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Biomedical subjects

Ying Xu

Publications and source records attributed to Ying Xu.

At least 73 records · Page 4Linked to original sources
PubMed2006

[Application of 16-slice spiral low-dose CT in the diagnosis of tracheobronchial stenosis and obstruction].

OBJECTIVE: To investigate the clinical values of 16-slice spiral low-dose CT (LDCT) in the diagnosis of the tracheobronchial stenosis and obstruction. METHODS: Both 16-slice spiral LDCT and fiberoptic bronchoscopy (FB) were used to examine the tracheobronchial stenosis and obstruction in 28 patients. With the FB findings as the gold standards, we calculated the sensitivity, specificity, and accuracy of 16-slice spiral LDCT in the diagnosis of the tracheobronchial stenosis and obstruction. RESULTS: The sensitivity, specificity, and accuracy of 16-slice spiral LDCT were 91.3%, 97.6%, and 97.9% in the diagnosis of stenosis and obstruction of central airways, and were 98.1%, 86.7% and 97.6% in the diagnosis of those conditions of segmental bronchi. Difference between 16-slice spiral LDCT and FB was not significant in diagnosing the central air ways (P = 0.257) , but was significant in diagnosing segmental bronchi (P = 0.035). Significant consistency existed between 16-slice spiral LDCT and FB in examining the normal structure, stenosis, and obstruction of tracheo-bronchi (P < 0.001). The consistency was good (Kappa = 0.846) for central airways and was moderate for segmental airways (Kappa = 0.694). CONCLUSION: 16-slice spiral LDCT can accurately detect the tracheobronchial stenosis and obstruction and therefore be a useful tool in clinical practice.

Adult↗
PubMed2006

[Study on the frequency of human papillomavirus type 6 and type 11 infection and L1 gene expression of the virus in biopsy samples of pointed condyloma patients].

OBJECTIVE: To determine the different rates of human papillomavirus types 6 (HPV-6) and 11 (HPV-11) infection in biopsy samples from pointed condyloma patients, and to construct prokaryotic expression system of the major capsid protein L1 of the virus so as to establish an ELISA for detecting the expression of L1 gene in the biopsy samples. METHODS: Using a double PCR based on the L1 gene of HPV-6 and HPV-11, the infection rates of HPV-6 and HPV-11 in the biopsy samples were determined. The whole length of HPV-6 L1 gene was amplified using PCR and the target amplification fragment was sequenced after T-A cloning. The prokaryotic expression system pET32a-L1-E. coli BL21 (DE3) was constructed and SDS-PAGE was used to measure the expression of the target recombinant protein rL1. Rabbit anti-rL1 serum was prepared and immuno-diffusion assay was applied to examine the antiserum titer. ELISA was established to detect the expression of L1 gene in the biopsy samples. RESULTS: In the biopsy samples from 116 pointed condyloma patients, 92.2% (107/116) were detectable for HPV-6 and/or HPV-11. Of the 107 positive samples, 70.1% (75/107) and 23.4% (25/107) were positive for HPV-6 or HPV-11 alone and 6.5% (7/107) were coinfected with both HPV-6 and HPV-11 respectively. When compared with the reported corresponding sequences, the homology of nucleotide and sequence of the cloned HPV-6 L1 gene was from 99.20% - 99.93% while its putative amino acid sequence homology was from 99.80% - 100%, suggesting IPTG could induce the expression of rL1. The immuno-diffusion titer of the rabbit anti-rL1 serum was 1:4. 88.8% (103/116) of the biopsy samples were the major capsid protein L1 detectable. CONCLUSION: A prokaryotic expression system of HPV-6 L1 gene, a double PCR assay for HPV-6 and HPV-11 genotyping, and an ELISA assay for detecting the major capsid protein L1 were successfully established in this study. The pointed condyloma patients in Zhejiang area mainly infected with HPV-6. The HPV in the focus frequently expressed major capsid protein L1.

Animals↗
PubMed2006

[Study on the environmental pollution of PCBs].

OBJECTIVE: To investigate the environmental pollution of PCBs from the place where the disused transformers were taken apart. METHODS: Take town F as the high exposed district for investigating and the town P which 100 kilometres is away from the town F as the low exposed district. At the same time, take town DXG which is 500 kilometres away from town F as the district for contrast. It was random and stated to extract samples of piped water, farmland rice and eggs. Then, the exceed-mark-quantity detecting methods were used to detect the PCBs and TEOs level in these samples. RESULTS: The content of PCBs in the samples was different except for piped water. Thediversity of the PCBs level in the hen's eggs was the most significant, duck's eggs took second place and farmland was the least. The order of PCBs level in the samples was: hen' s eggs > duck's eggs > farmland > rice > river water ( stream) > piped water. CONCLUSION: The content of PCBs in each sample from Town F was higher than town P and town DXG on different levels. So the industry of taking the disused transformer apart had caused pollution of local environment.

Animals↗
PubMed2006

[The expression of galectin-3 in nodular thyroid goitre].

OBJECTIVE: To investigate the expression of galectin-3 in benign and malignant thyroid nodules. METHODS: Galectin-3 expression was assayed with immunohistochemical and RT-PCR methods in thyroid specimens. RESULTS: The majority of the specimens of thyroid carcinomas expressed galectin-3 with immunohistochemical and RT-PCR methods (89.7% and 91.7%) and the expression was significantly in different histological types. Papillary and follicular thyroid malignancies showed high expression of galectin-3 (100% positive). Comparing the specimens of thyroid carcinomas with metastases and those without metastases, the expression of galectin-3 was significantly higher in the former than in the latter. Among 25 specimens of benign adenomas and 13 specimens of nodular hyperplasia, only 3 were weakly positive and other were negative. Neither 10 specimens of normal thyroid tissue nor 25 specimens of paracarcinomatous thyroid tissue expressed galectin-3. CONCLUSION: Galectin-3 may be used as a marker for differentiating benign and malignant thyroid nodules.

Adolescent↗
PubMed2006

[The emission mechanisms of two kinds of Tb complexes doped in PVK system].

Two kinds of new rare earth complexes Tb(p-MBA)3phen (sample I) and Tb(p-ClBA)3 phen (sample II) were synthesized, and photoluminescence (PL) and electroluminescence (EL) characteristics of the terbium complex and PVK blended system were investigated. As to the sample I , the emission of PVK was completely restrained in the EL spectra of the blended film; while in the PL spectra, obvious emission of PVK appeared besides the emission of Tb3+. But as to the sample II, only the green emission from Tb3+ can be observed in both PL and EL spectra of the doping system. So there are two processes that occur in sample I, one is the incomplete Förster energy transfer process from PVK to the Tb complex, and the other is the car rier charge trapping process. The main mechanism of sample II is the energy transfer process.

English Abstract↗
PubMed2006

[Protective effects of triptolide on the lipopolysaccharide-mediated degeneration of dopaminergic neurons in substantia nigra].

OBJECTIVE: To study the protective effects of triptolide (Tri) on the lipopolysaccharide (LPS)-mediated degeneration of dopaminergic neurons in substantia nigra. METHODS: Forty SD rats were randomly divided into four groups: the sham group, the LPS model group, the Tri group and the normal saline group, 10 in each group. Fourteen days later, the apomorphine-induced rotational behavior, the content of dopamine (DA) and its metabolites in the striatum of the injured side, the number of tyrosine-hydroxylase (TH) positive neurons and activation of microglia in rats were observed. RESULTS: Injection of LPS in substantia nigra could induce cerebral simulated immunoinflammatory reaction, leading to degeneration of dopaminergic neuron and induce ipsilateral directed rotational behavior of rats, which could be improved by Tri. Moreover, Tri could raise the lowered content of DA and its metabolites as well as the TH positive neurons in striatum, and suppress the activation of microglia significantly (P<0.01). CONCLUSION: Tri could protect the dopaminergic neurons from degeneration due to the inflammation mediated by LPS through inhibiting the activation of microglia.

Animals↗
PubMed2006

[Effects of PBD on the electroluminescence (EL) of Tb complex doped PVK system].

Electroluminescent (EL) properties of the terbium complex [Tb(m-MBA)3 phen]2 x 2H2O doped PVK system were investigated. Two kinds of devices with the structures of ITO/PVK: Tb complex/PBD/LiF/Al and ITO/PVK: Tb complex: PBD/PBD/LiF/Al were fabricated. PBD emission appears in the EL spectra of ITO/PVK: Tb complex/PBD/LiF/Al in comparison with ITO/PVK: Tb complex: PBD/PBD/LiF/Al. The reason is that PBD acts as a hole blocking material in the emitting layer (PVK: Tb complex: PBD) and thus the combination of excitons mostly occur within this layer. The energy of terbium complex emission comes from two different ways, namely energy transfer and direct combination of carriers. By altering the doping weight ratio of PBD, a set of devices were fabricated with the configuration of ITO/PVK: Tb complex: PBD/PBD/LiF/Al. Both the efficiency and brightness of these devices decrease with the rising of the PBD doping weight ratios. The efficiency of the carriers trapping may decrease with the rising of PBD doping ratios, for PBD may block the hoping of hole or electron between the PVK chains, causing a decrease in the brightness and efficiency. The PBD doping ratios have little effect on the efficiency of Förester energy transfer based on our synthesis.

English Abstract↗
PubMed2006

[High level expression of recombinant human sCD40L-IZ and identification of its biological activation].

AIM: To clone and express the recombinant human soluble CD40 ligand(CD40L) with biological activation. METHODS: The isoleucine zipper (IZ) gene was fused at N-terminal of CD40L gene coding E107-L261 contributing to form trimer. The gene coding hexahistidine was fused at the N-terminal of IZ because the sCD40L-IZ fusion protein could be purified by affinity chromatography. Then the fusion gene was amplified and cloned into expression plasmid pET30a. RESULTS: The protein sCD40L-IZ with His-tag at the N-terminal was effectively expressed in E. coli BL21 (DE3) as inclusion bodies and a denaturation and refolding procedure was performed to acquire soluble sCD40L-IZ. The fusion protein sCD40L-IZ was conveniently purified using HiTrap affinity column with above 95% purity. The gel filtration chromatography and non-reduced SDS-PAGE identified the trimeric structure of the recombinant protein. The microscope analysis showed the sCD40L-IZ interacted with the membrane CD40 on XG2, a multiple myeloma cell line. CONCLUSION: The recombinant human trimeric CD40L-IZ was expressed in prokaryotic cells successfully, which has provided a basis for further study of the relationship between CD40L and apoptosis, CD40L and pathogenesis of illness. It is also useful to clinical treatment.

Animals↗
PubMed2006

Fast de novo peptide sequencing and spectral alignment via tree decomposition.

De novo sequencing and spectral alignment are computationally important for the prediction of new protein peptides via tandem mass spectrometry (MS/MS). Both approaches are established upon the problem of finding the longest antisymmetric path on formulated graphs. The problem is of high computational complexity and the prediction accuracy is compromised when given spectra involve noisy data, missing mass peaks, or post translational modifications (PTMs) and mutations. This paper introduces a graphical mechanism to describe relationships among mass peaks that, through graph tree decomposition, yields linear and quadratic time algorithms for optimal de novo sequencing and spectral alignment respectively. Our test results show that, in addition to high efficiency, the new algorithms can achieve desired prediction accuracy on spectra containing noisy peaks and PTMs while allowing the presence of both b-ions and y-ions.

Algorithms↗
PubMed2006

A point-process model for rapid identification of post-translational modifications.

Post-translational modifications (PTMs) are very important to biological function, and yet are notoriously difficult to detect and identify, especially in a high-throughput manner. Most of the existing approaches rely on exhaustive searches which are highly time consuming and thus are currently limited to handling of a few types of PTMs. In this paper, we present a point-process model that aims to find the optimal mass shifts to maximize the spectra alignment between an experimental MS/MS spectrum and a candidate theoretical spectrum, through cross-correlation calculation, yields a rapid search for all types of PTMs in a blind mode, i.e., without giving the types of the searching PTMs in advance. The test results show that our new approach's performance is comparable to or better than the other blind search methods, but is more efficient computationally and simpler in its concept.

Algorithms↗
PubMed2005

Mapping of orthologous genes in the context of biological pathways: An application of integer programming.

Mapping biological pathways across microbial genomes is a highly important technique in functional studies of biological systems. Existing methods mainly rely on sequence-based orthologous gene mapping, which often leads to suboptimal mapping results because sequence-similarity information alone does not contain sufficient information for accurate identification of orthology relationship. Here we present an algorithm for pathway mapping across microbial genomes. The algorithm takes into account both sequence similarity and genomic structure information such as operons and regulons. One basic premise of our approach is that a microbial pathway could generally be decomposed into a few operons or regulons. We formulated the pathway-mapping problem to map genes across genomes to maximize their sequence similarity under the constraint that the mapped genes be grouped into a few operons, preferably coregulated in the target genome. We have developed an integer-programming algorithm for solving this constrained optimization problem and implemented the algorithm as a computer software program, p-map. We have tested p-map on a number of known homologous pathways. We conclude that using genomic structure information as constraints could greatly improve the pathway-mapping accuracy over methods that use sequence-similarity information alone.

Algorithms↗
PubMed2005

Structural genomics analysis of alternative splicing and application to isoform structure modeling.

Alternative splicing is a sophisticated nuclear process that regulates gene expression. It represents an important mechanism for enhancing the functional diversity of proteins. Our current knowledge of alternatively spliced variants is derived mainly from mRNA transcripts, and very little is known about their protein tertiary structures. We carried out a large-scale analysis of known alternatively spliced variants at both protein sequence and structure levels and have shown that threading is, in general, a viable approach for modeling structures of alternatively spliced variants. An examination of alternative splicing at the protein sequence level revealed that the size of splicing events follows the power law distribution and the majority of splicing isoforms harbor only one or two alternations. We examined alternative splicing in the context of protein 3D structures and found that the boundaries of alternative splicing events generally happen in coil regions of secondary structures and exposed residues and the majority of the sequences involved in splicing are located on the surface of proteins. In light of these findings, we then proceeded to demonstrate that threading represents a useful tool for structure prediction of alternative splicing isoforms and addressed the fold stability issue of threading-based structure prediction by molecular dynamics simulation. Our analysis and the insights gained have helped to establish a viable method for structure prediction of alternatively spliced isoforms at the genome scale.

Alternative Splicing↗
PubMed2005

Reproductive effects of prenatal exposure to nonylphenol on zebrafish (Danio rerio).

Mature female and male zebrafish were separated and exposed to nonylphenol (NP) at 0.1, 1, 10, 50, 100 and 500 microg/L, respectively, for 3 weeks. Gonadosomatic index (GSI) in both sexes and vitellogenin (VTG) induction in males was measured as the bioindicators for the impairment to the parents. The results indicated that 50 microg/L of NP was the non-observed effect concentration (NOEC) for GSI and VTG induction. Afterwards, the 50 microg/L NP exposed females and males, and the control females and males were cross-wise pair-bred in the control water for one week to examine the reproductive effects. The embryonic cathepsin D (CAT D) activity, eggshell thickness, fecundity, hatching rate and malformation (vertebral column flexure) rate of offspring were determined in the four pair-bred groups. While endpoints remained unchanged in the groups with exposed males, prenatal exposure of females to 50 microg/L of NP resulted in the impairment of reproduction in groups with exposed females including inhibition of CAT D activity (P < 0.05), decrease of eggshell thickness (by 23.6%) and elevation of malformation rate (P < 0.001). These results suggested NP could induce reproductive damage to zebrafish at NOEC for parents. The results also imply that alterations of CAT D activity and eggshell thickness may be more sensitive biomarkers to indicate the reproductive effects caused by endocrine disrupting chemicals.

Abnormalities, Drug-Induced↗
PubMed2005

libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

SUMMARY: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES, to facilitate a fast implementation of computer software for study of non-linear biochemical pathways. This library implements a (mu, lambda)-ES evolutionary optimization algorithm that uses stochastic ranking as the constraint handling technique. Considering the amount of computing time it might require to solve a parameter-estimation problem, an MPI version of libSRES is provided for parallel implementation, as well as a simple user interface. libSRES is freely available and could be used directly in any C program as a library function. We have extensively tested the performance of libSRES on various pathway parameter-estimation problems and found its performance to be satisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/

Algorithms↗
PubMed2005

The evolution of microbial phosphonate degradative pathways.

Phosphonate utilization by microbes provides a potential source of phosphorus for their growth. Homologous genes for both C-P lyase and phosphonatase degradative pathways are distributed in distantly related bacterial species. The phn gene clusters for the C-P lyase pathway show great structural and compositional variation among organisms, but all contain phnG-phnM genes that are essential for C-P bond cleavage. In the gamma-proteobacterium Erwinia carotovora, genes common to phosphonate biosyntheses were found in neighboring positions of those for the C-P lyase degradative pathway and in the same transcriptional direction. A gene encoding a hypothetical protein DUF1045 was found predominantly associated with the phn gene cluster and was predicted functionally related to C-P bond cleavage. Genes for phosphonate degradation are frequently located in close proximity of genes encoding transposases or other mobile elements. Phylogenetic analyses suggest that both degradative pathways have been subject to extensive lateral gene transfers during their evolution. The implications of plasmids and transposition in the evolution of phosphonate degradation are also discussed.

Bacteria↗
PubMed2005

[Analgesic effect of intrathecal transplant of immortalized rat astrocyte strain genetically modified by human preproenkephalin gene on rat chronic neuropathic pain].

OBJECTIVE: To observe the analgesic effect of intrathecal transplant of immortalized rat astrocyte genetically modified by human preproenkephalin gene (IAST/hPPE) on chronic neuropathic pain. METHODS: 40 adult male Sprague-Dawley rats were randomly divided into four groups, 10 rats for each group. Naive group, SNI group, SNI + IAST group and SNI + IAST/hPPE group. The immortalized rat astrocyte (IAST) or IAST/hPPE co-incubated with bromodeoxyuridine (BrdU) in vitro were transplanted in the lumbar 4 to 6 subarachnoid space near the spinal cord 1 week after right side spared nerve injury (SNI). All animals were tested for bilateral 50% hindpaw withdrawal threshold (PWT) to a graded series of Von Frey hairs stimulation once a week from one week before SNI to six weeks after transplant, the difference value for right 50% PWT minus left 50% PWT was calculated and the effect of intraperitoneal naloxone on the analgesic efficacies was also observed. The content of L-EK in the spinal cord of L4 - 6 and was determined using immunohistochemistry and radioimmunoassay, and the expression of BrdU in grafts was determined using immunohistochemistry. RESULTS: Allodynia-like behaviour after 1 week following SNI was observed. As compared with Naive group, the difference value for the right 50% PWT minus left 50% PWT in the other three groups was higher significantly (P < 0.01). The tactile allodynia induced by SNI was significantly alleviated during the 1 to 6 week period after transplantation of IAST/hPPE cells, but transplants of IAST cells had no effect on the allodynia-like behaviour. The difference value for the right 50% PWT minus left 50% PWT in SNI + IAST/hPPE group was lower significantly than that in the SNI and SNI +I AST group (P < 0.01), but there was no significant difference between SNI and SNI + IAST group (P > 0.05). The efficacies were reversed by intraperitoneal naloxone in SNI + IAST/hPPE group. The content of L-EK in the lumbar spinal cord in IAST/hPPE group (108.1 pg/mg +/- 12.5 pg/mg) was significantly higher than that in other three groups (P < 0.01), but there was no significant difference between SNI and SNI + IAST group (25.4 pg/mg +/- 1.9 pg/mg vs 28.0 pg/mg +/- 2.1 pg/mg, P > 0.05). Furthermore, The grafts in the surface of dorsal horn were still stained positively for BrdU, they survived greater than 6 weeks on the pia mater around the spinal cord. CONCLUSION: Intrathecal transplant of IAST/hPPE cells could alleviate the allodynia-like behaviour after chronic neuropathic pain, which is associated with enkephalin secreted continuously from the grafts and conducted via opiate receptors.

Animals↗