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author:("Li, zhikong")
1.  Fabrication of heterogeneous nanomaterial array by programmable heating and chemical supply within microfluidic platform towards multiplexed gas sensing application 
Scientific Reports  2015;5:8149.
A facile top-down/bottom-up hybrid nanofabrication process based on programmable temperature control and parallel chemical supply within microfluidic platform has been developed for the all liquid-phase synthesis of heterogeneous nanomaterial arrays. The synthesized materials and locations can be controlled by local heating with integrated microheaters and guided liquid chemical flow within microfluidic platform. As proofs-of-concept, we have demonstrated the synthesis of two types of nanomaterial arrays: (i) parallel array of TiO2 nanotubes, CuO nanospikes and ZnO nanowires, and (ii) parallel array of ZnO nanowire/CuO nanospike hybrid nanostructures, CuO nanospikes and ZnO nanowires. The laminar flow with negligible ionic diffusion between different precursor solutions as well as localized heating was verified by numerical calculation and experimental result of nanomaterial array synthesis. The devices made of heterogeneous nanomaterial array were utilized as a multiplexed sensor for toxic gases such as NO2 and CO. This method would be very useful for the facile fabrication of functional nanodevices based on highly integrated arrays of heterogeneous nanomaterials.
doi:10.1038/srep08149
PMCID: PMC4311253  PMID: 25634814
2.  Mosquito Saliva Serine Protease Enhances Dissemination of Dengue Virus into the Mammalian Host 
Journal of Virology  2014;88(1):164-175.
Dengue virus (DENV), a flavivirus of global importance, is transmitted to humans by mosquitoes. In this study, we developed in vitro and in vivo models of saliva-mediated enhancement of DENV infectivity. Serine protease activity in Aedes aegypti saliva augmented virus infectivity in vitro by proteolyzing extracellular matrix proteins, thereby increasing viral attachment to heparan sulfate proteoglycans and inducing cell migration. A serine protease inhibitor reduced saliva-mediated enhancement of DENV in vitro and in vivo, marked by a 100-fold reduction in DENV load in murine lymph nodes. A saliva-mediated infectivity enhancement screen of fractionated salivary gland extracts identified serine protease CLIPA3 as a putative cofactor, and short interfering RNA knockdown of CLIPA3 in mosquitoes demonstrated its role in influencing DENV infectivity. Molecules in mosquito saliva that facilitate viral infectivity in the vertebrate host provide novel targets that may aid in the prevention of disease.
doi:10.1128/JVI.02235-13
PMCID: PMC3911723  PMID: 24131723
3.  NF-κB inhibition alleviates carbon tetrachloride-induced liver fibrosis via suppression of activated hepatic stellate cells 
An effective treatment for hepatic fibrosis is not available clinically. Nuclear factor (NF)-κB plays a central role in inflammation and fibrosis. The aim of the present study was to investigate the effect of an NF-κB inhibitor, BAY-11–7082 (BAY), on mouse liver fibrosis. The effects of BAY on hepatic stellate cell (HSC) activation were measured in the lipopolysaccharide-activated rat HSC-T6 cell line. In addition, the therapeutic effect of BAY was studied in vivo using a model of hepatic fibrosis induced by carbon tetrachloride (CCl4) in mice. BAY effectively decreased the cell viability of activated HSC-T6 cells and suppressed HSC-T6 activation by downregulating the expression of collagen I and α-smooth muscle actin. BAY significantly inhibited the phosphorylation of phosphatidylinositol 3-kinase (PI3K) and serine/threonine kinase-protein kinase B (Akt) in activated HSC-T6 cells. In addition, administration of BAY attenuated mouse liver fibrosis induced by CCl4, as shown by histology and the expression of profibrogenic markers. BAY also significantly decreased the levels of serum alanine aminotransferase in this model of hepatic fibrosis. Therefore, the results of the present study demonstrate that BAY attenuates liver fibrosis by blocking PI3K and Akt phosphorylation in activated HSCs. Thus, BAY demonstrates therapeutic potential as a treatment for hepatic fibrosis.
doi:10.3892/etm.2014.1682
PMCID: PMC4061207  PMID: 24944604
nuclear factor-κB; BAY-11-7082; liver fibrosis; carbon tetrachloride
4.  Long-Term Effects of Liming on Health and Growth of a Masson Pine Stand Damaged by Soil Acidification in Chongqing, China 
PLoS ONE  2014;9(4):e94230.
In the last decades, the Masson pine (Pinus massoniana) forests in Chongqing, southwest China, have increasingly declined. Soil acidification was believed to be an important cause. Liming is widely used as a measure to alleviate soil acidification and its damage to trees, but little is known about long-term effects of liming on the health and growth of declining Masson pine forests. Soil chemical properties, health condition (defoliation and discoloration), and growth were evaluated following application of limestone powder (0 (unlimed control), 1, 2, 3, and 4 t ha−1) in an acidified and declining Masson pine stand at Tieshanping (TSP) of Chongqing. Eight years after liming, in the 0–20 cm and 20–40 cm mineral soil layers, soil pH values, exchangeable calcium (Ca) contents, and Ca/Al molar ratios increased, but exchangeable aluminum (Al) levels decreased, and as a result, length densities of living fine roots of Masson pine increased, with increasing dose. Mean crown defoliation of Masson pines (dominant, codominant and subdominant pines, according to Kraft classes 1–3) decreased with increasing dose, and it linearly decreased with length densities of living fine roots. However, Masson pines (Kraft classes 1–3) in all treatments showed no symptoms of discoloration. Mean current-year twig length, twig dry weight, needle number per twig, needle length per twig, and needle dry weight per twig increased with increasing dose. Over 8 years, mean height increment of Masson pines (Kraft classes 1–3) increased from 5.5 m in the control to 5.8, 6.9, 8.3, and 9.5 m in the 1, 2, 3, and 4 t ha−1 lime treatments, and their mean DBH (diameter at breast height) increment increased from 3.1 to 3.2, 3.8, 4.9, and 6.2 cm, respectively. The values of all aboveground growth parameters linearly increased with length densities of living fine roots. Our results show that liming improved tree health and growth, and these effects increased with increasing dose.
doi:10.1371/journal.pone.0094230
PMCID: PMC3984123  PMID: 24728089
5.  Alpha-enolase as a potential cancer prognostic marker promotes cell growth, migration, and invasion in glioma 
Molecular Cancer  2014;13:65.
Background
The success of using glycolytic inhibitors for cancer treatment relies on better understanding the roles of each frequently deregulated glycolytic genes in cancer. This report analyzed the involvement of a key glycolytic enzyme, alpha-enolase (ENO1), in tumor progression and prognosis of human glioma.
Methods
ENO1 expression levels were examined in glioma tissues and normal brain (NB) tissues. The molecular mechanisms of ENO1 expression and its effects on cell growth, migration and invasion were also explored by 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay, Transwell chamber assay, Boyden chamber assay, Western blot and in vivo tumorigenesis in nude mice.
Results
ENO1 mRNA and protein levels were upregulated in glioma tissues compared to NB. In addition, increased ENO1 was associated disease progression in glioma samples. Knocking down ENO1 expression not only significantly decreased cell proliferation, but also markedly inhibited cell migration and invasion as well as in vivo tumorigenesis. Mechanistic analyses revealed that Cyclin D1, Cyclin E1, pRb, and NF-κB were downregulated after stable ENO1 knockdown in glioma U251 and U87 cells. Conversely, knockdown of ENO1 resulted in restoration of E-cadherin expression and suppression of mesenchymal cell markers, such as Vimentin, Snail, N-Cadherin, β-Catenin and Slug. Furthermore, ENO1 suppression inactivated PI3K/Akt pathway regulating the cell growth and epithelial-mesenchymal transition (EMT) progression.
Conclusion
Overexpression of ENO1 is associated with glioma progression. Knockdown of ENO1 expression led to suppressed cell growth, migration and invasion progression by inactivating the PI3K/Akt pathway in glioma cells.
doi:10.1186/1476-4598-13-65
PMCID: PMC3994408  PMID: 24650096
ENO1; Glioma; Cell growth; EMT; PI3K/Akt
6.  Dynamic Multiobjective Optimization Algorithm Based on Average Distance Linear Prediction Model 
The Scientific World Journal  2014;2014:389742.
Many real-world optimization problems involve objectives, constraints, and parameters which constantly change with time. Optimization in a changing environment is a challenging task, especially when multiple objectives are required to be optimized simultaneously. Nowadays the common way to solve dynamic multiobjective optimization problems (DMOPs) is to utilize history information to guide future search, but there is no common successful method to solve different DMOPs. In this paper, we define a kind of dynamic multiobjectives problem with translational Paretooptimal set (DMOP-TPS) and propose a new prediction model named ADLM for solving DMOP-TPS. We have tested and compared the proposed prediction model (ADLM) with three traditional prediction models on several classic DMOP-TPS test problems. The simulation results show that our proposed prediction model outperforms other prediction models for DMOP-TPS.
doi:10.1155/2014/389742
PMCID: PMC3926970  PMID: 24616625
7.  Fuzi Attenuates Diabetic Neuropathy in Rats and Protects Schwann Cells from Apoptosis Induced by High Glucose 
PLoS ONE  2014;9(1):e86539.
Radix aconite lateralis preparata (Fuzi), a folk medicine, has long been used for the treatment of diabetes and paralysis in China. We examined the effect of Fuzi alone on diabetic rats and Schwann cells in high glucose and the components responsible for its activity. The major constituents of FZE were identified by HPLC-MS/MS data. Male Sprague Dawley rats (n = 36) were randomly divided into control, diabetic, FZE 1.75 g/kg, FZE 3.50 g/kg, FZE 7.00 g/kg, and methylcobalamin groups. After two weeks treatment, nerve conduction velocity and paw withdrawal latency were measured. In vitro, the Schwann cells were grouped according to exposure: normal glucose (NG), normal glucose plus mannitol (NG+M), high glucose (HG), and HG plus different concentrations of FZE (0.1 µg/ml, 1.0 µg/ml, and 10.0 µg/ml). Oxygen free radicals and apoptosis were evaluated through DCFH2DA, DHE and annexin-PE/7-AAD assay, respectively. Apoptosis factors (Bax, Bcl-2, CytoC, caspase-3, and caspase-9) were analyzed using immunofluorescence. Nine alkaloids were identified. The results from animal model showed that FZE was effective in accelerating nerve conduction velocity and shortening paw withdrawal latency in diabetic rats. And in vitro, FZE was also found to protect Schwann cells against high glucose injury. FZE could significantly decrease the apoptotic ratio, superoxide anion and peroxide level. Furthermore, the apoptosis factors, including Bax, Bcl-2, CytoC, caspase-3, and caspase-9 were ameliorated in FZE treated groups. The HPLC-MSn method is simple and suitable for the identification of alkaloids in Fuzi. FZE has a protective effect in diabetic neuropathic rats, which is probably achieved by the antiapoptotic effect of FZE on Schwann cells. Apoptosis factor data imply that FZE protected Schwann cells through the mitochondria pathway. Alkaloids are major components contributing to the protective effect.
doi:10.1371/journal.pone.0086539
PMCID: PMC3900563  PMID: 24466139
8.  Real-Time Tracking by Double Templates Matching Based on Timed Motion History Image with HSV Feature 
The Scientific World Journal  2014;2014:793769.
It is a challenge to represent the target appearance model for moving object tracking under complex environment. This study presents a novel method with appearance model described by double templates based on timed motion history image with HSV color histogram feature (tMHI-HSV). The main components include offline template and online template initialization, tMHI-HSV-based candidate patches feature histograms calculation, double templates matching (DTM) for object location, and templates updating. Firstly, we initialize the target object region and calculate its HSV color histogram feature as offline template and online template. Secondly, the tMHI-HSV is used to segment the motion region and calculate these candidate object patches' color histograms to represent their appearance models. Finally, we utilize the DTM method to trace the target and update the offline template and online template real-timely. The experimental results show that the proposed method can efficiently handle the scale variation and pose change of the rigid and nonrigid objects, even in illumination change and occlusion visual environment.
doi:10.1155/2014/793769
PMCID: PMC3921993  PMID: 24592185
9.  Identifying the Genome-Wide Sequence Variations and Developing New Molecular Markers for Genetics Research by Re-Sequencing a Landrace Cultivar of Foxtail Millet 
PLoS ONE  2013;8(9):e73514.
Foxtail millet (Setariaitalica) is a drought-resistant, barren-tolerant grain crop and forage. Currently, it has become a new model plant for cereal crops and biofuel grasses. Although two reference genome sequences were released recently, comparative genomics research on foxtail millet is still in its infancy. Using the Solexa sequencing technology, we performed genome re-sequencing on one important foxtail millet Landrace, Shi-Li-Xiang (SLX). Compared with the two reference genome sequences, the following genetic variation patterns were identified: 762,082 SNPs, 26,802 insertion/deletion polymorphisms of 1 to 5 bp in length (indels), and 10,109 structural variations (SVs) between SLX and Yugu1 genomes; 915,434 SNPs, 28,546 indels and 12,968 SVs between SLX and Zhang gu genomes. Furthermore, based on the Yugu1 genome annotation, we found out that ~ 40% SNPs resided in genes containing NB-ARC domain, protein kinase or leucine-rich repeats, which had higher non-synonymous to synonymous SNPs ratios than average, suggesting that the diversification of plant disease resistance proteins might be caused by pathogen pressure. In addition, out of the polymorphisms identified between SLX and Yugu1, 465 SNPs and 146 SVs were validated with more than 90% accuracy, which could be used as DNA markers for whole-genome genotyping and marker-assisted breeding. Here, we also represented an example of fine mapping and identifying a waxy locus in SLX using these newly developed DNA markers. This work provided important information that will allow a deeper understanding of the foxtail millet genome and will be helpful for dissecting the genetic basis of important traits in foxtail millet.
doi:10.1371/journal.pone.0073514
PMCID: PMC3769310  PMID: 24039970
10.  The Application of Closed Reduction Internal Fixation and Iliac Bone Block Grafting in the Treatment of Acute Displaced Femoral Neck Fractures 
PLoS ONE  2013;8(9):e75479.
Objective
This study aimed to evaluate the preliminary clinical and radiographic outcomes of acute displaced femoral neck fracture treated by closed reduction and internal fixation (CRIF) with free iliac bone block grafting with comparison to a routine protocol of CRIF without bone grafting.
Methods
From December 2008 to February 2010, 220 adult patients with acute displaced femoral neck fractures were enrolled in this study. In study group, there were 124 patients (57 males, 67 females) with a mean age of 44.8 years (range, 20-64 years). There were 70 transcervical fractures and 54 subcapital fractures. The patients were treated by CRIF and free iliac bone block grafting. The control group consisted of 96 adult patients (46 males, 50 females) with a mean age of 46.3 years (range, 23-64 years). There were 61 transcervical fractures and 35 subcapital fractures. The patients in control group were treated by CRIF without bone grafting.
Results
In study group, 112 patients were followed up for an average of 27.4 months (range, 24-34 months). All fractures healed within 5 months. However, 10 patients presented AVN of the femoral heads. The mean Harris score was 88.6 (range, 41-100). In control group, 68 patients were followed up for an average of 31.2 months (range, 24-42 months). The rates of AVN of the femoral head and fracture nonunion in control group were 26.5% (18/68) and 16.2% (11/68), respectively, significantly higher than those in study group (both P<0.05). The mean Harris score in control group was 83.8 (41–100), significantly lower than that in study group (P<0.05).
Conclusion
Acute displaced femoral neck fractures can be treated by CRIF and free iliac bone block grafting in a minimally invasive manner. This technique can guarantee uneventful fracture healing and significantly reduce the rate of femoral head osteonecrosis.
doi:10.1371/journal.pone.0075479
PMCID: PMC3769404  PMID: 24040414
11.  The Different Potential of Sponge Bacterial Symbionts in N2 Release Indicated by the Phylogenetic Diversity and Abundance Analyses of Denitrification Genes, nirK and nosZ 
PLoS ONE  2013;8(6):e65142.
Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N2O into N2 are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas.
doi:10.1371/journal.pone.0065142
PMCID: PMC3677918  PMID: 23762300
12.  Short hairpin RNA targeting of fibroblast activation protein inhibits tumor growth and improves the tumor microenvironment in a mouse model 
BMB Reports  2013;46(5):252-257.
Fibroblast activation protein (FAP) is a specific serine protease expressed in tumor stroma proven to be a stimulatory factor in the progression of some cancers. The purpose of this study was to investigate the effects of FAP knockdown on tumor growth and the tumor microenvironment. Mice bearing 4T1 subcutaneous tumors were treated with liposome-shRNA complexes targeting FAP. Tumor volumes and weights were monitored, and FAP, collagen, microvessel density (MVD), and apoptosis were measured. Our studies showed that shRNA targeting of FAP in murine breast cancer reduces FAP expression, inhibits tumor growth, promotes collagen accumulation (38%), and suppresses angiogenesis (71.7%), as well as promoting apoptosis (by threefold). We suggest that FAP plays a role in tumor growth and in altering the tumor microenvironment. Targeting FAP may therefore represent a supplementary therapy for breast cancer. [BMB Reports 2013; 46(5): 252-257]
doi:10.5483/BMBRep.2013.46.5.172
PMCID: PMC4133897  PMID: 23710635
Angiogenesis; Breast cancer; Fibroblast activation protein; RNA interference; Tumor microenvironment
13.  Phylogenetically Diverse ureC Genes and Their Expression Suggest the Urea Utilization by Bacterial Symbionts in Marine Sponge Xestospongia testudinaria 
PLoS ONE  2013;8(5):e64848.
Urea is one of the dominant organic nitrogenous compounds in the oligotrophic oceans. Compared to the knowledge of nitrogen transformation of nitrogen fixation, ammonia oxidization, nitrate and nitrite reduction mediated by sponge-associated microbes, our knowledge of urea utilization in sponges and the phylogenetic diversity of sponge-associated microbes with urea utilization potential is very limited. In this study, Marinobacter litoralis isolated from the marine sponge Xestospongia testudinaria and the slurry of X. testudinaria were found to have urease activity. Subsequently, phylogenetically diverse bacterial ureC genes were detected in the total genomic DNA and RNA of sponge X. testudinaria, i.e., 19 operative taxonomic units (OTUs) in genomic DNA library and 8 OTUs in cDNA library at 90% stringency. Particularly, 6 OTUs were common to both the genomic DNA library and the cDNA library, which suggested that some ureC genes were expressed in this sponge. BLAST and phylogenetic analysis showed that most of the ureC sequences were similar with the urease alpha subunit of members from Proteobacteria, which were the predominant component in sponge X. testudinaria, and the remaining ureC sequences were related to those from Magnetococcus, Cyanobacteria, and Actinobacteria. This study is the first assessment of the role of sponge bacterial symbionts in the regenerated utilization of urea by the detection of transcriptional activity of ureC gene, as well as the phylogenetic diversity of ureC gene of sponge bacterial symbionts. The results suggested the urea utilization by bacterial symbionts in marine sponge X. testudinaria, extending our understanding of nitrogen cycling mediated by sponge-associated microbiota.
doi:10.1371/journal.pone.0064848
PMCID: PMC3669342  PMID: 23741404
14.  Draft Genome Sequence of the Sponge-Associated Strain Bacillus atrophaeus C89, a Potential Producer of Marine Drugs 
Journal of Bacteriology  2012;194(16):4454.
Bacillus atrophaeus C89, isolated from the marine sponge Dysidea avara, is a potential producer of bioactive compounds, such as neobacillamide A and bacillamide C. Here, we present a 4.2-Mb assembly of its genome. The nonribosomal peptide synthetases (NRPSs) make it possible to produce the bioactive compounds.
doi:10.1128/JB.00835-12
PMCID: PMC3416270  PMID: 22843588
15.  Development of a Foot-and-Mouth Disease Virus Serotype A Empty Capsid Subunit Vaccine Using Silkworm (Bombyx mori) Pupae 
PLoS ONE  2012;7(8):e43849.
Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals that inflicts severe economic losses in the livestock industry. In 2009, FMDV serotype A caused outbreaks of FMD in cattle in China. Although an inactivated virus vaccine has proven effective to control FMD, its use may lead to new disease outbreaks due to a possible incomplete inactivation of the virus during the manufacturing process. Here, we expressed the P1-2A and the 3C coding regions of a serotype A FMDV field isolate in silkworm pupae (Bombyx mori) and evaluated the immunogenicity of the expression products. Four of five cattle vaccinated with these proteins developed high titers of FMDV-specific antibody and were completely protected against virulent homologous virus challenge with 10,000 50% bovine infectious doses (BID50). Furthermore, the 50% bovine protective dose (PD50) test was performed to assess the bovine potency of the empty capsid subunit vaccine and was shown to achieve 4.33 PD50 per dose. These data provide evidence that silkworm pupae can be used to express immunogenic FMDV proteins. This strategy might be used to develop a new generation of empty capsid subunit vaccines against a variety of diseases.
doi:10.1371/journal.pone.0043849
PMCID: PMC3428285  PMID: 22952788
16.  Impact of Coronary Tortuosity on Coronary Pressure: Numerical Simulation Study 
PLoS ONE  2012;7(8):e42558.
Background
Coronary tortuosity (CT) is a common coronary angiographic finding. Whether CT leads to an apparent reduction in coronary pressure distal to the tortuous segment of the coronary artery is still unknown. The purpose of this study is to determine the impact of CT on coronary pressure distribution by numerical simulation.
Methods
21 idealized models were created to investigate the influence of coronary tortuosity angle (CTA) and coronary tortuosity number (CTN) on coronary pressure distribution. A 2D incompressible Newtonian flow was assumed and the computational simulation was performed using finite volume method. CTA of 30°, 60°, 90°, 120° and CTN of 0, 1, 2, 3, 4, 5 were discussed under both steady and pulsatile conditions, and the changes of outlet pressure and inlet velocity during the cardiac cycle were considered.
Results
Coronary pressure distribution was affected both by CTA and CTN. We found that the pressure drop between the start and the end of the CT segment decreased with CTA, and the length of the CT segment also declined with CTA. An increase in CTN resulted in an increase in the pressure drop.
Conclusions
Compared to no-CT, CT can results in more decrease of coronary blood pressure in dependence on the severity of tortuosity and severe CT may cause myocardial ischemia.
doi:10.1371/journal.pone.0042558
PMCID: PMC3419180  PMID: 22905149
17.  Functional Gene-Guided Discovery of Type II Polyketides from Culturable Actinomycetes Associated with Soft Coral Scleronephthya sp 
PLoS ONE  2012;7(8):e42847.
Compared with the actinomycetes in stone corals, the phylogenetic diversity of soft coral-associated culturable actinomycetes is essentially unexplored. Meanwhile, the knowledge of the natural products from coral-associated actinomycetes is very limited. In this study, thirty-two strains were isolated from the tissue of the soft coral Scleronephthya sp. in the East China Sea, which were grouped into eight genera by 16S rDNA phylogenetic analysis: Micromonospora, Gordonia, Mycobacterium, Nocardioides, Streptomyces, Cellulomonas, Dietzia and Rhodococcus. 6 Micromonospora strains and 4 Streptomyces strains were found to be with the potential for producing aromatic polyketides based on the analysis of KSα (ketoacyl-synthase) gene in the PKS II (type II polyketides synthase) gene cluster. Among the 6 Micromonospora strains, angucycline cyclase gene was amplified in 2 strains (A5-1 and A6-2), suggesting their potential in synthesizing angucyclines e.g. jadomycin. Under the guidance of functional gene prediction, one jadomycin B analogue (7b, 13-dihydro-7-O-methyl jadomycin B) was detected in the fermentation broth of Micromonospora sp. strain A5-1. This study highlights the phylogenetically diverse culturable actinomycetes associated with the tissue of soft coral Scleronephthya sp. and the potential of coral-derived actinomycetes especially Micromonospora in producing aromatic polyketides.
doi:10.1371/journal.pone.0042847
PMCID: PMC3413676  PMID: 22880121
18.  Spatial distribution of prokaryotic symbionts and ammoxidation, denitrifier bacteria in marine sponge Astrosclera willeyana 
Scientific Reports  2012;2:528.
The present knowledge of microbial community mainly focus on total sponge, the spatial distribution of microbes in sponges is rarely known, especially those with potential ecological functions. In this study, based on gene library and ∫-LIBSHUFF analysis, the spatial distribution of prokaryotic symbionts and nitrogen cycling genes in the cortex and endosome sections of sponge Astrosclera willeyana were investigated. A significance difference of bacterial phylotypes between the cortex and endosome was revealed. For example Bacteroidetes, Frankineae and Propionibacterineae were detected only in the endosome, whereas Cyanobacteria, Planctomycetacia and Micrococcineae were only associated with the cortex. Some branches of α-Proteobacteria, γ-Proteobacteria, Corynebacterineae, Acidimicobidae, Crenarchaeota and Euryarchaeota also showed distribution difference. Bacterial denitrifiers and ammonia oxidizing bacteria (AOB) were observed using nirS and amoA genes as markers. Particularly, AOB were only associated with the endosome. This study highlighted the spatial distribution of bacterial symbionts especially those with ammonia oxidization function.
doi:10.1038/srep00528
PMCID: PMC3402844  PMID: 22829982
19.  Thrombotic risk assessment questionary helps increase the use of thromboprophylaxis for patients with pelvic and acetabular fractures 
Indian Journal of Orthopaedics  2012;46(4):413-419.
Background:
Pelvic and acetabular fractures have been known as one of the high risk factors for developing deep vein thrombosis (DVT), but thromboprophylaxis for patients with such fractures remains underused despite its widely accepted benefits. Current guidelines have not been universally adopted in clinical practice. The purpose of this study is to introduce a Thrombotic Risk Assessment Questionary (assessment table) according to evidence-based guidelines and evaluate its impact on the use of thromboprophylaxis for patients with pelvic and acetabular fractures.
Materials and Methods:
We retrospectively reviewed 305 consecutive patients with pelvic and acetabular fractures from August 1, 2008 through September 30, 2010. The control group without using the assessment table included 153 patients admitted during the first 13 months, and the assessment group using the assessment table included 152 patients admitted during the following months. Data on clinical outcomes of DVT, the number of patients receiving prophylaxis, and the time of the first dose of anticoagulant were collected.
Results:
Compared with the control group, Patients using the assessment table were more likely to be given DVT prophylaxis (84.2% vs. 37.3%, P < 0.05) and the time of the first dose of anticoagulant was reduced (4.32 days ± 4.78 days vs. 6.6 days ± 5.96 days, P < 0.05). Patients in the assessment group had lower risk of developing DVT (8.6% vs. 20.3%, P < 0.05).
Conclusion:
The assessment table can significantly improve the use of thromboprophylaxis after pelvic and acetabular fractures, which will likely reduce the incidence of DVT. Developing individual hospital prophylaxis strategy is an effective way to determine whether hospitalized patients should receive pharmacologic and/or mechanical prophylaxis or not.
doi:10.4103/0019-5413.98830
PMCID: PMC3421931  PMID: 22912516
Deep vein thrombosis; pelvic and acetabular fractures; risk assessment; thromboprophylaxis
20.  ZEB2 Mediates Multiple Pathways Regulating Cell Proliferation, Migration, Invasion, and Apoptosis in Glioma 
PLoS ONE  2012;7(6):e38842.
Background
The aim of the present study was to analyze the expression of Zinc finger E-box Binding homeobox 2 (ZEB2) in glioma and to explore the molecular mechanisms of ZEB2 that regulate cell proliferation, migration, invasion, and apoptosis.
Methodology/Principal Findings
Expression of ZEB2 in 90 clinicopathologically characterized glioma patients was analyzed by immunohistochemistry. Furthermore, siRNA targeting ZEB2 was transfected into U251 and U87 glioma cell lines in vitro and proliferation, migration, invasion, and apoptosis were examined separately by MTT assay, Transwell chamber assay, flow cytometry, and western blot.
Results
The expression level of ZEB2 protein was significantly increased in glioma tissues compared to normal brain tissues (P<0.001). In addition, high levels of ZEB2 protein were positively correlated with pathology grade classification (P = 0.024) of glioma patients. Knockdown of ZEB2 by siRNA suppressed cell proliferation, migration and invasion, as well as induced cell apoptosis in glioma cells. Furthermore, ZEB2 downregulation was accompanied by decreased expression of CDK4/6, Cyclin D1, Cyclin E, E2F1, and c-myc, while p15 and p21 were upregulated. Lowered expression of ZEB2 enhanced E-cadherin levels but also inhibited β-Catenin, Vimentin, N-cadherin, and Snail expression. Several apoptosis-related regulators such as Caspase-3, Caspase-6, Caspase-9, and Cleaved-PARP were activated while PARP was inhibited after ZEB2 siRNA treatment.
Conclusion
Overexpression of ZEB2 is an unfavorable factor that may facilitate glioma progression. Knockdown ZEB2 expression by siRNA suppressed cell proliferation, migration, invasion and promoted cell apoptosis in glioma cells.
doi:10.1371/journal.pone.0038842
PMCID: PMC3383704  PMID: 22761708
21.  Molecular characterization of China rabies virus vaccine strain 
Virology Journal  2011;8:521.
Background
Rabies virus (RV), the agent of rabies, can cause a severe encephalomyelitis in several species of mammals, including humans. As a human rabies vaccine strain employed in China, the genetic knowledge of the aG strain has not been fully studied. The main goal of the present study is to amplify the whole genome of aG strain, and genetic relationships between other vaccine strains and wild strains were analyzed.
Results
The entire genome of human rabies virus vaccine strain aG employed in China was sequenced; this is the second rabies virus vaccine strain from China to be fully characterized. The overall organization and the length of the genome were similar to that of other lyssaviruses. The length of aG strain was 11925nt, comprising a leader sequence of 58nt, nucleoprotein (N) gene of 1353nt, phosphoprotein (P) gene of 894 nt, matrix protein (M) gene of 609nt, glycoprotein (G) gene of 1575nt, RNA-dependent RNA polymerase (RdRp,L) gene of 6384nt, and a trailer region of 70 nt. There was TGAAAAAAA (TGA7) consensus sequence in the end of each gene, except AGA7 at the end of G gene. There was AACAYYYCT consensus start signal at the beginning of each gene.
Conclusions
In this report, we analyzed the full genome of China human rabies vaccine strain aG. Our studies indicated that the genome of aG retained the basic characteristics of RV. At gene level, N was the most conserved among the five coding genes, indicating this gene is the most appropriate for quantitative genotype definition. The phylogenetic analysis of the N indicated the aG strain clustered most closely with Japanese and Russian rabies vaccine strains, suggesting that they may share the same ancestor; also, the aG strain did not share high homology with wild strains isolated from China, making it may not be the best vaccine strain, more research is needed to elucidate the genetic relationship among the RV circulating in China.
doi:10.1186/1743-422X-8-521
PMCID: PMC3226571  PMID: 22093774
Rabies virus; aG; China; full-length genome
22.  Distribution and Abundance of Archaea in South China Sea Sponge Holoxea sp. and the Presence of Ammonia-Oxidizing Archaea in Sponge Cells 
Compared with bacterial symbionts, little is known about archaea in sponges especially about their spatial distribution and abundance. Understanding the distribution and abundance of ammonia-oxidizing archaea will help greatly in elucidating the potential function of symbionts in nitrogen cycling in sponges. In this study, gene libraries of 16S rRNA gene and ammonia monooxygenase subunit A (amoA) genes and quantitative real-time PCR were used to study the spatial distribution and abundance of archaea in the South China Sea sponge Holoxea sp. As a result, Holoxea sp. specific AOA, mainly group C1a (marine group I: Crenarchaeota) were identified. The presence of ammonia-oxidizing crenarchaea was observed for the first time within sponge cells. This study suggested a close relationship between sponge host and its archaeal symbionts as well as the archaeal potential contribution to sponge host in the ammonia-oxidizing process of nitrification.
doi:10.1155/2011/723696
PMCID: PMC3160109  PMID: 21869898
23.  Expression and antigenicity characterization for truncated capsid protein of porcine circovirus type 2 
Three pairs of specific primers were designed to amplify F2-1, F2-2, and XF2-2 truncated capsid protein genes of porcine circovirus type 2 (PCV-2). Amplified sequences were subcloned to pET-32a(+) vectors and expressed in Rosetta (DE3) Escherichia coli by induction of isopropy-β-D-thiogalactoside (IPTG). All of the fusion proteins had positive reactions to PCV-2 antiserum and His-XF2-2 showed the best reactivity. Proteins were used to immunize BALB/c mice to produce monoclonal antibodies (mAbs), and 7 mAbs were selected. Capsid protein N-terminal parts 55 to 96 amino acid (aa), 97 to 141 aa, and 143 to 211 aa were confirmed as binding regions of the 7 mAbs. Reactivity between His-XF2-2 and the 7 mAbs was detected, FmAb-8 showed the best reactivity. The dominant B-cell epitope was located at 97 to 141 aa. The PEPSCAN indicated that the P122–136 peptide contained the dominant B-cell epitope.
PMCID: PMC3003564  PMID: 21461197
24.  Advances in Marine Microbial Symbionts in the China Sea and Related Pharmaceutical Metabolites 
Marine Drugs  2009;7(2):113-129.
Marine animals and plants such as sponges, sea squirts, corals, worms and algae host diverse and abundant symbiotic microorganisms. Marine microbial symbionts are possible the true producers or take part in the biosynthesis of some bioactive marine natural products isolated from the marine organism hosts. Investigation of the pharmaceutical metabolites may reveal the biosynthesis mechanisms of related natural products and solve the current problem of supply limitation in marine drug development. This paper reviews the advances in diversity revelation, biological activity and related pharmaceutical metabolites, and functional genes of marine microbial symbionts from the China Sea.
doi:10.3390/md7020113
PMCID: PMC2707038  PMID: 19597576
Marine microbial symbionts; diversity; biological activity; natural products; gene
25.  Postsplenectomy reactive thrombocytosis 
Thrombocytosis is frequently encountered as an incidental laboratory finding. The most common etiology is reactive (secondary) thrombocytosis due to infections, trauma, surgery, or occult malignancy. Even though thrombocytosis is benign and self-limiting in most cases, it can result in hemorrhage or thrombosis. The hypercoagulable state is characterized by episodes of thrombosis and can be due to inherited or acquired conditions. Extreme thrombocytosis may result in thrombotic events such as acute myocardial infarction, mesenteric vein thrombosis, and pulmonary embolism. It is important for physicians to be familiar with the complications associated with thrombocytosis. Postsplenectomy reactive thrombocytosis has an incidence of about 75% to 82%. Thrombosis in association with elevated platelet count after splenectomy is well recognized, with an incidence of approximately 5%. This case report describes a 61-year-old patient who underwent emergent splenectomy and presented 1 week later with acute ST segment elevation myocardial infarction. Severe thrombocytosis, which was not present prior to splenectomy, was noted, and a diagnosis of reactive thrombocytosis was initially made. Involvement of the right coronary artery led to emergent percutaneous transluminal coronary angioplasty. Essential thrombocytosis was considered when treatment with hydroxyurea failed to lower the platelet count. A review of arterial and venous thrombosis in patients with severe thrombocytosis is presented, and the approach to the management of such patients is discussed.
PMCID: PMC2626351  PMID: 19169391

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