Biomedical subjects

Wenbin Liu

Publications and source records attributed to Wenbin Liu.

At least 19 recordsLinked to original sources

PubMed2025

Streptomyces huangiella sp. nov., an endophytic actinomycete isolated from Pheretima aspergillum, a promising candidate for biological pathogen control.

UNLABELLED: Pheretima aspergillum (E. Perrier) is an annelid of the genus Pheretima in the family Megascolecidae, a species of earthworm, whose dried body (Guang Dilong) is a traditional Chinese animal medicine. A new actinobacterium strain, named HD1123-B1T, was isolated from the gut contents of Pheretima aspergillum caught in the wild in Guangzhou, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was primarily identified as a member of the genus Streptomyces, sharing more than 98% sequence identity to Streptomyces endocoffeicus CA3R110T (98.80%), Streptomyces coffeae CA1R205T (98.47%), and Streptomyces iranensis HM35T (97.93%). The whole genome size of strain HD1123-B1T was approximately 8.9 Mbp, with 7,464 predicted genes and 71.42 mol% DNA C+G content. Comparative genomic analyses based on digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values revealed that strain HD1123-B1T represents a novel species within the genus Streptomyces. Additionally, 38 biosynthetic gene clusters for secondary metabolites were also predicted in the genome of strain HD1123-B1T. Based on LC-MS/MS analysis, the nigericin biosynthesis gene cluster has been completely characterized. The ethyl acetate crude extract of strain HD1123-B1T exhibited remarkable antibacterial activity against gram-positive bacteria (methicillin-resistant Staphylococcus aureus ATCC 25213, etc) and gram-negative bacteria Ralstonia solanacearum GIM 1.70. Based on these results, HD1123-B1T could be confirmed as an isolate that represents a novel species of the genus Streptomyces, for which the name Streptomyces huangiella sp. nov. is proposed. IMPORTANCE: As the largest genus of the phylum Actinomycetes, Streptomyces is a kind of microbial resources with great practical and economic value. Due to their unique physiological properties and metabolic capacity, Streptomyces have become an important source of bioactive compounds in the world and play an indispensable role in medical and industrial fields. With the advancement of molecular biology and genomics, researchers can more deeply explore the metabolic potential of Actinomycetes, discovering and developing new biologically active compounds. These new compounds may possess various biological activities, such as antibacterial, antiviral, antifungal, and antiparasitic properties, further promoting the development of medicine and related industries. Based on genomic analysis and antibacterial activity, the strain HD1123-B1T was indicated to be a promising candidate for biological pathogen control.

Streptomyces↗

PubMed2006

Gene expression profiling in embryonic mouse lenses.

PURPOSE: In this study, we used laser capture microdissection (LCM) and microarray hybridization technology to compare the gene expression profiles of mouse embryonic days 10 and 12 lenses (E10 and E12). METHODS: Lens cells of C57/BL6 mouse embryos at E10 and E12 were harvested using the PixCell II LCM System. Total RNA was extracted, amplified, labeled, and hybridized to the 430 2.0 mouse chip (Affymetrix) according to the manufacturer's instructions. Data extracted from the images were analyzed using different software programs. Regulated expression of selected genes was confirmed by real-time PCR (RT-PCR). RESULTS: Analysis of the microarray data from E10 and E12 lenses identified 1,573 genes that showed a two fold or greater change in expression level. Among these 1,573 genes, 956 genes were downregulated and 617 were upregulated in E12 lenses. In addition to the upregulated expression of beta- and gamma-crystallin genes, genes that regulate the cell cycle showed significant changes of gene expression during the E10 (lens pit) to E12 (primary fiber cell induction) time period. Genes involved in insulin-like growth factor (IGF) signaling and Wnt (a family of secreted glycoproteins related to the Drosophila segment polarity gene, wingless, and to the proto-oncogene, int-1) signaling were also differentially regulated. In particular, positive regulators of Wnt signaling were downregulated and negative regulators were upregulated, indicating that modulation of Wnt signaling is important for normal lens morphogenesis. CONCLUSIONS: Our results provide new information about differential regulation of gene expression during early lens development. Analysis of global gene expression profiles in embryonic mouse lenses has allowed us to identify several molecular pathways that are differentially regulated during early lens development.

Animals↗

PubMed2006

Structure of an accurate ab initio model of the aqueous Cl- ion at high temperatures.

The structure of an accurate ab initio model of aqueous chloride ion was calculated at two high-temperature state points (573 K, 0.725 g/cm(3) and 723 K, 0.0098 g/cm(3)) by a two-step procedure. First, the structure of an approximate model was calculated from a molecular dynamics simulation of the model. Then the difference between the structure of the ab initio model and the approximate model was calculated by non-Boltzmann weighting of a sample of configurations taken from the approximate model simulation. Radial distribution functions, average coordination numbers, the distribution of coordination numbers, an analysis of orientations of water in the first coordination shell, and the free energy of hydration of the chloride ion are reported for both state points. The most common water structure has one hydrogen close to the chloride ion and one pointing away (46% at 573 K and 57% at 723 K). Waters in the first coordination shell that are not strongly bound to the chloride ions are common. Several variations of the method were tested. Models in which the water-water interaction is calculated with ab initio methods predict only a slightly different structure than models in which water-water interactions are determined from the approximate models. Similarly, using the approximate model for solute-water interactions when the water is far from the chloride ion did not affect the results. Uncertainties due to the limited sample of configurations are estimated and found to be small. The results are in qualitative agreement with X-ray and neutron diffraction experiments and with simulations of approximate models.

Journal Article↗

PubMed2006

Evidence for the transfer of polychlorinated biphenyls, polychlorinated dibenzo-p-dioxins, and polychlorinated dibenzofurans from soil into biota.

The concentrations of six indicator and co-planar polychlorinated biphenyls (PCBs), 17 polychlorinated dibenzo-p-dioxins, and polychlorinated dibenzofurans (PCDD/Fs) were determined in soil and associated biota samples collected from a polluted and wasted farmland in southern China. The sum of six indicator PCBs (Nos 28, 52, 101, 138, 153 and 180) concentrations in biota samples were proportional to the total amount of PCBs that transferred from soil to the corresponding biota samples, and the sum six indicator PCB congeners in samples were about 20% of the total PCBs, respectively. The ratios of the sum six indicator PCBs and the total PCBs in samples collected in the same area were approximately equal. The sums of six indicator PCBs were proportional to the total PCBs that transferred from soil to plant, while the co-planar PCBs were not. Analysis of individual PCB and PCDD/F congener signatures in soil revealed the original pollutant source after transportation and biodegradation for 14 years using principal component analysis (PCA). The pattern of PCBs in soils and plants could reflect the original pollution source after transportation and biodegradation for 14 years, while the pattern of PCBs in the terrestrial animals could not reflect the primary source. The consumption foods in this region such as foraging chicken eggs, foraging duck eggs, and loach (Misgurnus anguillicaudatus) were highly contaminated, the total toxicity equivalent (TEQ) was up to 784 pg WHO-TEQ/g on basis lipid in foraging chicken eggs.

Animals↗

PubMed2006

Determination and assessment of HCHs and DDTs residues in sediments from Lake Dongting, China.

The contamination of organochlorine pesticides hexachlorocyclohexane (HCH) and Dichlorodiphenyltrichloroethane (DDT) and their eco-environmental assessment in surface sediments from Lake Dongting, the second-largest freshwater lake in China, were studied. Concentrations of summation HCH (=alpha-HCH + beta-HCH + gamma-HCH +delta-HCH) were 0.21-9.59 ng/g dry weight and those of summation DDT = p,p'-DDD+p,p'-DDE+o,p'-DDT+p,p'-DDT) ranged from under detectable limit to 10.15 ng/g dry weight. The ratios of alpha-HCH to gamma-HCH were above 7 at most sampling sites while no or a small amount of beta-HCH were found at all sites, suggesting the degradation of HCH used in the history and possibly current use of HCH in the region. The low ratios (below 2.0 in most cases) of (p,p'-DDE+p,p'-DDD) to p,p'-DDT and high levels of individual isomers of DDT at some sites also suggested that there have still been fresh inputs of DDT into Lake Dongting. Through the comparison between concentrations of HCH and DDT residues in sediments of Lake Dongting and those from other places in China and also from the results of our eco-environmental assessment, it can be concluded that Lake Dongting is the water body with high contamination of both HCH and DDT in its sediments in comparison with other water bodies in China.

China↗

PubMed2005

Dechlorination of hexachlorobenzene using ultrafine Ca-Fe composite oxides.

Ca-Fe composite oxides with different Ca/Fe atomic ratios were synthesized by co-precipitation method and characterized by X-ray diffraction (XRD), scanning electron microscopy with elemental X-ray analysis (SEM-EDX) and inductively coupled plasma optical emission spectrometer (ICP-OES). Their dechlorination activities were evaluated using hexachlorobenzene (HCB) as a model compound. The results indicate that the dechlorination activity is related to the composition of metal oxides. Different compositions lead to the formation of different phases of Ca-Fe composite oxides. When Ca/Fe atomic ratio was 3.4, the dechlorination activity reached 97%, which was the highest in the dechlorination of HCB at 300 degrees C for 0.5 h. This may be related to the formation of Ca(2)Fe(2)O(5) phase and small agglomerate size of oxide crystal of about 1 microm. The effect of reaction time on HCB dechlorination and the pathway of dechlorination were investigated using the Ca-Fe composite oxide with the highest activity. It was found that hydrodechlorination took place in the destruction of HCB, the dechlorination efficiency is almost 100% after 2 h reaction. After reaction, quantitative measurement of chloride ion and qualitative analysis of CaCO(3) indicate besides hydrodechlorination, other degradation routes may be present. The mechanism of synergic dechlorination using Ca-Fe composite oxides was discussed.

Adsorption↗

PubMed2005

Influence of metal oxides on PCDD/Fs formation from pentachlorophenol.

Chlorophenols (ClPhs) are considered as important precursors for PCDD/Fs formation. The influences of series of metal oxides including MgO, Al2O3, CaO, BaO, TiO2, V2O5, MnO2, Fe2O3, Co3O4, CuO, Ag2O, ZnO, HgO, SnO, PbO, La2O3, CeO2, and Eu2O3 on PCDD/Fs formation from pentachlorophenol (PCP) were investigated in a laboratory-scale reactor. The results indicated that most of the above metal oxides have obvious suppressing effects on the total amount of PCDD/Fs formation from precursor PCP except for CuO, ZnO, MnO2, TiO2 and Co3O4 with promotion effects at 280 degrees C for 2 h. Although MgO, Al2O3, Fe2O3, PbO, La2O3 and Eu2O3 could reduce the amount of octachlorinated dibenzo-p-dioxin (OCDD), they promote the formation of more toxic 1,2,3,4,6,7,8-HpCDD at the same time. The total suppressing efficiencies of several metal oxides including CaO, BaO, PbO, Ag2O, HgO and SnO which have lower Z/r (charge to radius ratio) <2 are all over 90%. The theories of generalized acid-base and atomic parameter (Z/r) were used to speculate the effecting mechanisms. The factors including time and temperature on suppressing efficiencies of CaO, BaO and PbO have also been studied in the present paper. The results showed that the total suppressing efficiencies of CaO, BaO and PbO increase with the increase of heated time and temperature.

Air Pollution↗

PubMed2005

Inhibition of PCDD/Fs formation from dioxin precursors by calcium oxide.

Research aimed at understanding the inhibition effect of CaO on polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) formation form dioxins precursors, such as chlorophenols (CPs) and chlorobenzenes (CBs). The results indicated that a clear dioxin inhibition effect occurred both in open and sealed system when CaO was used. In the open system, PCDDs were the main congeners and the inhibition efficiency was all over 99% in the experiments. In the experiments with CaO, less than 0.1% of the initial PCP was detected in the absorption tube and only about 1% of the initial PCP was examined as calcium pentachlorophenate in the reaction tube. In the sealed system, the inhibition efficiency was over 90% at temperature range between 280 and 450 degrees C when PCP was used as model precursor. When HCB and 2,3,4,5-T4CP replaced PCP, significant inhibition effect was also observed. As CaO has the advantageous properties of non-toxicity and non-volatile nature, it is our hope that the result will contribute to the development of a new technique to cope with the problem of dioxin pollution in MWIs.

Air Pollution↗

PubMed2005

Synergic effect of calcium oxide and iron (III) oxide on the dechlorination of hexachlorobenzene.

Dechlorination of hexachlorobenzene (HCB) was achieved by a mixture of commercial CaO and alpha-Fe2O3 (CaO/alpha-Fe2O3) in closed systems at temperatures of 300 degrees C and 350 degrees C, which exhibited a synergic effect compared to CaO or alpha-Fe2O3 alone, and the dechlorination efficiency was dramatically enhanced. When CaO and alpha-Fe2O3 coexisted, HCB was dechlorinated by about 98% after 0.5 h reaction at 300 degrees C. All TeCB-, TrCB-, and DCB-isomers were detected, showing the presence of more than one dechlorination pathway. The pathway to form 1,2,4-TrCB must be a major pathway because the greatest amount of 1,2,4-TrCB was detected. There existed discrepancy of the material balance between the starting and dechlorinated materials. It implies that besides dechlorination other decomposition processes may be present. The mechanism of synergic effect of calcium and iron oxides was investigated.

Calcium Compounds↗

PubMed2005

A spatial temporal assessment of pollution from PCBs in China.

This research represents an assessment of the current state of pollution from polychlorinated biphenyls (PCBs) in China. Various environmental media including sediment, water, organism and soil were analyzed and the spatial character of PCB pollution in each environmental medium was determined. On a national basis, PCB levels in all environmental media were relatively low, with little evidence of major contamination in China's main regions and rivers. However, there were some locations with high PCB concentrations. Sediments in Pearl River (83.1 ng/g) and its estuary (58.9 ng/g), Dalian Bay (58.1 ng/g) and Songhua River (36.8 ng/g) had relatively high level of PCBs. There were also some areas, which were mainly the industrial pollution sites or PCB equipment storage locations, remained seriously polluted with the highest PCB residue level of 150,000 ng/g. In addition, Minjiang Estuary (985.2 ng/g) and Taihu Lake (631 ng/g) had high levels of water pollution, while Pearl Estuary (635.7 ng/g) and Jiaozhou Bay (273.3 ng/g) had relatively high PCB levels in organisms. PCB pollution in soil was limited to a few special pollution areas with the highest PCB level of 4.5448 x 10(6) ng/g. Point source pollution was the common pattern of contamination, influenced primarily by local geographic, economic and historical factors. Analysis of PCB concentrations from the 1980s to 1990s shows an increasing trend, possibly due to the improper disposal of and leakage from PCB containers, chemical transfers, and the general rise of industrial pollution.

Animals↗

PubMed2005

Serial analysis of gene expression in the silkworm, Bombyx mori.

The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmental life cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, of which 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, and adult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes.

Animals↗

PubMed2005

Regulation of FoxO1 transcription factor by nitric oxide and cyclic GMP in cultured rat granulosa cells.

FoxO1 is a transcription factor implicated in a multitude of physiological processes including cell cycle progression, apoptosis and insulin signaling. Recent findings indicate that FoxO1 is a key regulator during the proliferation and maturation of granulosa cells. Over the past several years, it has become evident that nitric oxide (NO) and cGMP modulate ovarian function. There has been no information, however, about whether NO-cGMP affects FoxO1 expression or about the relationship between NO-cGMP and FoxO1. In the present study, we used immunoblot analysis to determine whether NO and cGMP affect FoxO1 expression in cultured granulosa cells. Our results clearly showed that FSH suppressed FoxO1 expression in a time-dependent manner, and that NO-cGMP stimulated FoxO1 expression in cultured granulosa cells. In addition, this stimulatory effects of NO and cGMP can be blocked by FSH in cultured granulosa cells. These findings demonstrate that NO and cGMP influence FoxO1 expression possibly through antagonizing the action of FSH in cultured granulosa cells. Results of both immunoblot analysis and immunohistochemistry also show that estradiol implantation do not affect the expression of FoxO1 in rat granulosa cells as gonadotrophins do, indicating that mechanism of estradiol on granulosa cells is different from gonadotrophins. Together, our experiments suggest that expression of FoxO1 in rat granulosa cells can be regulated by gonadotrophins and the NO/cGMP signaling pathway.

Animals↗

PubMed2004

A novel peptide isolated from a phage display peptide library with trastuzumab can mimic antigen epitope of HER-2.

Trastuzumab, a humanized antibody to HER-2, has been shown to be effective in the treatment of breast cancer in which HER-2 overexpression and metastasis occurs. In our search for an effective mimic epitope of HER-2 binding with trastuzumab and to develop HER-2 peptide vaccine, we screened a phage display 12-mer peptide library with trastuzumab as the target. A mimetic peptide (mimotope) H98 (LLGPYELWELSH) that could specifically recognize trastuzumab was isolated. The DNA encoding peptide H98 was cloned and expressed as the fusion protein GST-H98 in Escherichia coli BL21. The purified GST-H98 could specifically bind to trastuzumab and block the binding of trastuzumab to HER-2 protein. Moreover, H98 could significantly block the function of trastuzumab inhibiting the growth of cancer cells. Mice that were immunized with GST-H98 made specific antibody to H98 as well as to HER-2. In addition, T-cell proliferation occurred in mice immunized with GST-H98. Although no sequence homology was found between H98 and HER-2, through the use of structure analysis we were able to determine that peptide H98 contributed to a conformational epitope of HER-2. Furthermore, we determined that the last two amino acids at the C terminus, and the third together with the fourth amino acid at the N terminus of peptide H98 are critical to the binding of H98 to trastuzumab. As a result, we conclude that peptide H98 has potential for being developed as a HER-2 vaccine for biotherapy of cancer with HER-2 overexpression.

Animals↗

PubMed2004

Microarray analyses of gene expression during adventitious root development in Pinus contorta.

In order to investigate the gene expression pattern during adventitious root development, RNA of Pinus contorta hypocotyls, pulse-treated with the auxin indole-3-butyric acid and harvested at distinct developmental time points of root development, was hybridized to microarrays containing 2,178 cDNAs from Pinus taeda. Over the period of observation of root development, the transcript levels of 220 genes changed significantly. During the root initiation phase, genes involved in cell replication and cell wall weakening and a transcript encoding a PINHEAD/ZWILLE-like protein were up-regulated, while genes related to auxin transport, photosynthesis, and cell wall synthesis were down-regulated. In addition, there were changes in transcript abundance of genes related to water stress. During the root meristem formation phase the transcript abundances of genes involved in auxin transport, auxin responsive transcription, and cell wall synthesis, and of a gene encoding a B-box zinc finger-like protein, increased, while those encoding proteins involved in cell wall weakening decreased. Changes of transcript abundance of genes related to water stress during the root meristem formation and root formation phase indicate that the plant roots had become functional in water transport. Simultaneously, genes involved in auxin transport were up-regulated, while genes related to cell wall modification were down-regulated. Finally, during the root elongation phase down-regulation of transcripts encoding proteins involved in cell replication and stress occurred. Based on the observed changes in transcript abundances, we suggest hypotheses about the relative importance of various physiological processes during the auxin-induced development of roots in P. contorta.

Cell Division↗

PubMed2004

The effect of reduced glutathione on morphology and gene expression of white spruce (Picea glauca) somatic embryos.

Inclusions of reduced glutathione (GSH) in the maturation medium increased the conversion frequency of white spruce somatic embryos without the need of a partial drying treatment (PDT). This beneficial effect was the result of major alterations in morphology and gene expression during the maturation period. Compared with control embryos, GSH-treated embryos showed a differential accumulation of storage products, i.e. preferential deposition of starch, the reduced formation of protein bodies, and increased vacuolation of cells. These morphological changes correlated with extensive alterations of gene expression occurring throughout the maturation period. The transcript profiles of stage-specific embryos matured with or without GSH were analysed using a DNA microarray containing 2 178 cDNAs from loblolly pine (Pinus taeda). The efficiency of heterologous hybridization between spruce and pine species on microarrays has previously been documented. The results indicate that several genes involved in a variety of signal regulatory pathways were differentially expressed in developing GSH- treated embryos. The transcript levels of many genes involved in carbohydrate metabolism and protein synthesis were altered by the presence of GSH and denoted differences in physiology between treatments. Extensive changes in the expression of genes participating in hormone synthesis, nucleotide metabolism, and meristem formation were also observed and related to the post-embryonic performance of the embryos.

Desiccation↗

PubMed2004

Expression of CD80/CD86 and CTLA-4 mRNA in peripheral blood mononuclear cells of the patients with systemic lupus erythematosus.

The role of CD80/CD86 and CTLA-4 in the pathogenesis of systemic lupus erythematosus and their clinical significance was investigated. By using RT-PCR technique, the expression of CD80/CD86 and CTLA-4 mRNA in peripheral blood mononuclear cells (PBMC) were semiquantitatively detected in 32 patients with active SLE. The results showed that the percentage of positive CD86 expression in active SLE was increased significantly as compared with normal controls (90.63% vs 60.00%, P<0.01). The mean level of CD86 mRNA expression in active SLE group was markedly higher than in the normal controls (0.6410+0.0174 vs 0.4510+0.0402, P<0.001). Compared with normal controls, the percentage of positive CTLA-4 expression and the mean level of CTLA-4 mRNA expression in active SLE group were both increased significantly (both P<0.01). There was no statistical differences in positive rate of CD80 and the average level of CD80 mRNA between the two groups (both P>0.05). It was concluded that the aberrant expression of CD86 and CTLA-4 might play an important role in the activity and development of SLE.

Adolescent↗

PubMed2004

A new DNA computing model for the NAND gate based on induced hairpin formation.

Hairpin structure of DNA molecules has been widely employed in a variety of biosensors and in nanoscale molecular assembly applications. For example, the well known molecular beacons can report the presence of specific nucleic acids in homogeneous solutions with high accuracy. Recently, Smith et al. proposed the induction of hairpin formation through sequence-specific binding of a small-molecule ligand to a G-G mismatch. Not only did this method offer great flexibility in controlling hairpin formation, more importantly the induced hairpin maintains high degree of sensitivity toward specific hybridization. In this contribution, we present a theoretical model for the logical NAND gate based on induced hairpin formation.

Computer Simulation↗

PubMed2004

Formation of PCDD/Fs and PCBs in the process of production of 1,4-dichlorobenzene.

The occurrence and distribution of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and polychlorinated biphenyls (PCBs) in a typical process of production of 1,4-dichlorobenzene (p-DCB) were investigated systematically in this study. P5CDFs and H6CDFs were the main congeners of PCDD/Fs, while only low levels of other PCDD/Fs were detected in the samples. The concentrations of PCBs were up to 4614 ng/g in the semi-manufactured products, and 1797 ng/g in the product p-DCB. It was also found that high chlorinated PCB congeners increased with the further chlorination. The levels of PCDD/Fs decreased obviously in the purification process, while PCBs could not be removed effectively. Polychlorophenols and other important dioxin precursors (1,4-dichloro-2-phenoxybenzene and 2-phenyl-2',5,5'-trichlorophenol) were also analyzed. Polychlorophenols which ortho- and para-positions of the hydroxyl were substituted by chlorine were the main congeners. In addition, a possible pathway of the formation of PCDD/Fs and PCBs in the production of p-DCB was presented. The results of this article suggest that re-estimation on the risk of using p-DCB products, especially the products for daily use such as mothballs, is expected.

Benzofurans↗