetic model and degradation mechanisms. The kinetic data matched well with the Langmuir-Hinshelwood (L-H) kinetic model with the limiting rate constant and the adsorption constant in this case were 0.0064 mg l-1 min-1 and 9.2078 l mg-1, respectively. No gas-phase intermediates were detected by direct GC/FID analysis under the conditions despite the high benzene concentration. Ethyl acetate and (3-methyl-oxiran-2-yl)-methanol were two major identified intermediates which were accompanied by butylated hydroxytoluene, 2,6-bis(1,1-dimethylethyl)-4,4-dimethylycyclohe, 2,5-cyclohexadiene-1,4,dione,2,6-bis(1,1-dim). It is plausible that at least one of these less-reactive intermediates caused the deactivation of the photocatalyst. Finally, the photocatalytic oxidation mechanisms were speculated.

Benzene↗
PubMed2006

KCNE2, a down-regulated gene identified by in silico analysis, suppressed proliferation of gastric cancer cells.

It is important to identify the differentially expressed gene in gastric cancer for elucidating the molecular mechanisms of tumorigenesis of stomach. Here, 38 genes differentially expressed genes between gastric cancer and normal gastric mucosa by in silico approaches. A potassium channel protein KCNE2, identified as a down-regulated gene in gastric cancer, was chosen for further study. We investigated the expression of KCNE2 in gastric cancer tissues and cell lines and examined the effect of KCNE2 on proliferation of gastric cancer. The expression of KCNE2 was markedly down-regulated in gastric cancer tissues and cell lines. Forced overexpression of KCNE2 suppressed the growth of SGC7901 cells and cell cycle progression significantly, which might be related to the down-regulation of Cyclin D1. KCNE2 also inhibited SGC7901 cell growth in soft agar and its tumorigenicity in nude mice. Taken together, our work showed that in silico analysis approaches could be used to identify cancer-related genes effectively. KCNE2, as a novel down-regulated gene in gastric cancer, suppressed cell proliferation and tumorigenesis of stomach.

Animals↗
PubMed2006

Streptococcus gordonii utilizes several distinct gene functions to recruit Porphyromonas gingivalis into a mixed community.

Dental plaque biofilm formation proceeds through a developmental pathway initiated by the attachment of pioneer organisms, such as Streptococcus gordonii, to tooth surfaces. Through a variety of synergistic interactions, pioneer organisms facilitate the colonization of later arrivals including Porphyromonas gingivalis, a potential periodontal pathogen. We have investigated genes of S. gordonii required to support a heterotypic biofilm community with P. gingivalis. By screening a plasmid integration library of S. gordonii, genes were identified that are crucial for the accumulation of planktonic P. gingivalis cells into a multispecies biofilm. These genes were further investigated by specific mutation and complementation analyses. The biofilm-associated genes can be grouped into broad categories based on putative function as follows: (i) intercellular or intracellular signalling (cbe and spxB), (ii) cell wall integrity and maintenance of adhesive proteins (murE, msrA and atf), (iii) extracellular capsule biosynthesis (pgsA and atf), and (iv) physiology (gdhA, ccmA and ntpB). In addition, a gene for a hypothetical protein was identified. Biofilm visualization and quantification by confocal microscopy confirmed the role of these genes in the maturation of the multispecies community, including biofilm architectural development. The results suggest that S. gordonii governs the development of heterotypic oral biofilms through multiple genetic pathways.

Bacterial Adhesion↗
PubMed2005

Perfluorooctanesulfonate and related fluorochemicals in biological samples from the north coast of Colombia.

Perfluorinated compounds are widespread pollutants of toxicological importance that have been detected in environmental matrices. However, little is known on their distribution in South America. In this study, distribution of perfluorooctanesulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorohexanesulfonate (PFHxS), and perfluorooctanesulfonamide (PFOSA) was determined in the bile of mullet, Mugil incilis, and in tissues of pelicans (Pelecanus occidentalis) collected from North Colombia. Analysis was performed by HPLC mass spectrometry after ion-pair extraction. PFOS was found in all bile samples and PFOA and PFHxS were detected at lower frequency. Average concentrations of PFOS, PFOA, and PFHxS in bile of fish from Cartagena Bay, an industrialized site, and Totumo marsh, a reference site, were 3673, 370, 489 and 713, 47.4, 1.27 ng/mL, respectively. PFOS concentrations in pelican organs decreased in the order of spleen>liver>lung>kidney>brain>heart>muscle. These results suggest, for the first time, that perfluorinated compounds are also found in wildlife from Latin American countries.

Alkanesulfonic Acids↗
PubMed2005

Polycyclic musk compounds in higher trophic level aquatic organisms and humans from the United States.

Polycyclic musks, 1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta[g]-2-benzopyran (HHCB) and 7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene (AHTN), are used as fragrance ingredients in numerous consumer products such as cleaning agents and personal care products. Studies have reported the widespread occurrence of these musks in surface waters and fish from western European countries. Nevertheless, little is known about their accumulation in humans and wildlife in the United States. In this study, we measured concentrations of HHCB and AHTN in human adipose fat collected from New York City. Furthermore, tissues from marine mammals, water birds, and fish collected from US waters were analyzed to determine the concentrations of HHCB and AHTN. Concentrations of HHCB and AHTN in human adipose fat samples ranged from 12 to 798 and from <5 to 134 ng/g, on a lipid weight basis, respectively. A significant correlation existed between the concentrations of HHCB and AHTN in human adipose fat. Concentrations of HHCB and AHTN were not positively correlated with age or gender of the donors. HHCB was found in tissues of several wildlife species, but not in the livers of polar bear from the Alaskan Arctic. Among wildlife species analyzed, spinner and bottlenose dolphins collected from Florida coastal waters contained measurable concentrations of HHCB.

Adipose Tissue↗
PubMed2005

Perfluorinated compounds in aquatic organisms at various trophic levels in a Great Lakes food chain.

Trophic transfer of perfluorooctanesulfonate (PFOS) and other related perfluorinated compounds was examined in a Great Lakes benthic foodweb including water-algae-zebra mussel-round goby-smallmouth bass. In addition, perfluorinated compounds were measured in livers and eggs of Chinook salmon and lake whitefish, in muscle tissue of carp, and in eggs of brown trout collected from Michigan. Similarly, green frog livers, snapping turtle plasma, mink livers, and bald eagle tissues were analyzed to determine concentrations in higher trophic-level organisms in the food chain. PFOS was the most widely detected compound in benthic organisms at various trophic levels. Concentrations of PFOS in benthic invertebrates such as amphipods and zebra mussels were approximately 1000-fold greater than those in surrounding water, which suggested a bioconcentration factor (BCF; concentration in biota/concentration in water) of 1000 in benthic invertebrates. Concentrations of PFOS in round gobies were two- to fourfold greater than those in their prey organisms such as zebra mussels and amphipods. Concentrations of PFOS in predatory fishes (Chinook salmon and lake whitefish) were 10 to 20-fold greater than those in their prey species. Concentrations of PFOS in mink and bald eagles were, on average, 5- to 10-fold greater than those in Chinook salmon, carp, or snapping turtles. Because of the accumulation of PFOS in liver and blood, the biomagnification factor (BMF) of perfluorinated compounds in higher trophic-level organisms such as salmonid fishes, mink, and eagles were based on the concentrations in livers or plasma. Overall, these results suggest a BCF of PFOS of approximately 1000 (whole-body based) in benthic invertebrates, and a BMF of 10 to 20 in mink or bald eagles, relative to their prey items. Eggs of fish contained notable concentrations of PFOS, suggesting oviparous transfer of this compound. PFOA was found in water, but its biomagnification potential was lower than that of PFOS.

Animals↗
PubMed2005

DNA binding-uptake system: a link between cell-to-cell communication and biofilm formation.

DNA has recently been described as a major structural component of the extracellular matrix in biofilms. In streptococci, the competence-stimulating peptide (CSP) cell-to-cell signal is involved in competence for genetic transformation, biofilm formation, and autolysis. Among the genes regulated in response to the CSP are those involved in binding and uptake of extracellular DNA. We show in this study that a functional DNA binding-uptake system is involved in biofilm formation. A comGB mutant of Streptococcus mutans deficient in DNA binding and uptake, but unaffected in signaling, showed reduced biofilm formation. During growth in the presence of DNase I, biofilm was reduced in the wild type to levels similar to those found with the comGB mutant, suggesting that DNA plays an important role in the wild-type biofilm formation. We also showed that growth in the presence of synthetic CSP promoted significant release of DNA, with similar levels in the wild type and in the comGB mutant. The importance of the DNA binding-uptake system in biofilm formation points to possible novel targets to fight infections.

Bacterial Proteins↗
PubMed2005

Oral streptococci and cardiovascular disease: searching for the platelet aggregation-associated protein gene and mechanisms of Streptococcus sanguis-induced thrombosis.

BACKGROUND: Pathogenic mechanisms in infective endocarditis, disseminated intravascular coagulation, and cardiovascular events involve the aggregation of platelets into thrombi. Attendant infection by oral bacteria contributes to these diseases. We have been studying how certain oral streptococci induce platelet aggregation in vitro and in vivo. Streptococcus sanguis expresses a platelet aggregation-associated protein (PAAP), which contributes little to adhesion to platelets. When specific antibodies or peptides block PAAP, S. sanguis fails to induce platelet aggregation in vitro or in vivo. METHODS: We used subtractive hybridization to identify the gene encoding for PAAP. RESULTS: After subtraction of strain L50 (platelet aggregation-negative), four strain 133-79 specific sequences were characterized. Sequence agg4 encoded a putative collagen-binding protein (CbpA), which was predicted to contain two PAAP collagen-like octapeptide sequences. S. sanguis CbpA- mutants were constructed and tested for induction of platelet aggregation in vitro. Platelet aggregation was substantially inhibited when compared to the wild-type using platelet-rich plasma from the principal donor, but adhesion was unaffected. Other donor platelets responded normally to the CbpA- strain, suggesting additional mechanisms of response to S. sanguis. In contrast, CshA- and methionine sulfoxide reductase-negative (MsrA-) strains neither adhered nor induced platelet aggregation. CONCLUSIONS: CbpA was suggested to contribute to site 2 interactions in our two-site model of platelet aggregation in response to S. sanguis. Platelet polymorphisms were suggested to contribute to the thrombogenic potential of S. sanguis.

Amino Acid Sequence↗
PubMed2004

Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes.

BACKGROUND: Due to the high cost and low reproducibility of many microarray experiments, it is not surprising to find a limited number of patient samples in each study, and very few common identified marker genes among different studies involving patients with the same disease. Therefore, it is of great interest and challenge to merge data sets from multiple studies to increase the sample size, which may in turn increase the power of statistical inferences. In this study, we combined two lung cancer studies using microarray GeneChip, employed two gene shaving methods and a two-step survival test to identify genes with expression patterns that can distinguish diseased from normal samples, and to indicate patient survival, respectively. RESULTS: In addition to common data transformation and normalization procedures, we applied a distribution transformation method to integrate the two data sets. Gene shaving (GS) methods based on Random Forests (RF) and Fisher's Linear Discrimination (FLD) were then applied separately to the joint data set for cancer gene selection. The two methods discovered 13 and 10 marker genes (5 in common), respectively, with expression patterns differentiating diseased from normal samples. Among these marker genes, 8 and 7 were found to be cancer-related in other published reports. Furthermore, based on these marker genes, the classifiers we built from one data set predicted the other data set with more than 98% accuracy. Using the univariate Cox proportional hazard regression model, the expression patterns of 36 genes were found to be significantly correlated with patient survival (p < 0.05). Twenty-six of these 36 genes were reported as survival-related genes from the literature, including 7 known tumor-suppressor genes and 9 oncogenes. Additional principal component regression analysis further reduced the gene list from 36 to 16. CONCLUSION: This study provided a valuable method of integrating microarray data sets with different origins, and new methods of selecting a minimum number of marker genes to aid in cancer diagnosis. After careful data integration, the classification method developed from one data set can be applied to the other with high prediction accuracy.

Adenocarcinoma↗
PubMed2004

Identification and expression analysis of EST-based genes in the bud of Lycoris longituba.

To obtain a primary overview of gene diversity and expression pattern in Lycoris longituba, 4,992 ESTs (Expressed Sequence Tags) from L. longituba bud were sequenced and 4,687 cleaned ESTs were used for gene expression analysis. Clustered by the PHRAP program, 967 contigs and 1,343 singlets were obtained. Blast search showed that 179 contigs and 227 singlets (totally 1,066 ESTs) had homologues in GenBank and 3,621 ESTs were novel.

Base Composition↗
PubMed2004

Involvement of Streptococcus gordonii beta-glucoside metabolism systems in adhesion, biofilm formation, and in vivo gene expression.

Streptococcus gordonii genes involved in beta-glucoside metabolism are induced in vivo on infected heart valves during experimental endocarditis and in vitro during biofilm formation on saliva-coated hydroxyapatite (sHA). To determine the roles of beta-glucoside metabolism systems in biofilm formation, the loci of these induced genes were analyzed. To confirm the function of genes in each locus, strains were constructed with gene inactivation, deletion, and/or reporter gene fusions. Four novel systems responsible for beta-glucoside metabolism were identified, including three phosphoenolpyruvate-dependent phosphotransferase systems (PTS) and a binding protein-dependent sugar uptake system for metabolizing multiple sugars, including beta-glucosides. Utilization of arbutin and esculin, aryl-beta-glucosides, was defective in some mutants. Esculin and oligochitosaccharides induced genes in one of the three beta-glucoside metabolism PTS and in four other genetic loci. Mutation of genes in any of the four systems affected in vitro adhesion to sHA, biofilm formation on plastic surfaces, and/or growth rate in liquid medium. Therefore, genes associated with beta-glucoside metabolism may regulate S. gordonii in vitro adhesion, biofilm formation, growth, and in vivo colonization.

Bacterial Adhesion↗
PubMed2004

[Studies on the quality standard of "Lü Kang Yin Xing Ye Pian"].

OBJECTIVE: The quality control method of "Lü Kang Yin Xing Ye Pian" (LKYXYP) was studied and established. METHOD: The ginkgolides in LKYXYP were identified by TLC. The compounds of fatty acids in Perillae oil were determined by CC/MS. Flavones, ginkgolides and ginkgolic acids were determined by HPLC. RESULT: There were good linears relationship between the peak area and concentration, r = 0.999, RSD = 1.2% - 2.5% (n = 5), and recoveries of each composition was above 95%, the contation was stable in 24h. CONCLUSION: This method is proved to be accurate and able to be applied for the quality control of this preparation.

Bilobalides↗
PubMed2003

EST pipeline system: detailed and automated EST data processing and mining.

Expressed sequence tags (ESTs) are widely used in gene survey research these years. The EST Pipeline System, software developed by Hangzhou Genomics Institute (HGI), can automatically analyze different scalar EST sequences by suitable methods. All the analysis reports, including those of vector masking, sequence assembly, gene annotation, Gene Ontology classification, and some other analyses, can be browsed and searched as well as downloaded in the Excel format from the web interface, saving research efforts from routine data processing for biological rules embedded in the data.

Automation↗
PubMed2002

A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.

Arabidopsis↗
PubMed2002

RePS: a sequence assembler that masks exact repeats identified from the shotgun data.

We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4x to 6x, despite having up to 42.2% in exact repeats.

Cloning, Molecular↗