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Biomedical subjects

Jun Wang

Publications and source records attributed to Jun Wang.

At least 91 records · Page 5Linked to original sources
PubMed2006

MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution.

BACKGROUND: Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non-coding DNA depends on how well we are able to align non-coding DNA sequences. However, the alignment of non-coding DNA sequences is more difficult than aligning protein-coding sequences. RESULTS: Here we present an improved pair-hidden-Markov-Model (pair HMM) based method for performing global pairwise alignment of non-coding DNA sequences. The method uses an explicit model of indel length frequency distribution which can be specified, and allows any time reversible model of nucleotide substitution. The method uses a deterministic global optimiser to find the alignment with the highest posterior probability. We test MCALIGN2 in simulations, and compare it to a previous Monte Carlo based method (MCALIGN), to the pair HMM method of Knudsen and Miyamoto, and to a heuristic method (AVID) that performed very well in a previous simulation study. We show that the pair HMM methods have excellent performance for all combinations of parameter values we have considered. MCALIGN2 is up to ten times faster than MCALIGN. MCALIGN2 is more accurate in resolving indels given an accurate explicit model than heuristic methods, but is computationally slower. CONCLUSION: MCALIGN2 produces better quality alignments by explicitly using biological knowledge about the indel length distribution and time reversible models of nucleotide substitution. As a result, it can outperform other available sequence alignment methods for the cases we have considered to align non-coding DNA sequences.

Algorithms↗
PubMed2006

Neuronal SIRT1 activation as a novel mechanism underlying the prevention of Alzheimer disease amyloid neuropathology by calorie restriction.

Nicotinamide adenine dinucleotide (NAD)+-dependent sirtuins have been identified to be key regulators in the lifespan extending effects of calorie restriction (CR) in a number of species. In this study we report for the first time that promotion of the NAD+-dependent sirtuin, SIRT1-mediated deacetylase activity, may be a mechanism by which CR influences Alzheimer disease (AD)-type amyloid neuropathology. Most importantly, we report that the predicted attenuation of beta-amyloid content in the brain during CR can be reproduced in mouse neurons in vitro by manipulating cellular SIRT1 expression/activity through mechanisms involving the regulation of the serine/threonine Rho kinase ROCK1, known in part for its role in the inhibition of the non-amyloidogenic alpha-secretase processing of the amyloid precursor protein. Conversely, we found that the expression of constitutively active ROCK1 in vitro cultures significantly prevented SIRT1-mediated response, suggesting that alpha-secretase activity is required for SIRT1-mediated prevention of AD-type amyloid neuropathology. Consistently we found that the expression of exogenous human (h) SIRT1 in the brain of hSIRT1 transgenics also resulted in decreased ROCK1 expression and elevated alpha-secretase activity in vivo. These results demonstrate for the first time a role for SIRT1 activation in the brain as a novel mechanism through which CR may influence AD amyloid neuropathology. The study provides a potentially novel pharmacological strategy for AD prevention and/or treatment.

Alzheimer Disease↗
PubMed2006

RETRACTED: Investigation on photocatalytic degradation of ethyl violet dyestuff using visible light in the presence of ordinary rutile TiO2 catalyst doped with upconversion luminescence agent.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief. After careful investigations the editors have found that information in the paper is not reliable. Figure 4 appears similar to Figure 2 from another publication of the same authors in Dyes and Pigments 75 (2007) 335-343 https://doi.org/10.1016/j.dyepig.2006.06.007 which it is not describing the particles discussed in this Water Research paper. Although this article was published earlier than the Dyes and Pigments article, the Editor decided to retract this article given concerns about the reliability of the data.

Catalysis↗
PubMed2006

Platensimycin is a selective FabF inhibitor with potent antibiotic properties.

Bacterial infection remains a serious threat to human lives because of emerging resistance to existing antibiotics. Although the scientific community has avidly pursued the discovery of new antibiotics that interact with new targets, these efforts have met with limited success since the early 1960s. Here we report the discovery of platensimycin, a previously unknown class of antibiotics produced by Streptomyces platensis. Platensimycin demonstrates strong, broad-spectrum Gram-positive antibacterial activity by selectively inhibiting cellular lipid biosynthesis. We show that this anti-bacterial effect is exerted through the selective targeting of beta-ketoacyl-(acyl-carrier-protein (ACP)) synthase I/II (FabF/B) in the synthetic pathway of fatty acids. Direct binding assays show that platensimycin interacts specifically with the acyl-enzyme intermediate of the target protein, and X-ray crystallographic studies reveal that a specific conformational change that occurs on acylation must take place before the inhibitor can bind. Treatment with platensimycin eradicates Staphylococcus aureus infection in mice. Because of its unique mode of action, platensimycin shows no cross-resistance to other key antibiotic-resistant strains tested, including methicillin-resistant S. aureus, vancomycin-intermediate S. aureus and vancomycin-resistant enterococci. Platensimycin is the most potent inhibitor reported for the FabF/B condensing enzymes, and is the only inhibitor of these targets that shows broad-spectrum activity, in vivo efficacy and no observed toxicity.

3-Oxoacyl-(Acyl-Carrier-Protein) Synthase↗
PubMed2006

A rat model of bone cancer pain induced by intra-tibia inoculation of Walker 256 mammary gland carcinoma cells.

This study described a modified rat model of bone cancer pain. Syngeneic Walker 256 mammary gland carcinoma cells were injected into the tibia medullary cavity via intercondylar eminence. Series of tests were carried out including bone radiology, bone histology, ambulatory pain, thermal hyperalgesia, mechanical allodynia, weight bearing ability, and electrophysiological recording from primary afferent fibers. The rats inoculated with carcinoma cells showed significant ambulatory pain, mechanical allodynia, and reduction in weight bearing, as well as increased incidence of spontaneous activity in Abeta fibers in affected limb, whereas PBS (vehicle) or heat-killed cells (sham) injected rats showed no significant difference in comparison to normal rats. The pain hypersensitive behaviors were aggravated with time and destruction of bone. Interestingly, mechanical allodynia was also observed in the contralateral limb, indicating the involvement of 'mirror image' pain in bone cancer pain. In summary, the present study provided a useful and easily established rat model of bone cancer pain which will contribute to further study of the mechanisms underlying cancer pain.

Action Potentials↗
PubMed2006

Investigation on the sonocatalytic degradation of parathion in the presence of nanometer rutile titanium dioxide (TiO2) catalyst.

The nanometer rutile titanium dioxide (TiO2) powder was adopted to act as the sonocatalyst after treatment of high-temperature activation and the ultrasound of low power was used as an irradiation source to induce heat-treated TiO2 powder performing sonocatalytic degradation of parathion. Although there are many factors influencing sonocatalytic degradation of parathion, the experimental results demonstrate that the optimal degradation condition of parathion can be obtained when the experimental conditions such as initial concentration of 50 mg/L parathion, addition amount of 1000 mg/L nanometer rutile TiO2, ultrasonic of 30-50 kHz frequency and 50 W output power, acidity of pH 10.0 and temperature of 20 degrees C are adopted. The degradation ratio of parathion surpassed 90% within 120 min ultrasonic irradiation in these optimal experiment conditions. The total degradation process of parathion has been monitored by UV-vis spectra and ion chromatography. At last, the parathions in aqueous solution are completely degraded and become some simple inorganic ions such as NO3(-), PO4(3-), SO4(2-), etc. In addition, the sonocatalytic activities of reused TiO2 catalysts were also studied and found to decline gradually along with the reused times. In this paper, the research on sonocatalytic degradation kinetics was also been performed and found to follow pseudo first-order reaction. All experiments indicated that the sonocatalytic method in the presence of nanometer rutile TiO2 powder was an advisable choice for the treatments of non- or low-transparent organic wastewaters in future.

Catalysis↗
PubMed2006

The expression of monocyte chemoattractant protein-1 and C-C chemokine receptor 2 in post-kidney transplant patients and the influence of simvastatin treatment.

BACKGROUND: Inflammation is involved in the pathogenesis of chronic allograft nephropathy (CAN) and cardiovascular disease (CVD) in post-kidney transplantation. METHODS: Sixty patients, selected from 167 renal transplant patients, were divided into 2 groups: Group A (normal lipidemia group, n=30) and Group B (hyperlipidemia group, n=30). In addition, Control Group came from 30 healthy volunteers. In Group B, the patients were treated with simvastatin for 3 months. The mRNA expressions of MCP-1 and CCR2 were detected with reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: The mRNA expressions of MCP-1 and CCR2 of all post-kidney transplant patients were significantly higher than controls. Compare Group A with Group B and the mRNA expressions of MCP-1 and CCR2 in Group B were much higher than Group A. After simvastatin treatment, the mRNA expressions of MCP-1 and CCR2 were significantly reduced in one and a half months and decreased to the lowest levels in three months. CONCLUSIONS: Simvastatin decreased the expressions of MCP-1 and CCR2 in post-kidney transplant patients with hyperlipidemia.

Adult↗
PubMed2006

Depression of MAD2 inhibits apoptosis of gastric cancer cells by upregulating Bcl-2 and interfering mitochondrion pathway.

Mitotic arrest deficient 2 (MAD2) is an essential component of the mitotic spindle checkpoint pathway. It was previously shown to be associated with drug resistance of tumor cells. To further explore the roles of MAD2 in responses of gastric cancer cells to chemotherapy drugs, we constructed the siRNA vectors of MAD2 and transfected them into gastric cancer SGC7901 cells to inhibit expression of MAD2. MTT assay showed that the downregulation of MAD2 increased the resistance of SGC7901 cells to spindle inhibitors and DNA damaging agents. The apoptosis rates of gastric cancer cells transfected with MAD2-siRNA were 10.7% and 10%, respectively, after treated by 1.0microg/ml VCR and cisplatin. In contrast, the apoptosis rates of SGC7901 and SGC7901/psilencer3.1 induced by VCR were 43.2%, 38.7%; and that induced by cispaltin were 34.1%, 31.4%. The ratio of Bcl-2 to Bax was much higher in the MAD2-siRNA transfectants compared with the SGC7901/psilencer. In SGC7901/psilencer, cytochrome c and cleaved caspase 3 protein levels increased along with the exposure time increased. However, these protein levels of SGC7901/MAD2-siRNA had no changes during the drug treatment. These results indicate that down regulation of MAD2 could promote the drug resistance of gastric cancer cells and inhibit anticancer drugs induced-apoptosis by upregulating Bcl-2 and interfering the mitochondrion apoptosis pathway.

Antineoplastic Agents↗
PubMed2006

The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes.

The complete sequence of the 16,539 nucleotide mitochondrial genome from the single species of the catfish family Cranoglanididae, the helmet catfish Cranoglanis bouderius, was determined using the long and accurate polymerase chain reaction (LA PCR) method. The nucleotide sequences of C. bouderius mitochondrial DNA have been compared with those of three other catfish species in the same order. The contents of the C. bouderius mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region, the gene order of which is identical to that observed in most other vertebrates. Phylogenetic analyses for 13 otophysan fishes were performed using Bayesian method based on the concatenated mtDNA protein-coding gene sequence and the individual protein-coding gene sequence data set. The competing otophysan topologies were then tested by using the approximately unbiased test, the Kishino-Hasegawa test, and the Shimodaira-Hasegawa test. The results show that the grouping ((((Characiformes, Gymnotiformes), Siluriformes), Cypriniformes), outgroup) is the most likely but there is no significant difference between this one and the other alternative hypotheses. In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed.

Animals↗
PubMed2006

Physiochemical pathway for cyclic dehydrogenation and rehydrogenation of LiAlH4.

A five-step physiochemical pathway for the cyclic dehydrogenation and rehydrogenation of LiAlH4 from Li3AlH6, LiH, and Al was developed. The LiAlH4 produced by this physiochemical route exhibited excellent dehydrogenation kinetics in the 80-100 degrees C range, providing about 4 wt % hydrogen. The decomposed LiAlH4 was also fully rehydrogenated through the physiochemical pathway using tetrahydrofuran (THF). The enthalpy change associated with the formation of a LiAlH4.4THF adduct in THF played the essential role in fostering this rehydrogenation from the Li3AlH6, LiH, and Al dehydrogenation products. The kinetics of rehydrogenation was also significantly improved by adding Ti as a catalyst and by mechanochemical treatment, with the decomposition products readily converting into LiAlH4 at ambient temperature and pressures of 4.5-97.5 bar.

Journal Article↗
PubMed2006

The DNA sequence, annotation and analysis of human chromosome 3.

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

Animals↗
PubMed2006

Antisense angiopoietin-1 inhibits tumorigenesis and angiogenesis of gastric cancer.

AIM: To investigate the effect of angiopoietin-1 (Ang-1) on biological behaviors in vitro and tumorigenesis and angiogenesis in vitro of human gastric cancer cells. METHODS: Human full-length Ang-1 gene was cloned from human placental tissues by RT-PCR method. Recombinant human Ang-1 antisense eukaryotic expression vector was constructed by directional cloning, and transfected by lipofectin method into human gastric cancer line SGC7901 with high Ang-1 expression level. Inhibition efficiency was confirmed by semi- quantitative PCR and Western blot method. Cell growth curve and cell cycle were observed with MTT assays and flow cytometry, respectively. Nude mice tumorigenicity test was employed to compare in vitro tumorigenesis of cells with Ang-1 suppression. Microvessel density (MVD) of implanted tumor tissues was analyzed by immunohistochemistry for factor VIII staining. RESULTS: Full-length Ang-1 gene was successfully cloned and stable transfectants were established, namely 7Ang1- for antisenseìand 7901P for empty vector transfected. 7Ang1- cells showed down-regulated Ang-1 expression, while its in vitro proliferation and cell cycle distribution were not significantly changed. In contrast, xenograft of 7Ang1- cells in nude mice had lower volume and weight than those of 7901P after 30 days' implantation (P<0.01, 293.00+/-95.54 mg vs. 624.00+/-77.78 mg) accompanied with less vessel formation with MVD 6.00+/-1.73 compared to 7901P group 8.44+/-1.33 (P<0.01). CONCLUSION: Ang-1 may play an important role in tumorigenesis and angiogenesis of gastric cancer, and targeting its expression may be beneficial for the therapy of gastric cancer.

Angiopoietin-1↗
PubMed2006

A ketogenic diet as a potential novel therapeutic intervention in amyotrophic lateral sclerosis.

BACKGROUND: The cause of neuronal death in amyotrophic lateral sclerosis (ALS) is uncertain but mitochondrial dysfunction may play an important role. Ketones promote mitochondrial energy production and membrane stabilization. RESULTS: SOD1-G93A transgenic ALS mice were fed a ketogenic diet (KD) based on known formulations for humans. Motor performance, longevity, and motor neuron counts were measured in treated and disease controls. Because mitochondrial dysfunction plays a central role in neuronal cell death in ALS, we also studied the effect that the principal ketone body, D-beta-3 hydroxybutyrate (DBH), has on mitochondrial ATP generation and neuroprotection. Blood ketones were > 3.5 times higher in KD fed animals compared to controls. KD fed mice lost 50% of baseline motor performance 25 days later than disease controls. KD animals weighed 4.6 g more than disease control animals at study endpoint; the interaction between diet and change in weight was significant (p = 0.047). In spinal cord sections obtained at the study endpoint, there were more motor neurons in KD fed animals (p = 0.030). DBH prevented rotenone mediated inhibition of mitochondrial complex I but not malonate inhibition of complex II. Rotenone neurotoxicity in SMI-32 immunopositive motor neurons was also inhibited by DBH. CONCLUSION: This is the first study showing that diet, specifically a KD, alters the progression of the clinical and biological manifestations of the G93A SOD1 transgenic mouse model of ALS. These effects may be due to the ability of ketone bodies to promote ATP synthesis and bypass inhibition of complex I in the mitochondrial respiratory chain.

Amyotrophic Lateral Sclerosis↗
PubMed2006

Folding with downhill behavior and low cooperativity of proteins.

The downhill folding observed experimentally for a small protein BBL is studied using off-lattice Gō-like model. Our simulations show that the downhill folding has low cooperativity and is barrierless, which is consistent with the experimental findings. As an example of comparison in detail, the two-state folding behavior of proteins, for example, protein CI2, is also simulated. By observing the formation of contacts between the residues for these two proteins, it is found that the physical origin of the downhill folding is due to the deficiency of nonlocal contacts which determine the folding cooperatively. From a statistics on contacts of the native structures of 17 well-studied proteins and the calculation of their cooperativity factors kappa2 based on folding simulations, a strong correlation between the number of nonlocal contacts per residue NN and the factors kappa2 is obtained. Protein BBL with a value of NN = 0.73 has the lowest cooperativity factor kappa2 = 0.34 among all 17 proteins. A crossover around NNc approximately 0.9 could be defined to separate the two-state folders and the downhill folder roughly. A protein would behave downhill folding when its NN = NNc. For proteins with their NN values are about (or slightly larger than) NNc, the folding behaves with low cooperativity and the barriers are small, showing a weak two-state behavior or a downhill-like behavior. Furthermore, simulations on mutants of a two-state folder show that a mutant becomes a downhill folder when its NN is reduced to a value smaller than NNc. These could enable us to identify the downhill folding or the cooperative two-state folding behavior solely from the native structures of proteins.

Biophysical Phenomena↗
PubMed2006

[Effects of injecting urokinase via carotid artery in treatment of cerebral venous sinus thrombosis: an experiment with rabbit models].

OBJECTIVE: To study the effects of injection of urokinase via carotid artery in treatment of cerebral venous sinus thrombosis. METHODS: Thirty-nine New Zealand white rabbits were made into models of cerebral venous sinus thrombosis with the superior sagittal sinus ligated and injected with suspension of cephalin kaolin and cephalin, and then were randomly divided into three groups: control group (n = 15), anticoagulation group (n = 12, infused with heparin 2 mgxkg(-1)xd(-1) via external carotid venous for 5 days), and thrombolysis group (n = 12, injected with urokinase 4000 Uxkg(-1)xd(-1) via carotid artery for 5 days). Laser Doppler scanning was used to determine the local cerebral blood flow before ligation, 20 and 90 min after ligation, and at the end of experiment. Five rabbits of the control group per each of the 3 time points (before ligation, 12 h after ligation, and at the end of experiment) were killed to collect the tissues of cerebral cortex in front of the ligated part to determine the brain water content. All the remaining rabbits were killed within 24 hours after the end of experiment to determine the brain water content and undergo microscopy. RESULTS: The local cerebral blood flow of the thrombolysis group was 94.8% +/- 0.3%, significantly higher than those of the anticoagulation group (88.6% +/- 0.3%) and control group (80.9% +/- 0.3%) (both P < 0.01). The brain water content of the thrombolysis group was 78.9% +/- 0.3%, significantly lower than those of the anticoagulation group (81.8% +/- 0.7%) and control group (82.1% +/- 1.0%) (both P < 0.05). CONCLUSION: Improving the local blood flow and reducing the brain water content, injection of urokinase via carotid artery is effective in treatment of cerebral venous sinus thrombosis.

Animals↗
PubMed2006

Dispersion of SiO2-based nanocomposites with high performance liquid chromatography.

Core-shell structured Ag/SiO2 nanocomposite has been synthesized by a cyclohexane/Igepal/water reverse micelle system. The spherical nanocomposite particles were washed and concentrated with high performance liquid chromatography (HPLC) to remove the surfactant added during synthesis. Spherical SiO2 micrometer-scale particles were packed in the HPLC column as a stationary phase for the washing and dispersing of Ag/SiO2 nanocomposite particles. Surface modification of Ag/SiO2 nanocomposite particles and SiO2 microspheres with silane coupling agent enhanced the surface charge of the particles and improved the efficiency of washing with HPLC. Well-dispersed Ag/SiO2 stable suspensions were successfully attained in ethanol/water mixed solvents after HPLC washing. The state of dispersion for the Ag/SiO2 nanocomposite suspension was systematically assessed using dynamic light scattering (DLS) and transmission electron microscope (TEM) and spin coat/atomic force microscope (AFM) analyses. The mechanism of the enabling HPLC washing protocol for SiO2-based nanoparticles is discussed.

Journal Article↗
PubMed2006

[Preliminary screening and identification of a peptide that binds specifically to gastric cancers cells with high metastasis to peritoneum].

OBJECTIVE: To screen and identify peptides that binds specifically to gastric cancers cells with high metastasis to peritoneum so as to find appropriate vectors for targeting therapy for cancer. METHODS: Human gastric cancer cells of the line GC9811 and those with high metastasis to peritoneum of the line GC9811-P were co-incubated with the 12-mer bacteriophage random peptide library. After 3 round of repeated screening, phage clones were collected. Forty internalized phage single-stranded DNA that specifically binding to the GC98112-P cells were sequenced. GC9811 and GC9811-P cells were co-inoculated with 5 peptides with the N end marked with fluorescein isothiocyanate (FITC) and 1 un-related peptide not binding to GC9811 and GC9811-P cells. Fluorescence microscopy, ELISA, and flow cytometry were used to detect the binding activity. BALB/cnu/nu mice were inoculated intraperitoneally with GC9811 and GC9811-P cells and then randomly divided into. 2 equal groups: experimental group, inoculated with the peptide PIII-FITC and control group (inoculated with un-related peptide PC-FITC. Forty-eight hours later the mice were killed and the peritoneum and tumor masses in different organs were collected and under fluorescence microscopy. RESULTS: DNA sequencing showed that 45% (18/45) of the isolated phages displayed repeated sequence SMSIASPYIALE, and SMSI was defined as a conservative motif. Obvious fluorescence was seen in the GC9811-P cells co-incubated with PIII-FITC and weak fluorescence was seen in the GC9811 cells co-incubated with PIII-FITC. Un-marked un-related peptide PC and PIII-FITC did not influenced the fluorescence staining of the GC9811-P cells, however, no fluorescence could be seen in the GC9811-P cells co-incubated with un-marked PIII and PIII-FITC. The fluorescence positive cell rate was 5.9% in the GC9811 cells co-incubated with PIII-FITC, and was 90.2% in the GC9811-P cells co-incubated with PIII-FITC. The fluorescence positive cell rates of the GC9811 cells and GC9811-P cells co-incubated with PC-FITC were 10.1% and 9.9% respectively 10.1% and 9.9% respectively. The fluorescence strength of the GC9811-P cells co-incubated with PIII-FITC was significantly greater than that of the GC9811-P cells co-incubated with PC-FTIC at any time-point and dose (all P < 0.01), and increased along with the increase of co-incubation time and dose of PIII-FITC. The peritoneal tumor tissues caused by the GC9811-P cells of the mice showed strong fluorescence and those caused by GC9811 cells only showed very weak fluorescence. Weak fluorescence could be seen in the tumor masses in the lymph nodes, liver, and muscle of the mice inoculated with GC9811-P cells and was not seen in the tissues of the mice inoculated with GC9811 cells. CONCLUSION: The sequence SMSIASPYIALE that specifically binds to human gastric cancer cells with high metastasis has been screened that has the potential to be used as a marker and targeting vector in diagnosis and treatment of gastric cancer.

Amino Acid Sequence↗