Biomedical subjects

S Xu

Publications and source records attributed to S Xu.

At least 163 records · Page 9Linked to original sources

PubMed2000

Polychlorinated organic compounds in Yangtse River sediments.

Polychlorinated organic compounds (PCOCs) were analyzed in Yangtse River sediments. The results show that the concentrations of PCOCs in Yangtse River sediments followed the order of DDTs > HCB > HCHs > PCBs. High PCOCs concentrations were detected in sediments from station Y02a and Y02b, which are located in the main input of the Yangtse River (Nanjing section). Results also show that the PCOCs values were highly correlated with organic carbon content and heavy metal contamination.

China↗

PubMed2000

Historical record and sources of polycyclic aromatic hydrocarbons in core sediments from the Yangtze Estuary, China.

Polycyclic aromatic hydrocarbons (PAHs) in a sediment core taken from intertidal flat in the Yangtze Estuary were determined by gas chromatography-mass spectrometry. The results indicate that the total concentration of PAHs ranged from 0.08 to 11.74 microg/g. The concentration levels of total and individual PAHs changed dramatically with depth. The concentrations of PAHs were relatively high above 35 cm depth and remained constantly low below this depth. The historical record of PAHs in the core shows subsurface maximum (one or more peak values), followed by decreased levels to the surface and with depth. And, PAH sediment record in the core profile is in agreement with historically sewage discharge events during the 1980s to 1990s. The distribution of target molecule acenephthene, the fluoranthene/pyrene ratio, the proportion of 2-3-ring and 4-5-ring PAHs, and alkylated naphthalene to parent naphthalene in the core profile show that the sources in this area are characterized by petroleum-derived PAH contamination (mainly sewage discharge and the river runoff) and the incorporation of atmospheric inputs. Studies indicate the PAH profile pattern in this site in comparison with other regions appear to reflect its particular local position (near the sewage outlet). Moreover, physico-chemical conditions and sedimentation rate as well as biodegradation also affect the PAH concentration levels in the core sediments.

Journal Article↗

PubMed2000

Effects of allyl mercaptan and various allium-derived compounds on cholesterol synthesis and secretion in Hep-G2 cells.

The present study was undertaken to compare the effects of allyl mercaptan (AM), a major metabolite of garlic, with several garlic constituents and extracts on cytotoxicity, cholesterol synthesis and its secretion in Hep-G2 cells. The cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), and treated with 5, 25, 50, 125, 250 and 500 microg/ml of AM, diallyl disulfide (DD), diallyl trisulfide (DT), steam-distilled garlic oil (SD) or vinyl-dithiin oil of garlic (VD) for 4 h. At concentrations up to 50 microg/ml, no significant cytotoxic effect was found in any group, but at concentrations above 250 microg/ml, the cell viability decreased drastically in all groups compared to the control. The treatment of cells with 25 microg/ml (non-cytotoxic concentration) of AM, DD, DT, SD for 4 h significantly inhibited [3H]acetate incorporation into cholesterol compared to that of the control (P < 0.05). The secretion of cholesterol into the medium was also significantly decreased in all groups except for VD. The treatment of cells with those allium constituents had no effect on either [3H]acetate incorporation into fatty acids or [3H]glycerol incorporation into triglyceride or phospholipid.

Allium↗

PubMed2000

Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference.

In RNA-mediated interference (RNAi), externally provided mixtures of sense and antisense RNA trigger concerted degradation of homologous cellular RNAs. We show that RNAi requires duplex formation between the two trigger strands, that the duplex must include a region of identity between trigger and target RNAs, and that duplexes as short as 26 bp can trigger RNAi. Consistent with in vitro observations, a fraction of input dsRNA is converted in vivo to short segments of approximately 25 nt. Interference assays with modified dsRNAs indicate precise chemical requirements for both bases and backbone of the RNA trigger. Strikingly, certain modifications are well tolerated on the sense, but not the antisense, strand, indicating that the two trigger strands have distinct roles in the interference process.

Animals↗

PubMed2000

Mapping quantitative trait loci in tetraploid populations.

Knowledge of quantitative trait locus (QTL) mapping in polyploids is almost void, albeit many exquisite strategies of QTL mapping have been proposed and extensive investigations have been carried out in diploid animals and plants. In this paper we develop a simple algorithm which uses an iteratively reweighted least square method to map QTLs in tetraploid populations. The method uses information from all markers in a linkage group to infer the probability distribution of QTL genotype under the assumption of random chromosome segregation. Unlike QTL mapping in diploid species, here we estimate and test the compound 'gametic effect', which consists of the composite 'genic effect' of alleles and higher-order gene interactions. The validity and efficiency of the proposed method are investigated through simulation studies. Results show that the method can successfully locate QTLs and separates different sources (e.g. additive and dominance) of variance components contributed by the QTLs.

Algorithms↗

PubMed2000

Nanofabrication of self-assembled monolayers using scanning probe lithography.

This Account focuses on our recent and systematic effort in the development of generic scanning probe lithography (SPL)-based methodologies to produce nanopatterns of self-assembled monolayers (SAMs). The key to achieving high spatial precision is to keep the tip-surface interactions strong and local. The approaches used include two AFM-based methods, nanoshaving and nanografting, which rely on the local force, and two STM-based techniques, electron-induced diffusion and desorption, which use tunneling electrons for fabrication. In this Account we discuss the principle of these procedures and the critical steps in controlling local tip-surface interactions. The advantages of SPL will be illustrated through various examples of production and modification of SAM nanopatterns and their potential applications.

Chemistry↗

PubMed2000

Granulocyte colony-stimulating factor (G-CSF) induces the production of cytokines in vivo.

Granulocyte colony-stimulating factor (G-CSF) is a haematopoietic growth factor required for the proliferation and differentiation of haematopoietic precursors of neutrophil granulocytes and is now used to overcome congenital and acquired neutropenia. In addition to increasing the numbers of neutrophils in vivo and modulating neutrophil functions, G-CSF may induce the production of cytokines such as tumour necrosis factor alpha (TNF-alpha). In the present study, the plasma levels of granulocyte-macrophage colony-stimulating factor (GM-CSF) in six healthy volunteers given G-CSF at 10 microgram/kg once daily for 6 d were measured and found to be elevated. The elevated levels (P < 0.05) were detected on day 2, peaked on days 6-7 and returned to baseline on day 12. In vitro, G-CSF did not enhance the secretion of TNF-alpha and GM-CSF from mononuclear cells, whole blood or endothelial cells. However, in the co-presence of whole blood and endothelial cells, the secretion of TNF-alpha was significantly enhanced by G-CSF at low concentrations. The GM-CSF secretion, however, was unaltered. G-CSF pretreatment of whole blood suppressed lipopolysaccharide (LPS)-induced secretion of TNF-alpha and GM-CSF in a dose-dependent manner. These results together with our previous findings suggest that G-CSF induces the production of TNF-alpha and GM-CSF in vivo, and that this production may be due to the co-effects of endothelial cells and whole blood under the influence of G-CSF through an as yet unknown network of cells and cytokines. Treatment of whole blood with G-CSF suppresses LPS-induced secretion of TNF-alpha and GM-CSF.

Adult↗

PubMed2000

Maximum likelihood analysis of quantitative trait loci under selective genotyping.

Selective genotyping is a cost-saving strategy in mapping quantitative trait loci (QTLs). When the proportion of individuals selected for genotyping is low, the majority of the individuals are not genotyped, but their phenotypic values, if available, are still included in the data analysis to correct the bias in parameter estimation. These ungenotyped individuals do not contribute much information about linkage analysis and their inclusion can substantially increase the computational burden. For multiple trait analysis, ungenotyped individuals may not have a full array of phenotypic measurements. In this case, unbiased estimation of QTL effects using current methods seems to be impossible. In this study, we develop a maximum likelihood method of QTL mapping under selective genotyping using only the phenotypic values of genotyped individuals. Compared with the full data analysis (using all phenotypic values), the proposed method performs well. We derive an expectation-maximization (EM) algorithm that appears to be a simple modification of the existing EM algorithm for standard interval mapping. The new method can be readily incorporated into a standard QTL mapping software, e.g. MAPMAKER. A general recommendation is that whenever full data analysis is possible, the full maximum likelihood analysis should be performed. If it is impossible to analyse the full data, e.g. sample sizes are too large, phenotypic values of ungenotyped individuals are missing or composite interval mapping is to be performed, the proposed method can be applied.

Algorithms↗

PubMed2000

Bayesian mapping of quantitative trait loci for complex binary traits.

A complex binary trait is a character that has a dichotomous expression but with a polygenic genetic background. Mapping quantitative trait loci (QTL) for such traits is difficult because of the discrete nature and the reduced variation in the phenotypic distribution. Bayesian statistics are proved to be a powerful tool for solving complicated genetic problems, such as multiple QTL with nonadditive effects, and have been successfully applied to QTL mapping for continuous traits. In this study, we show that Bayesian statistics are particularly useful for mapping QTL for complex binary traits. We model the binary trait under the classical threshold model of quantitative genetics. The Bayesian mapping statistics are developed on the basis of the idea of data augmentation. This treatment allows an easy way to generate the value of a hypothetical underlying variable (called the liability) and a threshold, which in turn allow the use of existing Bayesian statistics. The reversible jump Markov chain Monte Carlo algorithm is used to simulate the posterior samples of all unknowns, including the number of QTL, the locations and effects of identified QTL, genotypes of each individual at both the QTL and markers, and eventually the liability of each individual. The Bayesian mapping ends with an estimation of the joint posterior distribution of the number of QTL and the locations and effects of the identified QTL. Utilities of the method are demonstrated using a simulated outbred full-sib family. A computer program written in FORTRAN language is freely available on request.

Algorithms↗

PubMed2000

Multipoint mapping of viability and segregation distorting loci using molecular markers.

In line-crossing experiments, deviations from Mendelian segregation ratios are usually observed for some markers. We hypothesize that these deviations are caused by one or more segregation-distorting loci (SDL) linked to the markers. We develop both a maximum-likelihood (ML) method and a Bayesian method to map SDL using molecular markers. The ML mapping is implemented via an EM algorithm and the Bayesian method is performed via the Markov chain Monte Carlo (MCMC). The Bayesian mapping is computationally more intensive than the ML mapping but can handle more complicated models such as multiple SDL and variable number of SDL. Both methods are applied to a set of simulated data and real data from a cross of two Scots pine trees.

Alleles↗

PubMed2000

Bayesian mapping of quantitative trait loci under the identity-by-descent-based variance component model.

Variance component analysis of quantitative trait loci (QTL) is an important strategy of genetic mapping for complex traits in humans. The method is robust because it can handle an arbitrary number of alleles with arbitrary modes of gene actions. The variance component method is usually implemented using the proportion of alleles with identity-by-descent (IBD) shared by relatives. As a result, information about marker linkage phases in the parents is not required. The method has been studied extensively under either the maximum-likelihood framework or the sib-pair regression paradigm. However, virtually all investigations are limited to normally distributed traits under a single QTL model. In this study, we develop a Bayes method to map multiple QTL. We also extend the Bayesian mapping procedure to identify QTL responsible for the variation of complex binary diseases in humans under a threshold model. The method can also treat the number of QTL as a parameter and infer its posterior distribution. We use the reversible jump Markov chain Monte Carlo method to infer the posterior distributions of parameters of interest. The Bayesian mapping procedure ends with an estimation of the joint posterior distribution of the number of QTL and the locations and variances of the identified QTL. Utilities of the method are demonstrated using a simulated population consisting of multiple full-sib families.

Alleles↗

PubMed2000

Meiosis and the evolution of recombination at low mutation rates.

The classical understanding of recombination is that in large asexual populations with multiplicative fitness, linkage disequilibrium is negligible, and thus there is no selective agent driving an allele for recombination. This has led researchers to recognize the importance of synergistic epistatic selection in generating negative linkage disequilibrium that thereby renders an advantage to recombination. Yet data on such selection is equivocal, and various works have shown that synergistic epistasis per se, when left unquantified in its magnitude or operation, is not sufficient to drive the evolution of recombination. Here we show that neither it, nor any mechanism generating negative linkage disequilibrium among fitness-related loci, is necessary. We demonstrate that a neutral gene for recombination can increase in frequency in a large population under a low mutation rate and strict multiplicative fitness. We work in a parameter range where individuals have, on average, less than one mutation each, yet recombination can still evolve. We demonstrate this in two ways: first, by examining the consequences of recombination correlated with misrepaired DNA damage and, second, by increasing the probability of recombination with declining fitness. Interestingly, the allele spreads without repairing even a single DNA mutation.

Alleles↗

PubMed2000

B cell development and activation defects resulting in xid-like immunodeficiency in BLNK/SLP-65-deficient mice.

Engagement of the B cell receptor (BCR) leads to the activation of tyrosine kinases and other signaling molecules that ultimately determine the type and magnitude of the B lymphocyte's cellular response. The adaptor protein BLNK/SLP-65 plays a pivotal role in BCR signal transduction by coupling Syk activation to downstream elements such as Grb2, phospholipase C-gamma, Vav and Nck. We have generated BLNK(-/-) mice to determine the physiological role of this protein in B cell development and activation. BLNK(-/-) mice exhibit an incomplete block in B cell development with a severe inhibition of pro-B to pre-B cell differentiation. BLNK(-/-) sIgM(+) cells can develop, seed the peripheral lymphoid tissues and accumulate in numbers overtime. However, these mutant B cells failed to mature and are non-responsive to BCR cross-linking in terms of proliferation and up-regulation of activation markers such as CD69 and CD86 (B7-2). In addition, the CD5(+) subset of B cells is absent. The immune response to T cell-independent antigen but not T cell-dependent antigen is also impaired. Overall, the phenotype of BLNK(-/-) mice bears a striking resemblance to that of xid mice which is the murine model of human XLA that has a mutation in Bruton's tyrosine kinase. This raises the interesting possibility that mutation in BLNK/SLP-65 may be responsible for certain human immunodeficiencies.

Adaptor Proteins, Signal Transducing↗

PubMed2000

Phylogenetic analysis under reticulate evolution.

The usual assumption that species have evolved from a common ancestor by a simple branching process--where each branch is genetically isolated--has been challenged by the observation of frequent hybridization between species in natural populations. In fact, most plant species are thought to have hybrid origins. This reticulate pattern of species evolution has posed problems in the definition of speciation and in phylogenetic reconstruction, especially when molecular data are used. As a result, hybridization has been largely treated as an evolutionary accident or statistical error in phylogenetic analysis. In this paper, I explicitly incorporate hybridization as an evolutionary occurrence and then conduct phylogenetic reconstruction. I first examine the reticulate evolution under a pure drift model, and then extend the theory to fit a mutation model. A least-squares method is developed for reconstructing a reticulate phylogeny using gene frequency data. The efficacy of the method under the pure drift model is verified via Monte Carlo simulations.

Evolution, Molecular↗

PubMed2000

Low-dose whole-body irradiation (LD-WBI) changes protein expression of mouse thymocytes: effect of a LD-WBI-enhanced protein RIP10 on cell proliferation and spontaneous or radiation-induced thymocyte apoptosis.

Low-dose radiation (LDR) can potentiate cellular metabolic activities or immune functions in vivo (hormesis), and can render cells resistant to DNA or chromosome damage caused by subsequent high-dose radiation (adaptive response). Protein synthesis was required for these cellular responses to LDR. In the present study, the early expression of proteins by thymocytes in response to low-dose whole-body irradiation (LD-WBI) was investigated. The expression of novel and previously existing proteins was found in the nucleus, cytoplasm, and extracellular fluid of thymocytes at 4 hours after WBI with 75-mGy X-rays. A 10 kD protein (RIP10) was seen in the cytoplasm of thymocytes after LD-WBI was further investigated. The fraction containing RIP10 separated by Sephadex G 100 gel filtration potentiated spontaneous thymocyte, and mitogen-induced splenocyte proliferation. Western blotting demonstrated that an anti-RIP10 antibody could react with a 10-kD cytoplasm protein and also with a 13-kD nuclear protein in thymocytes at 4 h after LD-WBI. Immunocytochemical staining showed the existence of RIP10 in several immune tissues including thymus, spleen, and lymph node. RIP10 expression, as determined by immunocytochemical staining and flow cytometry, was enhanced at 4-8 h after LD-WBI. Cell-cycle arrest (G(0)/G(1) block with decreased percentage of S-phase cells), and increased levels of spontaneous or radiation-induced apoptosis were observed in thymocytes incubated with RIP10 antibody in vitro for 4 h or 24 h. These results directly demonstrated the role of RIP10 in modulating cell proliferation and apoptosis. This finding is important to understand the mechanisms underlying LDR-induced hormesis and adaptive response.

Adaptation, Physiological↗

PubMed2000

Isolation and characterization of a Helicobacter sp. from the gastric mucosa of dolphins, Lagenorhynchus acutus and Delphinus delphis.

Gastric ulcerations in dolphins have been reported for decades. Some of these lesions were associated with parasitic infections. However, cases of nonparasitic gastric ulcers with no clearly defined etiology also have been reported in wild and captive dolphins. Considerable speculation exists as to whether dolphins have Helicobacter-associated gastritis and peptic ulcer disease. The stomachs of seven stranded Atlantic white-sided dolphins, Lagenorhynchus acutus, and 1 common dolphin, Delphinus delphis, were assessed for the presence of Helicobacter species. Novel Helicobacter species were identified by culture in the gastric mucosa of two of the eight dolphins studied and by PCR in seven of the eight dolphins. The gram-negative organisms were urease, catalase, and oxidase positive. Spiral to fusiform bacteria were detected in gastric mucosa by Warthin Starry staining. Histopathology revealed mild to moderate diffuse lymphoplasmacytic gastritis within the superficial mucosa of the main stomach. The pyloric stomach was less inflamed, and bacteria did not extend deep into the glands. The lesions parallel those observed in Helicobacter pylori-infected humans. Bacteria from two dolphins classified by 16S rRNA analysis clustered with gastric helicobacters and represent a novel Helicobacter sp. most closely related to H. pylori. These findings suggest that a novel Helicobacter sp. may play a role in the etiopathogenesis of gastritis and gastric ulcers in dolphins. To our knowledge this represents the first isolation and characterization of a novel Helicobacter sp. from a marine mammal and emphasizes the wide host distribution and pathogenic potential of this increasingly important genus.

Animals↗

PubMed2000

Helicobacter aurati sp. nov., a urease-positive Helicobacter species cultured from gastrointestinal tissues of Syrian hamsters.

A novel helicobacter with the proposed name Helicobacter aurati (type strain MIT 97-5075c) has been isolated from the inflamed stomachs and ceca of adult Syrian hamsters. The new species is fusiform with multiple bipolar sheathed flagella and periplasmic fibers; it contains urease and gamma-glutamyl transpeptidase. By 16S rRNA sequencing and repetitive element PCR-based DNA fingerprinting, it was found that H. aurati represents a distinct taxon and clusters with Helicobacter muridarum, Helicobacter hepaticus, and Helicobacter sp. MIT 94-022. H. aurati was recovered from hamsters housed in various research and vendor facilities. Further studies are necessary to define its association with disease and other microbiota in hamsters, as well as its impact on research projects involving hamsters. H. aurati (GenBank accession number AF297868) can be used in animal experiments to define the factors that are important for gastric helicobacter pathogenesis.

Animals↗

PubMed2000

Characteristics of complexes composed of sodium hyaluronate and bovine serum albumin.

Complexes composed of sodium hyaluronate (NaHA) and bovine serum albumin (BSA) were studied to elucidate the exact composition of the complex, the phase separation, the electrophoretic mobility and the size using dynamic light scattering (DLS) and electrophoretic light scattering (ELS), etc. The phase diagram of the mixed solutions was determined. The complexes were soluble in neutral or weakly acidic pH regions and showed phase separation in the more acidic pH region. From the concentration of Na+ released from NaHA when it binds to BSA, the ratios of BSA to NaHA of the complexes were determined. In the region of soluble complexes, one BSA molecule was determined to bind with 15 carboxylic groups of NaHA and in the region of insoluble complexes to bind with 6 carboxylic groups. At the phase separation point, 117 BSA molecules bound with one NaHA molecule and 17% of the carboxylic groups of NaHA did not contribute to the binding of BSA. The sizes of the complexes decreased from several microm to several hundred nm as the binding ratio of BSA increases. Decreases in the viscosities of the mixed solutions were consistent with the decreases of the sizes. From these results, a model of complex formation is proposed.

Animals↗