Biomedical subjects

Hui Yu

Publications and source records attributed to Hui Yu.

At least 37 records · Page 2Linked to original sources

PubMed2006

[Latest advances on the nomenclature for factors of the SLA class-I system].

A new nomenclature system for the SLA class-I system based on DNA sequencing and phylogenetic analysis has been published recently. The naming conventions of SLA class-I loci, allele groups, alleles and haplotypes are particular represented, and the requirements for naming a new allele are also recapitulatively described in this paper. Considering the nomenclature system of SLA class-I, it will has important significance towards human transplantation immunology, swine immunogenetics and breeding for pig disease resistance in the future.

Alleles↗

PubMed2006

[Adsorption and partition of PAHS on particles of the Yellow River].

Experiments were carried out to study the sorption of PAHs Benzo(a)pyrene, chrysene and Benzo(g, h, i)perylene on particles of the Yellow River. The contributions of adsorption and partition to the sorption of PAHs were investigated. Several significant results were obtained from the study: (1) The total sorption capacity increases with the particle content while the sorption capacity of unit weight particle decreases; the isotherms of Benzo(a)pyrene depend on the particle content. (2) Isotherms of Benzo(a) pyrene can be fitted with the Dual Adsorption-Partition model under different particle content; the measured value of the adsorption and partition are in accord with the theoretical value of the Dual Adsorption-Partition model. (3) The adsorption is predominant in the sorption of Benzo(a)pyrene. When the particle contents are 3, 8 and 15 g/L and the liquid equilibrium concentrations are 2.84, 2.35 and 3.4 microg/L, respectively, the contributions of adsorption are 67.8%, 65.6% and 62.69%, respectively. In addition, the contributions of adsorption have a decreasing trend with the increase of the particle content. (4) The sorption capacity of Benzo (a) pyrene being alone are bigger than that with other PAHs chrysene and Benzo(g, h, i)perylene coexisting in the water system, this also proves that the adsorption is predominant in the sorption of PAHs.

Adsorption↗

PubMed2006

[Familiar hypertrophic cardiomyopathy caused by a IVS15-1G > A mutation in cardiac myosin-binding protein C gene].

OBJECTIVE: To detect the disease-causing gene mutation of hypertrophic cardiomyopathy (HCM) in a Chinese family and to analyze the correlation of the genotype and the phenotype. METHODS: One family affected with HCM was studied. The clinical data including symptom, physical examination, echocardiography and electrocardiography were collected. The full encoding exons and flanking sequences of beta-myosin heavy chain gene (MYH7) and cardiac myosin-binding protein C gene (MYBPC3) were amplified with PCR and the products were sequenced. RESULTS: A G8887A mutation, which is an acceptor splicing site of intron 15 (IVS15-1G > A) in MYBPC3 (gi: Y10129) was identified in 6 out of 11 family members. Three mutation carriers developed HCM at 48 - 75 years old with mild chest pain, chest distress and asymmetric septal hypertrophy (13 - 14 mm) and remaining mutation carriers are free of HCM. No mutation was identified in MYH7 gene. CONCLUSION: HCM caused by the IVS15-1G > A mutation is a benign phenotype. It is helpful to screen MYBPC3 gene mutation in late-onset HCM patients with mild symptoms.

Adult↗

PubMed2006

[Biodegradability and degradation mechanism of 3-fluorophenol by the activated sludge].

An acclimated activated sludge was examined for its ability to degrade 3-fluorophenol in aerobic batch cultures. The result indicated that the organism degrades up to 100 mg/L 3-fluorophenol completely with approximately 100% fluoride anion release within 16 h. 3-Fluorophenol can serve as the sole carbon source and energy source for the organism. The acclimated activated sludge can degrade 3-fluorophenol effectively. The degradation mechanism study reveal that the initial step in the aerobic biodegradation of 3-fluorophenol is its transformation to fluorocatechol. Following transformation of the fluorophenol to fluorocatechol, ring cleavage by catechol 1, 2-dioxygenase proceedes via an ortho-cleavage pathway, then defluorination occurres.

Acclimatization↗

PubMed2006

[Detection of class I integron and its relation to antimicrobial resistance of Shigella flexneri in children].

OBJECTIVE: To investigate class I integron of Shigella flexneri, its prevalence in children, and its relation to bacterial resistance to antimicrobial agents. METHODS: Totally 51 strains of Shigella flexneri were isolated from fecal samples of children suffering from bacterial diarrhea seen between June 2004 and November 2004 at Children's Hospital of Fudan University. Polymerase chain reaction (PCR) was employed to amplify various integron markers, including intI1, gene cassette region and 3' conserved region of class I intrgron; susceptibility of Shigella flexneri strains to 7 antimicrobial agents was determined by K-B (Kriby-Bauer) method. RESULTS: Forty-six strains of Shigella flexneri had intI gene with a positive rate of 90.2% (46/51); 24 strains of Shigella flexneri were positive for qacEDelta1-sul1, the positive rate was 47.1% (24/51); proportion of the isolates positive for all the three regions of class I integron was 43.1% (22/51); 46 strains of intI positive Shigella flexneri were all positive for ant (3'')-I. Among 46 strains of intI positive isolates, proportions of the isolates positive and negative for qacEDelta1-sul1 were 47.8% (22/46) and 52.2% (24/46), respectively. In the class I integron positive Shigella flexneri, the resistance rates of ampicillin (chi(2) = 10.13, P < 0.01) and chloramphenicol (chi(2) = 19.97, P < 0.01) were significantly higher than those in the class I integron-negative group. CONCLUSIONS: Class I integron was detected in 90.2% of Shigella flexneri in children; carriage of class I integron is related to antimicrobial resistance of Shigella flexneri.

Anti-Bacterial Agents↗

PubMed2006

[Multiple analysis of the relationship between correlation of gene function and expression by GeneHub software].

GeneHub software developed by us can be applied to evaluate the significance of expression similarity of genes in each functional unit of different gene function classification systems, and thus to select experiment condition related gene functional units. With different expression similarity measurement and different experiment data, we have applied GeneHub to analyze the expression correlation of functional related genes classified respectively with gene chromosome location, celluar location and interaction, metabolic pathway and signal transduction pathway relationship of protein products of genes. Genes classified according to these multiple ways all showed significant experimental condition related co-expression in our analysis. Our results provide further evidence for the assumption that functional related genes express similarly, which is widely adopted in gene expression profile analysis.

Chromosome Mapping↗

PubMed2005

A multifunctional Pasteurella multocida sialyltransferase: a powerful tool for the synthesis of sialoside libraries.

A multifunctional sialyltransferase has been cloned from Pasteurella multocida strain P-1059 and expressed in E. coli as a truncated C-terminal His6-tagged recombinant protein (tPm0188Ph). Biochemical studies indicate that the obtained protein is (1) an alpha2,3-sialyltransferase (main function), (2) an alpha2,6-sialyltransferase, (3) an alpha2,3-sialidase, and (4) an alpha2,3-trans-sialidase. The recombinant tPm0188Ph is a powerful tool in the synthesis of structurally diverse sialoside libraries due to its relaxed substrate specificity, high solubility, high expression level, and multifunctionality.

Carbohydrate Sequence↗

PubMed2005

Hematopoietic stem cell exhaustion impacted by p18 INK4C and p21 Cip1/Waf1 in opposite manners.

Transplantation-associated stress can compromise the hematopoietic potential of hematopoietic stem cells (HSCs). As a consequence, HSCs may undergo "exhaustion" in serial transplant recipients, for which the cellular and molecular bases are not well understood. Hematopoietic exhaustion appears to be accelerated in the absence of p21(Cip1/Waf1) (p21), a cyclin-dependent kinase inhibitor (CKI) in irradiated hosts. Our recent study demonstrated that unlike loss of p21, deletion of p18(INK4C) (p18), a distinct CKI, results in improved long-term engraftment, largely because of increased self-renewing divisions of HSCs in vivo. We show here that HSCs deficient in p18 sustained their competitiveness to wild-type HSCs from unmanipulated young mice, and retained multilineage differentiation potential after multiple rounds of serial bone marrow transfer over a period of more than 3 years. Further, p18 absence significantly decelerated hematopoietic exhaustion caused by p21 deficiency. Such an effect was shown to occur at the stem cell level, likely by a counteracting mechanism against the cellular senescence outcome. Our current study provides new insights into the distinct impacts of these cell-cycle regulators on HSC exhaustion and possibly HSC aging as well under proliferative stress, thereby offering potential pharmacologic targets for sustaining the durability of stressed HSCs in transplantation or elderly patients.

Aged↗

PubMed2005

Relationship between cytokines gene polymorphism and susceptibility to hepatitis B virus intrauterine infection.

BACKGROUND: The influences of genomic background are confirmed in more diseases. Immunologic tolerance after intrauterine infection of hepatitis B virus is considered to occur in T cells. Cytokines work effectively in eliminating virus by immune system after hepatitis B virus infection. To explore the relationship between cytokines (tumor necrosis factor-alpha, interferon-gamma, interleukin-4 and interleukin-10), which expressed abnormal quantity in the peripheral blood to intrauterine hepatitis B virus infectious children, gene single nucleotide polymorphism (SNP) and susceptibility to hepatitis B virus intrauterine infection. METHODS: This is a cross sectional study of molecular clinical epidemiology. The subjects in this study were selected from outpatients of hepatitis B vaccine follow-up special clinics of our hospital in the period. According to intrant criteria, the high risk children of hepatitis B virus (HBV) intrauterine infection were divided into immune failure group (group I); and immune effective group (group II) and non high risk children belonged to the control group. Four gene SNP sites of TNF-alpha -238, IFN-gamma +874, IL-4 -590 and IL-10 -1082 were determined by real-time quantitative fluorescent polymerase chain reaction (PCR). RESULTS: The significant differences of TNF-alpha -238 A allele frequency were found between group I and group II (chi(2) = 6.797, P < 0.05) and between group I and the control group (chi(2) = 9.513, P < 0.05). No evident differences of TNF-alpha -238 A were found between group II and control group (chi(2) = 0.047, P > 0.05); the significant differences of IFN-gamma +874 A allele frequency were found between group I and group II (chi(2) = 7.238, P < 0.05), and between group I and the control group (chi(2) = 5.199, P < 0.05). No evident differences were found between group II and the control group (chi(2) = 0.602, P > 0.05); the significant differences of IL-4 -590 C/T allele frequency were not found between group I and group II (chi(2) = 0.632, P > 0.05), also group I and the control group (chi(2) = 0.584, P > 0.05), and the group II and the control group (chi(2) = 0.004, P > 0.05) respectively; The significant differences of IL-10 -1082 G allele frequency were found between group II and group I (chi(2) = 10.359, P < 0.001), and between group II and the controls (chi(2) = 35.418, P < 0.001), but the significant differences were not found between group I and the control group (chi(2) = 1.759, P > 0.05). CONCLUSIONS: This study suggested the possibility that the TNF-alpha -238 A allele and IFN-gamma +874 A allele were associated with HBV intrauterine infection. There was no evident relationship between IL-4 -590 C/T allele SNP and susceptibility to HBV intrauterine infection, but the IL-10 -1082 G allele was associated with preventive efficacy to HBV intrauterine infection.

Cross-Sectional Studies↗

PubMed2005

Evidence that azide occupies the chloride binding site near the manganese cluster in photosystem II.

The effect of adding azide to photosystem II (PS II) membrane samples (BBY preparation), with or without chloride, has been investigated using continuous wave (CW) and pulsed EPR spectroscopy. In the BBY samples with 25 mM chloride, we observed that the inhibition induced by azide is partly recovered by the addition of bicarbonate. Electron spin-echo envelope modulation (ESEEM) was used to search for spin transitions of 15N nuclei magnetically coupled to the S2 state Mn cluster (multiline EPR signal form) in 15N (single terminal label) azide-treated samples with negative results. However, an 15N ESEEM peak was observed in parallel chloride-depleted PS II samples when the 15N-labeled azide is added. However, this peak is absent in chloride-depleted samples incubated in buffer containing both chloride and [15N]azide. Thus these results demonstrate an azide binding site in the immediate vicinity of the Mn cluster, and since this site appears to be competitive with chloride, these results provide further evidence that chloride is bound proximal to the Mn cluster as well. Discussion on the possible interplay between azide, chloride, and bicarbonate is provided.

Azides↗

PubMed2005

Beam expansion in thermo-optic-effect-induced total internal reflection and its applications in optical switches.

The beam-propagation characteristics of the total internal reflection (TIR) induced by the thermo-optic effect are investigated. Based on the Fourier heat-transmission principle and the variable separation method, we derive an analytical transient expression of the thermal field for general thermo-optic devices. With the analytical expression, the time response and steady-state temperature distribution of thermo-optic devices are presented. The beam expansion rule of TIR in the thermal field is developed mathematically, and a quantitative calculation is given as well. To illustrate the application of the rule, an X-junction 2 x 2 TIR switch with high reflection efficiency is designed through theoretical calculation. The simulation shows that the structure exhibits a high reflection coefficient; the reflection loss is only -0.76 dB. The simulation results agree well with the theoretical calculation.

Journal Article↗

PubMed2005

Correlation of anaerobic biodegradability and the electrochemical characteristic of azo dyes.

Some experiments were conducted to study some electrochemical factors affecting the bacterial reduction (cleavage) of azo dyes, knowledge of which will be useful in the wastewater treatments of azo dyes. A common mixed culture was used as a test organism and the reductions of Acid Yellow 4, 11, 17 and Acid Yellow BIS were studied. It was found that the azo dyes were reduced at different rates, which could be correlated with the reduction potential of the azo compounds in cyclic voltammetric experiments. Acid Yellow BIS (E (r)--616.75 mV) was reduced at the highest rate of 0.0284 mol g dry cell weight(-1) h(-1), Acid Yellow 11 (E (r)--593.25 mV) at 0.0245 mol g dry cell weight(-1) h(-1) and Acid Yellow 4 (E (r)--513 mV) at 0.0178 mol g dry cell weight(-1) h(-1). At the same time, the decolorization rate of Acid Yellow 17 (E (r)--627.5 mV) was 0.0238 mol g dry cell weight(-1) h(-1), which was affected by the nature of chlorine substituent. Reduction of these azo dyes did not occur under aeration conditions. These studies with a common mixed culture indicate that the reduction of azo dyes may be influenced by the chemical nature of the azo compound. The reduction potential is a preliminary tool to predict the decolorization capacity of oxidative and reductive biocatalysts.

Azo Compounds↗

PubMed2005

Influence of the 33 kDa manganese-stabilizing protein on the structure and substrate accessibility of the oxygen-evolving complex of photosystem II.

The 33 kDa manganese-stabilizing extrinsic protein binds to the lumenal side of photosystem II (PS II) close to the Mn(4)Ca cluster of the oxygen-evolving complex, where it limits access of small molecules to the metal site. Our previous finding that the removal of this protein did not alter the magnetic coupling regime within the manganese cluster, measured by electron spin-echo envelope modulation [Gregor, W., and Britt, R. D. (2000) Photosynth. Res. 65, 175-185], prompted us to examine whether this accessibility control is also true for substrate water, using the same pulsed EPR technique. Comparing the deuteron modulation of the S(2)-state multiline signal of PS II membranes, equilibrated with deuterated water (D(2)O) after removal or retention of the 33 kDa protein, we observed no change in the number and the distance of deuterons magnetically coupled to manganese, indicating that the number and distance of water molecules bound to the manganese cluster are independent of bound 33 kDa protein in the S(1) state, in which the sample was poised prior to cryogenic illumination. A simple modulation depth analysis revealed a distance of 2.5-2.6 A between the closest deuteron and manganese. These results are in agreement with our refined X-ray absorption analysis. The manganese K-edge positions, reflecting their oxidation states, and the extended X-ray absorption fine structure amplitudes and distances between the manganese ions and their oxygen and nitrogen ligands (1.8, 2.7, and 3.3-3.4 A) were independent of bound 33 kDa protein.

Binding Sites↗

PubMed2005

Broadly predicting specific gene functions with expression similarity and taxonomy similarity.

Previous studies on computational gene functional prediction have not fully exploited the taxonomy structure of Gene Ontology (GO). They just select a few classes from GO into a set, and conduct classwise learning of these classes. The pre-selection of learning classes, often done according to the annotation sizes, limits the prediction breadth and depth. This way of pre-selecting learning classes ignores the taxonomy relations among classes, and so wastes the valuable functional knowledge encoded in the DAG structure of GO. This paper proposes GESTS, a novel gene functional prediction approach based on both gene expression similarity and GO taxonomy similarity, which circumvents the problem of arbitrary learning class pre-selection. GESTS is a semi-supervised approach that reasonably and efficiently incorporates the ontology-formed gene functional knowledge into automated functional analyses of local gene clustering. By integrating both expression similarity and taxonomy similarity into the learning process, GESTS achieves better prediction breadth, depth, and precision than previous studies on the fibroblast serum response dataset and the yeast expression dataset.

Computational Biology↗

PubMed2005

Automated measurement of cell motility and proliferation.

BACKGROUND: Time-lapse microscopic imaging provides a powerful approach for following changes in cell phenotype over time. Visible responses of whole cells can yield insight into functional changes that underlie physiological processes in health and disease. For example, features of cell motility accompany molecular changes that are central to the immune response, to carcinogenesis and metastasis, to wound healing and tissue regeneration, and to the myriad developmental processes that generate an organism. Previously reported image processing methods for motility analysis required custom viewing devices and manual interactions that may introduce bias, that slow throughput, and that constrain the scope of experiments in terms of the number of treatment variables, time period of observation, replication and statistical options. Here we describe a fully automated system in which images are acquired 24/7 from 384 well plates and are automatically processed to yield high-content motility and morphological data. RESULTS: We have applied this technology to study the effects of different extracellular matrix compounds on human osteoblast-like cell lines to explore functional changes that may underlie processes involved in bone formation and maintenance. We show dose-response and kinetic data for induction of increased motility by laminin and collagen type I without significant effects on growth rate. Differential motility response was evident within 4 hours of plating cells; long-term responses differed depending upon cell type and surface coating. Average velocities were increased approximately 0.1 microm/min by ten-fold increases in laminin coating concentration in some cases. Comparison with manual tracking demonstrated the accuracy of the automated method and highlighted the comparative imprecision of human tracking for analysis of cell motility data. Quality statistics are reported that associate with stage noise, interference by non-cell objects, and uncertainty in the outlining and positioning of cells by automated image analysis. Exponential growth, as monitored by total cell area, did not linearly correlate with absolute cell number, but proved valuable for selection of reliable tracking data and for disclosing between-experiment variations in cell growth. CONCLUSION: These results demonstrate the applicability of a system that uses fully automated image acquisition and analysis to study cell motility and growth. Cellular motility response is determined in an unbiased and comparatively high throughput manner. Abundant ancillary data provide opportunities for uniform filtering according to criteria that select for biological relevance and for providing insight into features of system performance. Data quality measures have been developed that can serve as a basis for the design and quality control of experiments that are facilitated by automation and the 384 well plate format. This system is applicable to large-scale studies such as drug screening and research into effects of complex combinations of factors and matrices on cell phenotype.

Automation↗

PubMed2005

Towards precise classification of cancers based on robust gene functional expression profiles.

BACKGROUND: Development of robust and efficient methods for analyzing and interpreting high dimension gene expression profiles continues to be a focus in computational biology. The accumulated experiment evidence supports the assumption that genes express and perform their functions in modular fashions in cells. Therefore, there is an open space for development of the timely and relevant computational algorithms that use robust functional expression profiles towards precise classification of complex human diseases at the modular level. RESULTS: Inspired by the insight that genes act as a module to carry out a highly integrated cellular function, we thus define a low dimension functional expression profile for data reduction. After annotating each individual gene to functional categories defined in a proper gene function classification system such as Gene Ontology applied in this study, we identify those functional categories enriched with differentially expressed genes. For each functional category or functional module, we compute a summary measure (s) for the raw expression values of the annotated genes to capture the overall activity level of the module. In this way, we can treat the gene expressions within a functional module as an integrative data point to replace the multiple values of individual genes. We compare the classification performance of decision trees based on functional expression profiles with the conventional gene expression profiles using four publicly available datasets, which indicates that precise classification of tumour types and improved interpretation can be achieved with the reduced functional expression profiles. CONCLUSION: This modular approach is demonstrated to be a powerful alternative approach to analyzing high dimension microarray data and is robust to high measurement noise and intrinsic biological variance inherent in microarray data. Furthermore, efficient integration with current biological knowledge has facilitated the interpretation of the underlying molecular mechanisms for complex human diseases at the modular level.

Algorithms↗

PubMed2005

MEGO: gene functional module expression based on gene ontology.

Existing analysis tools to study the collective properties of gene functional modules cannot return highly homogeneous modules and do not provide quantitative measures of module activity level. By partitioning genes according to multiple gene functional categorization principles and summarizing gene expression values into module expression values, MEGO (module expression based on gene ontology), a standalone microarray data analysis program, is able to extract highly activated gene functional modules that are of much interest to microarray experimenters. With multiple functional categorization principles simultaneously introduced in MEGO, the partition of genes is more delicate, and the collective property of a group of genes is sharpened and easier to capture. The quantitative measures of module activity levels returned by MEGO give users a quick impression of the direction and degree of module regulation. MEGO efficiently determines the answers to frequently asked questions, such as which functional classes have been induced or repressed under a specific experiment and to which levels these functional classes have been affected. MEGO is available free of charge for academic use and may be downloaded from http://www.dxy.cn/mego/MEGOInstall.EXE. Supplementary information can be found on the authors' web page at http://www.dxy.cn/mego/ and at the BioTechniques' web site at http://www. BioTechniques.com/February2005/TuSupplementary.html.

Algorithms↗

PubMed2005

[MAPK signal pathway plays a role in proliferation of Jurkat cells induced by ouabain].

The object was to study the effect of ouabain on Jurkat cells and its possible mechanism. The effect of ouabain of low concentration on Jurkat cells was confirmed by MTT, while c-myc gene transcription was measured by RT-PCR, and the phosphorylation of MAPK (ERK1/2) as well as the expression of c-myc gene was tested by Western blot respectively. The results showed that ouabain at low concentration could induce the proliferation of Jurkat in a time-and dose-dependent manner. At the same time, the phosphorylation of MAPK (ERK1/2) and the expression of c-myc gene was enhanced. In conclusion, ouabain stimulates the intracellular MAPK signal pathway by acting on the Na, K-ATPase, and thus induce the proliferation of Jurkat cells, in which the regulation of c-myc gene expression may be involved.

Blotting, Western↗