Biomedical subjects

Jie Yang

Publications and source records attributed to Jie Yang.

At least 55 records · Page 3Linked to original sources

PubMed2006

Inversion vibration of PH3+(X2A2") studied by zero kinetic energy photoelectron spectroscopy.

We report the first rotationally resolved spectroscopic studies on PH3+(X2A2") using zero kinetic energy photoelectron spectroscopy and coherent VUV radiation. The spectra about 8000 cm(-1) above the ground vibrational state of PH3+(X2A2") have been recorded. We observed the vibrational energy level splittings of PH3+(X2A2") due to the tunneling effect in the inversion (symmetric bending) vibration (nu2+). The energy splitting for the first inversion vibrational state (0+/0-) is 5.8 cm(-1). The inversion vibrational energy levels, rotational constants, and adiabatic ionization energies (IEs) for nu2+ = 0-16 have been determined. The bond angles between the neighboring P-H bonds and the P-H bond lengths are also obtained using the experimentally determined rotational constants. With the increasing of the inversion vibrational excitations (nu2+), the bond lengths (P-H) increase a little and the bond angles (H-P-H) decrease a lot. The inversion vibrational energy levels have also been calculated by using one dimensional potential model and the results are in good agreement with the experimental data for the first several vibrational levels. In addition to inversion vibration, we also observed firstly the other two vibrational modes: the symmetric P-H stretching vibration (nu1+) and the degenerate bending vibration (nu4+). The fundamental frequencies for nu1+ and nu4+ are 2461.6 (+/-2) and 1043.9 (+/-2) cm(-1), respectively. The first IE for PH3 was determined as 79670.9 (+/-1) cm(-1).

Journal Article↗

PubMed2006

The Amino-terminal domain of tntegrin beta3 functions as a transcriptional activator in yeast.

A deletion mutant encoding the integrin beta3(4I-F56) with an additional Gln at the carboxyl terminus was found occassionally when we were constructing a counterselection yeast two-hybrid assay modle. This mutant exhibited strong transcriptional activation in yeast cells, bearing the Escherichia coli lacZ reporter gene encoding the beta-galactosidase under the transcriptional control of GAL4 promoter and TATA box. Further analysis revealed that the region between the amino acid residues 23C to S77, an acidic domain involved in the function of several transcriptional activators were critical for optimal level of transactivation.

Amino Acid Sequence↗

PubMed2006

A comparison of elderly and adult multiple organ dysfunction syndrome in the rat model.

Multiple organ dysfunction syndrome (MODS) in the elderly is the most common cause of mortality in critically ill elderly patients, and it is different from MODS in the adult in clinic. Rare studies have been done on its pathogenesis and the comparison between adult and elderly MODS animal models. This work aimed at exploring the mechanisms mediating elderly MODS and compared this with adult MODS. Male Sprague-Dawley aged and adult rats were intraperitoneally injected with zymosan for incitement of MODS. Aged rats receiving zymosan showed severer pulmonary, cardiac and renal dysfunctions than adult rats. Likewise, the tissue lesions under light microscope in major organs of zymosan treated aged rats were much worse than those of zymosan treated adult rats. Moreover, zymosan treated aged rats showed 142% and 64% greater increase in pulmonary alveolar macrophages (AMs) apoptotic rate and serum TNF-alpha level, respectively, whereas 43% smaller increase in serum IL-10 level compared to zymosan treated adult rats. Furthermore, lung injury was much worse than that in other organs in zymosan treated aged rats. Overall, these results suggest that zymosan can be used in aged rats to incite MODS in the elderly. In the animal model of elderly MODS, there are (1) severer injury in lung, heart and kidney vs adult; (2) easier to develop severe systemic inflammatory response syndrome (SIRS) instead of compensatory anti-inflammatory response syndrome (CARS) compared to the adult; and (3) severer inflammation in lung than other organs indicative of the possible roles of lung in triggering MODS in the elderly.

Aging↗

PubMed2006

PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance.

Phylogenetic Tree Reconstruction (PTreeRec) is a web-based tool for automatic phylogeny inferences from whole-genome sequences, which accepts files of DNA sequences in the FASTA format and allows users to save the output tree file, and displays the inferred tree through an applet in a web browser. PTreeRec involves three basic steps. First, regions of maximal segment pairs (MSPs) based on an all-against-all pairwise comparison of genomes are located. Second, a distance matrix is calculated from MSP scores or coverage. Finally, a phylogenetic tree is reconstructed by the neighbor-joining method.

Algorithms↗

PubMed2006

TRAIL-induced apoptosis proceeding from caspase-3-dependent and -independent pathways in distinct HeLa cells.

The apoptotic pathway in higher eukaryotes remains controversial with respect to the necessity of activation of caspase-3 in TRAIL (tumor necrosis factor-related apoptosis-inducing ligand)-treated cells. In this study, a fluorescence resonance energy transfer (FRET) probe was developed to image the activation of caspase-3 and the related apoptotic pathway in TRAIL-treated cells in real time. Both kinds of apoptotic pathways were observed simultaneously in the same experiment proceeding from activation and non-activation of caspase-3. The total apoptotic rate was 56.08%, the apoptotic rates for activation and non-activation of caspase-3 pathways were 21.5% and 34.58%, respectively, which were examined later for Hoechst 33258 staining and morphological characteristics. The apoptotic rate due to the activation of caspase-3 pathways in TRAIL-treated cells has been independently measured to be around 25.11% by capillary electrophoresis (CE) analysis, which confirmed the apoptotic rate due to activation of caspase-3 pathways as found by FRET analysis. This result also suggests that rest apoptosis is preceded by caspase-3-independent pathways, as CE has the ability to quantitatively detect caspase-dependent apoptosis. The observation of the coexistence of caspase-3-dependent and caspase-3-independent apoptotic pathways in the TRAIL-treated cells was unusual in comparison with the previous reports.

Apoptosis↗

PubMed2006

Using stacked generalization to predict membrane protein types based on pseudo-amino acid composition.

Membrane proteins are vitally important for many biological processes and have become an attractive target for both basic research and drug design. Knowledge of membrane protein types often provides useful clues in deducing the functions of uncharacterized membrane proteins. With the unprecedented increasing of newly found protein sequences in the post-genomic era, it is highly demanded to develop an automated method for fast and accurately identifying the types of membrane proteins according to their amino acid sequences. Although quite a few identifiers have been developed in this regard through various approaches, such as covariant discriminant (CD), support vector machine (SVM), artificial neural network (ANN), and K-nearest neighbor (KNN), classifier the way they operate the identification is basically individual. As is well known, wise persons usually take into account the opinions from several experts rather than rely on only one when they are making critical decisions. Likewise, a sophisticated identifier should be trained by several different modes. In view of this, based on the frame of pseudo-amino acid that can incorporate a considerable amount of sequence-order effects, a novel approach called "stacked generalization" or "stacking" has been introduced. Unlike the "bagging" and "boosting" approaches which only combine the classifiers of a same type, the stacking approach can combine several different types of classifiers through a meta-classifier to maximize the generalization accuracy. The results thus obtained were very encouraging. It is anticipated that the stacking approach may also hold a high potential to improve the identification quality for, among many other protein attributes, subcellular location, enzyme family class, protease type, and protein-protein interaction type. The stacked generalization classifier is available as a web-server named "SG-MPt_Pred" at: http://202.120.37.186/bioinf/wangsq/service.htm.

Algorithms↗

PubMed2006

Intelligence and information processing during a visual search task in children: an event-related potential study.

To investigate the differences in event-related potential parameters related to children's intelligence, we selected 15 individuals from an experimental class of intellectually gifted children and 13 intellectually average children as control to finish three types of visual search tasks (Chinese words, English letters and Arabic numbers). We recorded the electroencephalogram and calculated the peak latencies and amplitudes. Our results suggest comparatively increased P3 amplitudes and shorter P3 latencies in brighter individuals than in less intelligent individuals, but this expected neural efficiency effect interacted with task content. The differences were explained by a more spatially and temporally coordinated neural network for more intelligent children.

Brain Mapping↗

PubMed2006

Digitally reconstructed radiograph generation by an adaptive Monte Carlo method.

Digitally reconstructed radiograph (DRR) generation is an important step in several medical imaging applications such as 2D-3D image registration, where the generation of DRR is a rate-limiting step. We present a novel DRR generation technique, called the adaptive Monte Carlo volume rendering (AMCVR) algorithm. It is based on the conventional Monte Carlo volume rendering (MCVR) technique that is very efficient for rendering large medical datasets. In contrast to the MCVR, the AMCVR does not produce sample points by sampling directly in the entire volume domain. Instead, it adaptively divides the entire volume domain into sub-domains using importance separation and then performs sampling in these sub-domains. As a result, the AMCVR produces almost the same image quality as that obtained with the MCVR while only using half samples, and increases projection speed by a factor of 2. Moreover, the AMCVR is suitable for fast memory addressing, which further improves processing speed. Independent of the size of medical datasets, the AMCVR allows for achieving a frame rate of about 15 Hz on a 2.8 GHz Pentium 4 PC while generating reasonably good quality DRR.

Algorithms↗

PubMed2006

Chlamydia infection induces ICOS ligand-expressing and IL-10-producing dendritic cells that can inhibit airway inflammation and mucus overproduction elicited by allergen challenge in BALB/c mice.

Our previous study has shown that the adoptive transfer of dendritic cells (DCs) freshly isolated from Chlamydia-infected mice (iIDCs), unlike those from control naive mice (iNDCs), can inhibit systemic and cutaneous eosinophilia induced by OVA exposure. In the present study, we examined the mechanism by which iIDC inhibits allergen-specific Th2 cell differentiation in vitro and in vivo. The study revealed that iIDCs exhibited higher surface expression of CD8alpha and the ICOS ligand (ICOS-L), as well as higher IL-10 and IL-12 production than iNDCs. In vitro DC:CD4(+) T cell coculture experiments showed that iIDCs could inhibit allergen-specific Th2 cell differentiation and that the inhibitory effect could be abolished by the blockage of IL-10 or IL-12 activity. More interestingly, the coblockade of IL-10 and the ICOS-L showed synergistic effect in enhancing allergen-driven Th2 cytokine production. Furthermore, adoptive transfer of iIDCs, but not iNDCs, to OVA sensitized mice significantly inhibited airway eosinophilia and mucus overproduction following intranasal challenge with OVA. Overall, the data demonstrate a critical role played by ICOS-L-expressing and IL-10-producing DCs from Chlamydia-infected mice in the infection-mediated inhibition of allergic responses.

Allergens↗

PubMed2006

Mandibular morphological changes in low bone mass edentulous females: evaluation of panoramic radiographs.

OBJECTIVE: The objective of this study was to evaluate morphological changes of the mandible in osteopenic and osteoporotic edentulous females. STUDY DESIGN: Fifty-two female edentulous patients underwent panoramic radiography and dual-energy x-ray absorptiometry of the lumbar spine and femoral neck. Measurements of the gonial angle, antegonial angle, antegonial depth, antegonial index (AI), and mental index (MI) were performed. Patients were classified as normal (T-score > -1.0), osteopenic (T-score of -1.0 to 0 -2.5), or osteoporotic (T-score < -2.5). RESULTS: The gonial angle did not show differences among the three categories of skeletal bone status (P > .05). The antegonial angle was significantly smaller in individuals with low bone mass (P < .05). The antegonial depth was significantly greater in osteoporotic (P < .05) and osteopenic individuals (P < .05). The AI and MI were significantly smaller in individuals with low bone mass (P < .05); however, after age adjustment there were no differences among the groups (P > .05). CONCLUSIONS: Edentulous females with low bone mass have a deeper antegonial region. The thickness of the cortical mandibular bone is highly influenced by age.

Absorptiometry, Photon↗

PubMed2006

Application of FTTP to alpha-helix or beta-strand motifs.

Information concerning protein structure is widely dispersed and cannot easily and rapidly be processed by the biological community. We present a database of tendentious factors of three states of tripeptide units from PDB database, called a bank of tendentious factors of three states of three-peptide units (FTTP). The FTTP database was constructed based on conformational dihedral angle (varphi,psi) library of 20(3) peptide triplets by exhaustively searching through PDB databases. We introduce the FTTP database for the analysis of characteristics common to relative conformational biases of all peptide triplets, especially finding some motifs apt to alpha-helix and beta-strand. Our results show that this will provide a platform for studies of short peptide motifs, folding codons, secondary structure and three-dimensional (3D) structure of proteins. Moreover, FTTP is a unique resource that will allow a comprehensive characterization of peptide triplets and thus improve our understanding of sequence-structure relationship, refined domains, 3D structures, and their associated function. We believe the FTTP database will help biologists in increasing the efficiency of finding useful and relevant information regarding structure-function relationship of proteins. Therefore, this approach will play an important role in protein folding, protein engineering, molecular design, and proteomics.

Amino Acid Motifs↗

PubMed2006

Alteration of subcellular redox equilibrium and the consequent oxidative modification of nuclear factor kappaB are critical for anticancer cytotoxicity by emodin, a reactive oxygen species-producing agent.

We previously found that emodin produced reactive oxygen species (ROS) intracellularly. In various tumor cells at low doses it enhances the cytotoxicity of As(2)O(3), and at higher doses it renders cytotoxicity independently in vitro and in vivo. The effects involve redox-mediated inhibition of NF-kappaB activation. In this study, we focus on the mechanisms by which emodin inhibits NF-kappaB activation. Results in HeLa cells demonstrated that emodin at high doses or in combination with As(2)O(3), via generation of ROS especially in the nucleus, altered subcellular redox equilibrium and thus oxidized the redox-sensitive site on NF-kappaB and prevented its binding to the target DNA. In vivo study showed that tumors exposed to the arsenic/emodin cotreatment had dramatically smaller sizes and weaker antioxidant capacity, compared with arsenic alone. NF-kappaB binding and transactivation were inhibited in these tumors. These data help in the understanding of the mechanisms by which manipulation of cellular redox and NF-kappaB activation may enhance chemotherapy.

Antineoplastic Agents↗

PubMed2006

Association of smoking, alcohol drinking and dietary factors with esophageal cancer in high- and low-risk areas of Jiangsu Province, China.

AIM: To study the main environmental and lifestyle factors that account for the regional differences in esophageal cancer (EC) risk in low- and high-risk areas of Jiangsu Province, China. METHODS: Since 2003, a population-based case-control study has been conducted simultaneously in low-risk (Ganyu County) and high-risk (Dafeng County) areas of Jiangsu Province, China. Using identical protocols and pre-tested standardized questionnaire, following written informed consent, eligible subjects were inquired about their detail information on potential determinants of EC, including demographic information, socio-economic status, living conditions, disease history, family cancer history, smoking, alcohol drinking, dietary habits, frequency, amount of food intake, etc. Conditional logistic regression with maximum likelihood estimation was used to obtain Odds ratio (OR) and 95 % confidence interval (95% CI), after adjustment for potential confounders. RESULTS: In the preliminary analysis of the ongoing study, we recruited 291 pairs of cases and controls in Dafeng and 240 pairs of cases and controls in Ganyu, respectively. In both low-risk and high-risk areas, EC was inversely associated with socio-economic status, such as level of education, past economic status and body mass index. However, this disease was more frequent among those who had a family history of cancer or encountered misfortune in the past 10 years. EC was also more frequent among smokers, alcohol drinkers and fast eaters. Furthermore, there was a geographic variation of the associations between smoking, alcohol drinking and EC risk despite the similar prevalence of these risk factors in both low-risk and high-risk areas. The dose-response relationship of smoking and smoking related variables, such as age of the first smoking, duration and amount were apparent only in high-risk areas. On the contrary, a dose-response relationship on the effect of alcohol drinking on EC was observed only in low-risk areas. CONCLUSION: The environmental risk factors, together with genetic factors and gene-environmental interactions might be the main reason for this high-risk gradient in Jiangsu Province, China.

Aged↗

PubMed2006

NMR and HPLC-MS/MS analysis of synthetically prepared linoleic acid diol glucuronides.

Hydroxylated fatty acids are important mediators of many physiological and pathophysiological processes in a variety of human tissues. Recent evidence shows that in humans many of these are ultimately excreted in the urine as the glucuronide conjugates. In this paper we describe a general approach for the chemical synthesis of glucuronide conjugate derivatives of fatty acids. The synthesis strategy employs three steps (epoxidation, hydrolysis and glucuronidation) using methyl linoleate as a model non-hydroxylated starting compound. Hydroxylated starting compounds would require only the glucuronidation step. NMR and HPLC-MS/MS experiments were used to help determine the structure of the synthesized glucuronide conjugates and to identify fragmentation product ions useful for discriminating positional isomers in biological samples. This synthetic strategy should prove useful for generating analytical standards in order to identify and quantify glucuronide metabolites of hydroxylated fatty acids in humans.

Chemical Phenomena↗

PubMed2006

Specific targeting of pancreatic islet cells in vivo by insulin-promoter-driven adenoviral conjugated reporter genes.

BACKGROUND: The objective of this study was to determine whether rat insulin promoter (RIP) could, in a mouse model, direct expression of an adenovirus-mediated reporter gene specifically into pancreatic islets via systemic delivery. METHODS: Five hundred and eight base pairs of the RIP DNA sequence were constructed into an adenoviral vector containing a lacZ reporter gene (Adeno-RIP-lacZ). The cytomegalovirus (CMV) promoter was constructed to drive lacZ reporter-gene expression (Adeno-CMV-lacZ) and used as controls. In vitro transient transfection assays were performed to determine levels of reporter-gene expression and compared with that of liposome-mediated plasmid transfection. SCID mice were bred and housed in the barrier BL-4 animal facility. At 2 months of age, the human pancreatic cancer cell PANC-1 was intraperitoneally injected into male mice. Two months after the tumor cell inoculation, mice were injected with 10(7) adenoviral particles via tail veins. After gene delivery, mice were sacrificed at different time points to determine transgene expression levels. Complete necropsies were performed. Morphological alterations were determined using hematoxylin and eosin (H&E) staining, and distribution of the reporter lacZ gene was determined by immunohistochemistry analyses. RESULTS: Adenoviral-driven reporter-gene expression resulted in more than 5 times higher transgene expression compared with conventional plasmid transfections. In Adeno-RIP-lacZ-injected mice, lacZ expression was specifically detected in pancreatic islets. By contrast, in Adeno-CMV-lacZ-injected mice, lacZ gene expression was observed in multiple organs and tissues. Mononuclear cell infiltration and liver cell inflammation were found in Adeno-CMV-lacZ-treated mice. Similar phenomena were observed in islet cells of Adeno-RIP-lacZ-treated mice. A significantly higher level of reporter-gene expression was also found at the edge of in-vivo-inoculated human pancreatic tumors. CONCLUSION: These results demonstrate that RIP-directed reporter-gene expression was found specifically in mouse pancreatic islets and implanted human pancreatic cancer cells. These data thus demonstrate that the combination of an adenoviral vector and a tissue-specific promoter could lead to an enhanced and more specific transgene expression in vivo.

Adenoviridae↗

PubMed2006

Degree prediction of malignancy in brain glioma using support vector machines.

The degree of malignancy in brain glioma needs to be assessed by MRI findings and clinical data before operations. There have been previous attempts to solve this problem with a fuzzy rule extraction algorithm based on fuzzy min-max neural networks. We utilize support vector machines with floating search method to select relevant features and to predict the degree of malignancy. Computation results show that the feature subset selected by our techniques can yield better classification performance. In contrast with the base line method, which generated two rules and obtained 83.21% accuracy on the whole data set, our method generates one rule to yield 88.21% accuracy.

Algorithms↗

PubMed2006

Lung damage may induce thrombocytopenia.

Thrombocytopenia is common in patients with lung diseases. Lung injury is associated with deranged platelet homeostasis. The potential mechanisms underlying this association were investigated in this study. The number and morphology of circulating megakaryocytes (MK) were investigated in vivo during cardiopulmonary bypass (CPB) in patients undergoing elective cardiac surgery for heart disease. The association between lung injury and thrombocytopenia was further investigated in vitro in rats with lung injury. MK and platelet counts, and platelet activation between the prepulmonary (right atrial) and postpulmonary (left atrial) blood were also compared. In human, the total number of MK in central venous was higher than those of peripheral arteries during normal circulation. During CPB, the total MK and Type-4 MK of central venous and peripheral arteries were significant increased when compared with that in normal circulation. In healthy rats, the postpulmonary blood had lower MK count, higher platelet count, and similar P-selectin expression. However, the lung-damaged animals showed no such differences in either MK or platelet count, but P-selectin expression was greater in the postpulmonary blood. Peripheral platelets in the lung-injured rats were significantly lower than those in their respective controls. The lungs may play an active role in the regulation of MK levels and the lung damage may reduce circulating platelets.

Animals↗

PubMed2006

Identification of Hepatitis B virus putative intergenotype recombinants by using fragment typing.

Eight hundred and thirty-seven human Hepatitis B virus (HBV) genomes were categorized into pure genotypes and potential intergenotypes, according to their fragment types which were determined based on similarity and phylogenetic analyses of 13 contrived fragments of 250 bp against the corresponding fragments of the consensus sequences of genotypes A-H. Twenty-five intergenotypes, including 171 genomes, were revealed from the potential intergenotype recombinants by phylogenetic analysis of the precisely derived mosaic fragments. Among these, four new intergenotypes were discovered. Many genomes were revealed as putative intergenotype recombinants for the first time. About 87 % of the putative recombinants were B/C (120) and A/D (29) hybrids. The other recombinants comprised A/B/C, A/C, A/E, A/G, C/D, C/F, C/G, C/U (U for unknown genotype) and B/C/U hybrids. Genotypes A and C showed a higher recombination tendency than did other genotypes. The results also demonstrated region priority and breakpoint hot spots in the intergenotype recombination. Recombination breakpoints were found to be concentrated mainly in the vicinity of the DR1 region (nt 1640-1900), the pre S1/S2 region (nt 3150-100), the 3'-end of the C gene (nt 2330-2450) and the 3'-end of the S gene (nt 650-830). These results support the suggestion that intergenotype recombinants may result from co-infection with different genotypes.

Cluster Analysis↗