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Tao Liu

Publications and source records attributed to Tao Liu.

At least 37 records · Page 2Linked to original sources
PubMed2006

High resolution electron momentum spectroscopy of dichlorodifluoromethane: unambiguous assignments of outer valence molecular orbitals.

On account of controversial orbital assignment that appeared in previous works, [J. Chem. Phys. 120, 7933 (2004), and references therein] high resolution electron momentum spectroscopy (EMS) measurements on dichlorodifluoromethane has been carried out using a newly developed high resolution energy-momentum dispersive multichannel spectrometer employing asymmetric noncoplanar geometry at an impact energy of 2500 eV plus binding energy. Four resolved structures and two shoulders were obviously observed in high resolution binding energy spectrum in energy range covering eight outermost valence orbitals, whereas only two broad lobes were resolved in previous EMS studies [J. Chem. Phys. 120, 7933 (2004); Chin. Phys. 14, 2467 (2005)]. The ordering of these orbitals was reassigned unambiguously by simple comparison of experimental momentum distributions with theoretical ones.

Journal Article↗
PubMed2006

Effect of lead on the sorption of 2,4,6-trichlorophenol on soil and peat.

The effect of lead on the sorption of 2,4,6-trichlorophenol (2,4,6-TCP) on soil and peat was investigated using a batch equilibration method. Lead markedly diminished the sorption of 2,4,6-TCP, and 2,4,6-TCP had little effect on lead sorption. Peat was a more effective adsorbent for 2,4,6-TCP than soil. The desorption hysteresis of 2,4,6-TCP verified the presence of high-energy sorption sites. Mechanisms of lead suppression effect on the 2,4,6-TCP sorption included the following: Firstly, lead accelerated the aggregation of colloids, the aggregates covered the surface in part and shrunk the pore sizes of the adsorbents, hence decreased the sorption of 2,4,6-TCP. Secondly, X-ray absorption and Fourier transform infrared spectroscopy study suggested that lead competed with 2,4,6-TCP for carboxylic, phenolic and Si-OH groups of organic matter and clay minerals. Such competition was partly responsible for the overall suppression effect of lead on the sorption of 2,4,6-TCP.

Adsorption↗
PubMed2006

Highly sensitive gold nanoparticles biosensor chips modified with a self-assembled bilayer for detection of Con A.

In this paper, an improved method for detection of Concanavalin A (Con A) with label-free optical biosensors is reported. 1-Dodecanethiol (DDT) was self-assembled onto gold nanoparticles which were deposited on glass slides, and then glycolipid molecules were inserted into dodecanethiol by physical interactions only. The recognition between Con A and carbohydrate was observed by UV-vis spectrophotometry. The absorption spectrum shifted when Con A was bound to the sugar residues of glycolipids immobilized onto nanogold slides, while almost no spectrum change was observed when another nonspecific protein molecule met the nanogold slides. The self-assembled bilayer on nanogold substrates had very high sensitivity for Con A, the minimum detection concentration of Con A can be down to 0.1 nM. In addition to the ultra sensitivity for investigating carbohydrate-lectin interaction, the self-assembled bilayer structure, is expected to replace many receptors which require time-consuming organic syntheses for the fixation to the transducer. The simplicity and sensitivity of this biosensor architecture once again show the prospect of nanogold application in biosensor.

Biosensing Techniques↗
PubMed2006

Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags.

BACKGROUND: Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a recognized pathogen for humans, little is known about how its transcriptional pattern is related to development of the fungus and establishment of disease. It is therefore necessary to identify genes whose expression is relevant to growth, metabolism and virulence of T. rubrum. RESULTS: We generated 10 cDNA libraries covering nearly the entire growth phase and used them to isolate 11,085 unique expressed sequence tags (ESTs), including 3,816 contigs and 7,269 singletons. Comparisons with the GenBank non-redundant (NR) protein database revealed putative functions or matched homologs from other organisms for 7,764 (70%) of the ESTs. The remaining 3,321 (30%) of ESTs were only weakly similar or not similar to known sequences, suggesting that these ESTs represent novel genes. CONCLUSION: The present data provide a comprehensive view of fungal physiological processes including metabolism, sexual and asexual growth cycles, signal transduction and pathogenic mechanisms.

Arthrodermataceae↗
PubMed2006

Genetic variation of Chinese PRRSV strains based on ORF5 sequence.

Thirteen isolates of porcine reproductive and respiratory syndrome virus (PRRSV) from different provinces of China were studied and compared with several PRRSV isolates from other countries. Phylogenetic analysis shows that all Chinese isolates of PRRSV in this study belong to the American genotype, except for one strain, B13, which clustered as a European genotype. Sequence analysis revealed that PRRSV Chinese isolates of the American genotype were highly similar in the ORF5 sequence and could be classified into two subclades. One contains PRRSV isolates that are more closely related to the American vaccine strain MLV Resp and its parent strain VR-2332, and the other contains ones only distantly related to them. Within the Chinese isolates slight genetic variation occurred, and some strains may originate directly from the vaccine virus.

Amino Acid Sequence↗
PubMed2006

Effect of example weights on prediction of protein-protein interactions.

Protein-protein interactions (PPIs) prediction is an important issue in biology. Recently many computational methods have been proposed to determine PPIs. However, there is no golden standard dataset for these methods now. Furthermore, there exists different quality among training examples and the quality is always ignored by the current methods. In the condition of low-quality examples, the system should tolerate the data noise. Example weighting strategy is used in this paper to build a robust system and solve the problem of data noise. Training examples are investigated and a new example selecting/using strategy is proposed. Training example weighting method based on confidence is proposed. Different weight setting strategies are discussed and the corresponding results are given in the experiment. A new model integrating example weighting strategy, attraction-repulsion (AR) weight model, is proposed. Experimental results on Saccharomyces cerevisiae demonstrate that the new model outperforms the original AR model in the ROC score measure by over 8%. Furthermore, the example weighting strategy is applied to another domain-based PPIs prediction method, maximum likelihood estimation (MLE) method, and the modified MLE method obtains better performance than the original MLE method. At same time, our examples weighting strategy can be applied to any other training example based PPIs prediction methods.

Algorithms↗
PubMed2006

Rhinosinusitis derived Staphylococcal enterotoxin B plays a possible role in pathogenesis of food allergy.

BACKGROUND: Staphylococcal enterotoxin B (SEB) is a potent immunomodulator and implicated with pathogenesis of inflammatory diseases mediated by Th1 or Th2 dominant immune responses. The objective of this study is to determine a possible association between rhinosinusitis derived SEB and pathogenesis of food allergy (FA). METHODS: The study included chronic rhinosinusitis (CRS) patients with FA (N = 46) or without FA (N = 33). Controls included FA patients without CRS (N = 26) and healthy volunteers (N = 25). In CRS patients, we assessed the parameters associated with FA including prick skin test (PST) reactivity to food allergens, serum levels of allergen-specific IgE and cytokines (IL-4, IL-13, IFN-I3), and the number/reactivity of food-allergen specific Th1/Th2 cells in the peripheral blood before and 2 months after sinus surgery. Changes of these parameters were evaluated in comparison with changes in SEB concentration in the sinus lavage and stool samples and also in vitro reactivity to SEB. In CRS patients with FA, we also assessed changes in reactivity to oral challenge of offending food before and after sinus surgery. RESULTS: Two months following sinus surgery, we observed statistically significant reduction in PST and oral challenge reactivity in CRS patients with FA in parallel to decrease in serum levels of Th2 cytokines (IL-4 and IL-13) and allergen specific IgE. Improvement of reactivity to food allergens was positively associated with decline in SEB concentrations in the sinus lavage and stool samples. In vitro study results also indicated a role of SEB in aggravation of Th2 skewed responses to food allergens. Such changes were not observed in CRS-non FA patients or control FA patients. CONCLUSION: The rhinosinusitis derived SEB plays a certain role in the pathogenesis of FA by augmenting and/or maintaining polarized Th2 responses. Removal of SEB-producing pathogens from the rhinosinuses may be beneficial for attenuating the FA symptoms in patients with CRS-FA.

Adult↗
PubMed2006

Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications.

Recent advances in proteomics technologies provide tremendous opportunities for biomarker-related clinical applications; however, the distinctive characteristics of human biofluids such as the high dynamic range in protein abundances and extreme complexity of the proteomes present tremendous challenges. In this review we summarize recent advances in LC-MS-based proteomics profiling and its applications in clinical proteomics as well as discuss the major challenges associated with implementing these technologies for more effective candidate biomarker discovery. Developments in immunoaffinity depletion and various fractionation approaches in combination with substantial improvements in LC-MS platforms have enabled the plasma proteome to be profiled with considerably greater dynamic range of coverage, allowing many proteins at low ng/ml levels to be confidently identified. Despite these significant advances and efforts, major challenges associated with the dynamic range of measurements and extent of proteome coverage, confidence of peptide/protein identifications, quantitation accuracy, analysis throughput, and the robustness of present instrumentation must be addressed before a proteomics profiling platform suitable for efficient clinical applications can be routinely implemented.

Biomarkers↗
PubMed2006

Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry.

Strategies for removal of high abundance proteins have been increasingly utilized in proteomic studies of serum/plasma and other body fluids to enhance the detection of low abundance proteins and achieve broader proteome coverage; however, both the reproducibility and specificity of the high abundance protein depletion process still represent common concerns. Here we report a detailed evaluation of immunoaffinity subtraction performed applying the ProteomeLab IgY-12 system that is commonly used in human serum/plasma proteome characterization in combination with high resolution LC-MS/MS. Plasma samples were repeatedly processed using this approach, and the resulting flow-through fractions and bound fractions were individually analyzed for comparison. The removal of target proteins by the immunoaffinity subtraction system and the overall process was highly reproducible. Non-target proteins, including one spiked protein standard (rabbit glyceraldehyde-3-phosphate dehydrogenase), were also observed to bind to the column at different levels but also in a reproducible manner. The results suggest that multiprotein immunoaffinity subtraction systems can be readily integrated into quantitative strategies to enhance detection of low abundance proteins in biomarker discovery studies.

Biomarkers↗
PubMed2006

Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.

Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small non-coding transcriptome of Caenorhabditis elegans, microRNAs excepted. As a substantial fraction of the ncRNAs is located in introns of protein-coding genes in C.elegans, we also analysed the relationship between ncRNA and host gene expression. To this end, we designed a combined microarray, which included probes against ncRNA as well as host gene mRNA transcripts. The microarray revealed pronounced differences in expression profiles, even among ncRNAs with housekeeping functions (e.g. snRNAs and snoRNAs), indicating distinct developmental regulation and stage-specific functions of a number of novel transcripts. Analysis of ncRNA-host mRNA relations showed that the expression of intronic ncRNA loci with conserved upstream motifs was not correlated to (and much higher than) expression levels of their host genes. Even promoter-less intronic ncRNA loci, though showing a clear correlation to host gene expression, appeared to have a surprising amount of 'expressional freedom', depending on host gene function. Taken together, our microarray analysis presents a more complete and detailed picture of a non-coding transcriptome than hitherto has been presented for any other multicellular organism.

Animals↗
PubMed2006

Role of the olivo-cerebellar system in timing.

Timing has been proposed as a basic function of the cerebellar cortex (particularly the climbing fiber afferents and their sole source, the inferior olive) that explains the contribution of the cerebellum to both motor control and nonmotor cognitive functions. However, whether the olivo-cerebellar system mediates time perception without motor behavior remains controversial. We used event-related functional magnetic resonance imaging to dissociate the neural correlates of the perceptual from the motor aspects of timing. The results show activation of multiple areas within the cerebellar cortex during both perception and motor performance of temporal sequences. The results further show that the inferior olive was activated only when subjects perceived the temporal sequences without motor activity. This finding is most consistent with electrophysiological studies showing decreased responsiveness of the inferior olivary neurons to sensory input during expected, self-produced movement. Our results suggest that the primary role of the inferior olive and the climbing fiber system in timing is the encoding of temporal information independent of motor behavior.

Adult↗
PubMed2006

High dynamic range characterization of the trauma patient plasma proteome.

Although human plasma represents an attractive sample for disease biomarker discovery, the extreme complexity and large dynamic range in protein concentrations present significant challenges for characterization, candidate biomarker discovery, and validation. Herein we describe a strategy that combines immunoaffinity subtraction and subsequent chemical fractionation based on cysteinyl peptide and N-glycopeptide captures with two-dimensional LC-MS/MS to increase the dynamic range of analysis for plasma. Application of this "divide-and-conquer" strategy to trauma patient plasma significantly improved the overall dynamic range of detection and resulted in confident identification of 22,267 unique peptides from four different peptide populations (cysteinyl peptides, non-cysteinyl peptides, N-glycopeptides, and non-glycopeptides) that covered 3,654 different proteins with 1,494 proteins identified by multiple peptides. Numerous low abundance proteins were identified, exemplified by 78 "classic" cytokines and cytokine receptors and by 136 human cell differentiation molecules. Additionally a total of 2,910 different N-glycopeptides that correspond to 662 N-glycoproteins and 1,553 N-glycosylation sites were identified. A panel of the proteins identified in this study is known to be involved in inflammation and immune responses. This study established an extensive reference protein database for trauma patients that provides a foundation for future high throughput quantitative plasma proteomic studies designed to elucidate the mechanisms that underlie systemic inflammatory responses.

Blood Proteins↗
PubMed2006

A possible link between sinusitis and lower airway hypersensitivity: the role of Staphylococcal enterotoxin B.

BACKGROUND AND AIMS: The prevalence of asthma has been keeping arising with unknown etiology. The cumulative evidence indicates that chronic rhinosinusitis (CRS) closely relates to asthma, but the detailed mechanisms remain unclear. The present study aimed to take insight into the role of Staphylococcus enterotoxin B (SEB) in a possible association between CRS and asthma. METHODS: 38 patients with both CRS and asthma underwent functional endoscopic sinus surgery. Serum specific IgE and cytokines, clinical symptoms of CRS and asthma were evaluated before and after the surgery. Peripheral blood mononuclear cells (PBMCs) were separated from the patients and cultured. Th2 response of the cultured PBMCs in the presence or absence of specific antigens and SEB was evaluated. RESULTS: Besides the improvement of CRS symptoms, amelioration of asthma was also observed in the patients with both CRS and asthma after the sinus surgery. The preoperatively elevated Th2 cytokines, IL-4 and IL-5, normalized postoperatively. Th2 response was generated with separated PBMCs in the presence of specific antigens. SEB was required for maintaining Th2 response in these separated PBMCs. CONCLUSION: The present results indicate that a possible link exists between CRS and lower airway hypersensitivity. Sinusitis derived SEB may play a role in sustaining Th2 responses in the low airway hypersensitivity related to sinusitis.

Journal Article↗
PubMed2006

Identification of up-regulated genes after complete spinal cord transection in adult rats.

Spinal cord injury (SCI) initiates a cascade of events and these responses to injury are likely to be mediated and reflected by changes in mRNA concentrations. As a step towards understanding the complex mechanisms underlying repair and regeneration after SCI, the gene expression pattern was examined 4.5 days after complete transection at T8-9 level of rat spinal cord. Improved subtractive hybridization was used to establish a subtracted cDNA library using cDNAs from normal rat spinal cord as driver and cDNAs from injured spinal cord as tester. By expressed sequence tag (EST) sequencing, we obtained 73 EST fragments from this library, representing 40 differentially expressed genes. Among them, 32 were known genes and 8 were novel genes. Functions of all annotated genes were scattered in almost every important field of cell life such as DNA repair, detoxification, mRNA quality control, cell cycle control, and signaling, which reflected the complexity of SCI and regeneration. Then we verified subtraction results with semiquantitative RT-PCR for eight genes. These analyses confirmed, to a large extent, that the subtraction results accurately reflected the molecular changes occurring at 4.5 days post-SCI. The current study identified a number of genes that may shed new light on SCI-related inflammation, neuroprotection, neurite-outgrowth, synaptogenesis, and astrogliosis. In conclusion, the identification of molecular changes using improved subtractive hybridization may lead to a better understanding of molecular mechanisms responsible for repair and regeneration after SCI.

Animals↗
PubMed2006

Mechanisms of competitive adsorption of Pb, Cu, and Cd on peat.

Combined use of batch equilibration adsorption and X-ray absorption spectroscopy (XAS) was employed to study the mechanisms of competitive adsorption of Pb, Cu, and Cd on Danish and Heilongjiang peat in single- and multi-solute systems. The adsorption capacity and initial adsorption rate on the same peat in single-solute systems followed the order Pb>Cu>Cd. Both the adsorbed amount of each metal (q'm) and its initial adsorption rate were decreased in multi-solute systems. It was observed that the adsorbed amounts of metals at low-energy adsorption sites (qm,1) decreased pronouncedly compared to those at high-energy adsorption sites (qm,2), indicating that the competitive adsorption of Pb, Cu and Cd occurred mainly at the low-energy adsorption sites. XAS study revealed that both Pb and Cu were coordinated in peat predominantly to carboxylic moieties without excluding the hydroxyl groups, thereby providing an insight into the mechanism of competitive adsorption of Pb and Cu on peat.

Adsorption↗
PubMed2006

Effect of Chinese medicine Qinggan Huoxuefang on inducing HSC apoptosis in alcoholic liver fibrosis rats.

AIM: To investigate the effect of Qinggan Huoxuefang (QGHXF) on improvement of liver function and pathology in rats, and to analyze the mechanism. METHODS: Wistar rats were divided into three groups at random: normal control group (12),micro-amount carbon tetrachloride group (CCl(4))(12) and model group A (60). The model group A was ingested with the mixture (500 mL/L alcohol, 8 mL/kg per day; corn oil, 2 mL/kg per day; pyrazole, 24 mg/kg per day) once a day and intraperitoneal injections of 0.25 mL/kg of a 250 mL/L solution of CCl(4) in olive oil twice a week for 12 wk. The CCl(4) group received intraperitoneal injections only. At the end of 8 wk the model group A (60) was divided into 5 subgroups: model group, Xiaochaihu Chongji (XCH) group, QGHXF high dose group, moderate dose group and low dose group, and were given the drugs respectively. At the end of 12 wk, all the rats were killed and blood samples collected, as well as liver tissue. Blood samples were used for evaluation of alanine transaminase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), gamma-glutamyltransferase (gamma-GT). Liver specimens were obtained for routine HE, apoptosis gene array and flow cytometry analysis. RESULTS: A liver fibrosis animal model was successfully established. Fibrosis was obviously reduced in QGHXF high dose group, and no fibrosis formed in CCl(4) group. Compared with model group the QGHXF group and XCH group could obviously decrease the level of ALT, AST, ALP, and GGT (P<0.05). QGHXF high dose group was better than XCH group in ALT (615+/-190 vs 867+/-115), and AST(1,972+/-366 vs 2,777+/-608). Moreover, QGHXF could reduce liver inflammation, fibrosis-induced hepatic stellate cell (HSC) apoptosis and regulate apoptosis gene expression. The HSC apoptosis rates of QGHXF groups were 22.4+/-3.13, 13.79+/-2.26 and 10.07+/-1.14, higher than model group, 6.58+/-1.04 (P<0.05). Compared to model group, 39 genes were up-regulated, 11 solely expressed and 17 down-regulated in high dose group. CONCLUSION: QGHXF can improve liver fibrosis and induce HSC apoptosis.

Animals↗
PubMed2006

Mass spectrometric analysis of enzymatic digestion of denatured collagen for identification of collagen type.

Collagen type II and I from bovine were thermally denatured and digested with trypsin. The digest mixture was analyzed with liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS). Peptides in the digest mixture were identified by mass spectrometry/mass spectrometry (MS/MS) sequencing. The results indicated that the digest mixtures of collagen type II and I contained lots of specific peptides and common peptides. Specific peptides could be used as index for identifying collagen type. Articular cartilage from bovine was pretreated and analyzed with the same method to determine the collagen types. The result indicated that the method developed was effective for identification of collagen types. The research provided a possible approach for collagen identification in particular tissues.

Animals↗