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author:("Gao, heiming")
1.  Reduced pulmonary function and increased pro-inflammatory cytokines in nanoscale carbon black-exposed workers 
Background
Although major concerns exist regarding the potential consequences of human exposures to nanoscale carbon black (CB) particles, limited human toxicological data is currently available. The purpose of this study was to evaluate if nanoscale CB particles could be responsible, at least partially, for the altered lung function and inflammation observed in CB workers exposed to nanoscale CB particles.
Methods
Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), and Brunauer-Emmett-Teller were used to characterize CB. Eighty-one CB-exposed male workers and 104 non-exposed male workers were recruited. The pulmonary function test was performed and pro-inflammatory cytokines were evaluated. To further assess the deposition and pulmonary damage induced by CB nanoparticles, male BALB/c mice were exposed to CB for 6 hours per day for 7 or 14 days. The deposition of CB and the pathological changes of the lung tissue in mice were evaluated by paraffin sections and TEM. The cytokines levels in serum and lung tissue of mice were evaluated by ELISA and immunohistochemical staining (IHC).
Results
SEM and TEM images showed that the CB particles were 30 to 50 nm in size. In the CB workplace, the concentration of CB was 14.90 mg/m3. Among these CB particles, 50.77% were less than 0.523 micrometer, and 99.55% were less than 2.5 micrometer in aerodynamic diameter. The reduction of lung function parameters including FEV1%, FEV/FVC, MMF%, and PEF% in CB workers was observed, and the IL-1β, IL-6, IL-8, MIP-1beta, and TNF- alpha had 2.86-, 6.85-, 1.49-, 3.35-, and 4.87-folds increase in serum of CB workers, respectively. In mice exposed to the aerosol CB, particles were deposited in the lung. The alveolar wall thickened and a large amount of inflammatory cells were observed in lung tissues after CB exposure. IL-6 and IL-8 levels were increased in both serum and lung homogenate.
Conclusions
The data strongly suggests that nanoscale CB particles could be responsible for the lung function reduction and pro-inflammatory cytokines secretion in CB workers. These results, therefore, provide the first evidence of a link between human exposure to CB and long-term pulmonary effects.
Electronic supplementary material
The online version of this article (doi:10.1186/s12989-014-0073-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s12989-014-0073-1
PMCID: PMC4318129  PMID: 25497989
Carbon black; Nanoparticles; Occupational exposure; Pro-inflammatory cytokines; Pulmonary function
2.  A dual sensor for real-time monitoring of glucose and oxygen 
Biomaterials  2013;34(38):10.1016/j.biomaterials.2013.09.031.
A dual glucose and oxygen sensor in a polymer format was developed. The dual sensor composed of a blue emitter as the glucose probe, a red emitter as an oxygen probe, and a yellow emitter as a built-in reference probe which does not respond to either glucose or oxygen. All the three probes were chemically immobilized in a polyacrylamide-based matrix. Therefore, the dual sensor possesses three well separated emission colors and ratiometric approach is applicable for analysis of the glucose and oxygen concentration at biological conditions. The sensor was applied for real-time monitoring of glucose and oxygen consumption of bacterial cells, Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis), and mammalian cells of mouse macrophage J774 and human cervical cancer HeLa cell lines. On the other hand, in order to achieve satisfactory sensing performance for glucose, compositions of the matrices among poly(2-hydroxyethyl methacrylate), polyacrylamide, and poly(6-aminohexyl methacrylamide) which is a linker polymer for grafting the glucose probe, were optimized.
doi:10.1016/j.biomaterials.2013.09.031
PMCID: PMC3878311  PMID: 24090834
sensor; oxygen sensor; glucose sensor; dual sensor; ratiometric
3.  Effects of Formaldehyde on Lymphocyte Subsets and Cytokines in the Peripheral Blood of Exposed Workers 
PLoS ONE  2014;9(8):e104069.
Formaldehyde (FA) is a well-known irritant, and it is suggested to increase the risk of immune diseases and cancer. The present study aimed to evaluate the distribution of major lymphocyte subsets and cytokine expression profiles in the peripheral blood of FA-exposed workers. A total of 118 FA-exposed workers and 79 controls were enrolled in the study. High performance liquid chromatography, flow cytometry, and cytometric bead array were used to analyze FA in air sample and formic acid in urine, blood lymphocyte subpopulations, and serum cytokines, respectively. The FA-exposed workers were divided into low and high exposure groups according to their exposure levels. The results showed that both the low and high FA-exposed groups had a significant increase of formic acid in urine when compared to the controls. Both the low and high exposure groups had a significant increase in the percentage of B cells (CD19+) compared to the control group (p<0.01). A significant increase in the percentage of the natural killer (NK) cells (CD56+) was observed in the low exposure group compared to the control (p = 0.013). Moreover, the FA-exposed workers in both exposure groups showed a significant higher level of IL-10 but lower level of IL-8 than the control (p<0.01). Subjects in the high exposure group had a higher level of IL-4 but a lower level of IFN-γ than the control (p<0.05). Finally, there is a significant correlation between the levels of IL-10, IL-4, and IL-8 and formic acid (p<0.05). The findings from the present study may explain, at least in part, the association between FA exposure and immune diseases and cancer.
doi:10.1371/journal.pone.0104069
PMCID: PMC4144836  PMID: 25157974
4.  A Minimally Invasive Method for Retrieving Single Adherent Cells of Different Types from Cultures 
Scientific Reports  2014;4:5424.
The field of single-cell analysis has gained a significant momentum over the last decade. Separation and isolation of individual cells is an indispensable step in almost all currently available single-cell analysis technologies. However, stress levels introduced by such manipulations remain largely unstudied. We present a method for minimally invasive retrieval of selected individual adherent cells of different types from cell cultures. The method is based on a combination of mechanical (shear flow) force and biochemical (trypsin digestion) treatment. We quantified alterations in the transcription levels of stress response genes in individual cells exposed to varying levels of shear flow and trypsinization. We report optimal temperature, RNA preservation reagents, shear force and trypsinization conditions necessary to minimize changes in the stress-related gene expression levels. The method and experimental findings are broadly applicable and can be used by a broad research community working in the field of single cell analysis.
doi:10.1038/srep05424
PMCID: PMC4067612  PMID: 24957932
5.  Curcumin and Vitamin E Protect against Adverse Effects of Benzo[a]pyrene in Lung Epithelial Cells 
PLoS ONE  2014;9(3):e92992.
Benzo[a]pyrene (BaP), a well-known environmental carcinogen, promotes oxidative stress and DNA damage. Curcumin and vitamin E (VE) have potent antioxidative activity that protects cells from oxidative stress and cellular damage. The objectives of the present study were to investigate the adverse effects of BaP on normal human lung epithelial cells (BEAS-2B), the potential protective effects of curcumin and VE against BaP-induced cellular damage, and the molecular mechanisms of action. MTT assay, flow cytometry, fluorescence microplate assay, HPLC, qRT-PCR, and western blot were performed to analyze cytotoxicity, cell cycle, reactive oxygen species (ROS), BaP diol-epoxidation (BPDE)-DNA adducts, gene expression, and protein expression, respectively. Curcumin or VE prevented cells from BaP-induced cell cycle arrest and growth inhibition, significantly suppressed BaP-induced ROS levels, and decreased BPDE-DNA adducts. While CYP1A1 and 1B1 were induced by BaP, these inductions were not significantly reduced by curcumin or VE. Moreover, the level of activated p53 and PARP-1 were significantly induced by BaP, whereas this induction was markedly reduced after curcumin and VE co-treatment. Survivin was significantly down-regulated by BaP, and curcumin significantly restored survivin expression in BaP-exposed cells. The ratio of Bax/Bcl-2 was also significantly increased in cells exposed to BaP and this increase was reversed by VE co-treatment. Taken together, BaP-induced cytotoxicity occurs through DNA damage, cell cycle arrest, ROS production, modulation of metabolizing enzymes, and the expression/activation of p53, PARP-1, survivin, and Bax/Bcl-2. Curcumin and VE could reverse some of these BaP-mediated alterations and therefore be effective natural compounds against the adverse effects of BaP in lung cells.
doi:10.1371/journal.pone.0092992
PMCID: PMC3963982  PMID: 24664296
6.  Integrated Metagenomic and Metatranscriptomic Analyses of Microbial Communities in the Meso- and Bathypelagic Realm of North Pacific Ocean 
Marine Drugs  2013;11(10):3777-3801.
Although emerging evidence indicates that deep-sea water contains an untapped reservoir of high metabolic and genetic diversity, this realm has not been studied well compared with surface sea water. The study provided the first integrated meta-genomic and -transcriptomic analysis of the microbial communities in deep-sea water of North Pacific Ocean. DNA/RNA amplifications and simultaneous metagenomic and metatranscriptomic analyses were employed to discover information concerning deep-sea microbial communities from four different deep-sea sites ranging from the mesopelagic to pelagic ocean. Within the prokaryotic community, bacteria is absolutely dominant (~90%) over archaea in both metagenomic and metatranscriptomic data pools. The emergence of archaeal phyla Crenarchaeota, Euryarchaeota, Thaumarchaeota, bacterial phyla Actinobacteria, Firmicutes, sub-phyla Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria, and the decrease of bacterial phyla Bacteroidetes and Alphaproteobacteria are the main composition changes of prokaryotic communities in the deep-sea water, when compared with the reference Global Ocean Sampling Expedition (GOS) surface water. Photosynthetic Cyanobacteria exist in all four metagenomic libraries and two metatranscriptomic libraries. In Eukaryota community, decreased abundance of fungi and algae in deep sea was observed. RNA/DNA ratio was employed as an index to show metabolic activity strength of microbes in deep sea. Functional analysis indicated that deep-sea microbes are leading a defensive lifestyle.
doi:10.3390/md11103777
PMCID: PMC3826135  PMID: 24152557
deep-sea microbial community; metagenomics; metatranscriptomics; strength of metabolic activity
7.  Monitoring the Single-Cell Stress Response of the Diatom Thalassiosira pseudonana by Quantitative Real-Time Reverse Transcription-PCR 
Directly monitoring the stress response of microbes to their environments could be one way to inspect the health of microorganisms themselves, as well as the environments in which the microorganisms live. The ultimate resolution for such an endeavor could be down to a single-cell level. In this study, using the diatom Thalassiosira pseudonana as a model species, we aimed to measure gene expression responses of this organism to various stresses at a single-cell level. We developed a single-cell quantitative real-time reverse transcription-PCR (RT-qPCR) protocol and applied it to determine the expression levels of multiple selected genes under nitrogen, phosphate, and iron depletion stress conditions. The results, for the first time, provided a quantitative measurement of gene expression at single-cell levels in T. pseudonana and demonstrated that significant gene expression heterogeneity was present within the cell population. In addition, different expression patterns between single-cell- and bulk-cell-based analyses were also observed for all genes assayed in this study, suggesting that cell response heterogeneity needs to be taken into consideration in order to obtain accurate information that indicates the environmental stress condition.
doi:10.1128/AEM.03399-12
PMCID: PMC3592218  PMID: 23315741
8.  Interaction between IGF-IR and ER Induced by E2 and IGF-I 
PLoS ONE  2013;8(5):e62642.
Estrogen receptor (ER) is a nuclear receptor and the insulin-like growth factor-I (IGF-I) receptor (IGF-IR) is a transmembrane tyrosine kinase receptor. Estrogen and IGF-I are known to have synergistic effects on the growth of breast cancer cells. Recently, non-nuclear effects of ER have been under investigation. To study the mechanism involved in this process, we have used MCF-7 breast cancer cell lines transfected with IGF-IR anti-sense cDNA (SX13, MCF-7SX13) that resulted in 50% reduction of IGF-IR. In MCF-7 cells, estradiol (E2) and IGF-I induced the rapid association of ER to IGF-IR, however, the interaction was abrogated in MCF-7SX13 cells. In addition, NWTB3 cells (NIH3T3 cells overexpressing IGF-IR) were transiently transfected with ERα, the ER-IGF-IR interaction was induced by both E2 and IGF-I. Moreover, ERα regulated the IGF-I signaling pathways through phosphorylation of ERK1/2 and Akt and the interaction of ER-IGF-IR potentiated the cell growth. Finally, E2 and IGF-I stimulated translocation of ER from the nucleus to the cytoplasm. Taken together, these findings reveal that the interaction of the ER and IGF-IR is important for the non-genomic effects of ER.
doi:10.1371/journal.pone.0062642
PMCID: PMC3660452  PMID: 23704881
9.  Microbe observation and cultivation array (MOCA) for cultivating and analyzing environmental microbiota 
Microbiome  2013;1:4.
Background
The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contrast to this great achievement is the current difficulty in cultivating the majority of bacterial species or phylotypes revealed by molecular approaches. Although recent new technologies such as metagenomics and metatranscriptomics can provide more functionality information about the microbial communities, it is still important to develop the capacity to isolate and cultivate individual microbial species or strains in order to gain a better understanding of microbial physiology and to apply isolates for various biotechnological applications.
Results
We have developed a new system to cultivate bacteria in an array of droplets. The key component of the system is the microbe observation and cultivation array (MOCA), which consists of a Petri dish that contains an array of droplets as cultivation chambers. MOCA exploits the dominance of surface tension in small amounts of liquid to spontaneously trap cells in well-defined droplets on hydrophilic patterns. During cultivation, the growth of the bacterial cells across the droplet array can be monitored using an automated microscope, which can produce a real-time record of the growth. When bacterial cells grow to a visible microcolony level in the system, they can be transferred using a micropipette for further cultivation or analysis.
Conclusions
MOCA is a flexible system that is easy to set up, and provides the sensitivity to monitor growth of single bacterial cells. It is a cost-efficient technical platform for bioassay screening and for cultivation and isolation of bacteria from natural environments.
doi:10.1186/2049-2618-1-4
PMCID: PMC3869193  PMID: 24468000
Microbe observation and cultivation array (MOCA); Cultivation; Growth; Microbiota
10.  Triazacryptand-Based Fluorescent Sensors for Extracellular and Intracellular K+ Sensing 
Biomaterials  2011;32(33):8574-8583.
A 4-amino-naphthalimide derived fluorophore with a triazacryptand moiety ligand was synthesized as a potassium ion (K+) sensor (KS1). This sensor is a monomer possessing a polymerizable vinyl group. By taking advantage of the polymerizable characteristics of the vinyl group, KS1 was polymerized with 2-hydroxyethyl methacrylate (HEMA) and acrylamide (AM) to form K+-sensing films for extracellular sensing. The sensitivity of the films to potassium ions can be further tuned through the adjustment of the HEMA and AM weight ratios as well as introduction of positive or negative charge-containing segments. KS1 and its poly(2-hydroxyethyl methacrylate)-co-poly(acrylamide) (PHEMA-co-PAM) thin films show high selectivity for K+ over competing sodium ions (Na+) at physiological concentrations. Extracellular sensing was demonstrated using a KS1-conjugated PHEMA-co-PAM thin film to measure the K+ efflux of Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis) stimulated by lysozyme. Meanwhile, KS1 itself permeates human glioblastoma U87MG and human esophagus premalignant CP-A cell lines. KS1 was used to monitor K+ efflux stimulated by adenosine-5'-triphosphate (ATP), amphotericin, and a mixture of nigericin, bumetanide and ouabain, demonstrating application of this material as an intracellular potassium ion sensor.
doi:10.1016/j.biomaterials.2011.07.081
PMCID: PMC3177004  PMID: 21855134
Potassium ion sensor; Amino-naphthalimide; Intracellular sensing; Extracellular sensing; Fluorescent probe
11.  Green Tea Polyphenols Reduce Body Weight in Rats by Modulating Obesity-Related Genes 
PLoS ONE  2012;7(6):e38332.
Beneficial effects of green tea polyphenols (GTP) against obesity have been reported, however, the mechanism of this protection is not clear. Therefore, the objective of this study was to identify GTP-targeted genes in obesity using the high-fat-diet-induced obese rat model. A total of three groups (n = 12/group) of Sprague Dawley (SD) female rats were tested, including the control group (rats fed with low-fat diet), the HF group (rats fed with high-fat diet), and the HF+GTP group (rats fed with high-fat diet and GTP in drinking water). The HF group increased body weight as compared to the control group. Supplementation of GTP in the drinking water in the HF+GTP group reduced body weight as compared to the HF group. RNA from liver samples was extracted for gene expression analysis. A total of eighty-four genes related to obesity were analyzed using PCR array. Compared to the rats in the control group, the rats in the HF group had the expression levels of 12 genes with significant changes, including 3 orexigenic genes (Agrp, Ghrl, and Nr3c1); 7 anorectic genes (Apoa4, Cntf, Ghr, IL-1β, Ins1, Lepr, and Sort); and 2 genes that relate to energy expenditure (Adcyap1r1 and Adrb1). Intriguingly, the HF+GTP group restored the expression levels of these genes in the high-fat-induced obese rats. The protein expression levels of IL-1β and IL-6 in the serum samples from the control, HF, and HF+GTP groups confirmed the results of gene expression. Furthermore, the protein expression levels of superoxide dismutase-1 (SOD1) and catechol-O-methyltransferase (COMT) also showed GTP-regulated protective changes in this obese rat model. Collectively, this study revealed the beneficial effects of GTP on body weight via regulating obesity-related genes, anti-inflammation, anti-oxidant capacity, and estrogen-related actions in high-fat-induced obese rats.
doi:10.1371/journal.pone.0038332
PMCID: PMC3371013  PMID: 22715380
12.  Chemotherapeutic Sensitization of Leptomycin B Resistant Lung Cancer Cells by Pretreatment with Doxorubicin 
PLoS ONE  2012;7(3):e32895.
The development of novel targeted therapies has become an important research focus for lung cancer treatment. Our previous study has shown leptomycin B (LMB) significantly inhibited proliferation of lung cancer cells; however, p53 wild type lung cancer cells were resistant to LMB. Therefore, the objective of this study was to develop and evaluate a novel therapeutic strategy to sensitize LMB-resistant lung cancer cells by combining LMB and doxorubicin (DOX). Among the different treatment regimens, pretreatment with DOX (pre-DOX) and subsequent treatment with LMB to A549 cells significantly decreased the 50% inhibitory concentration (IC50) as compared to that of LMB alone (4.4 nM vs. 10.6 nM, P<0.05). Analysis of cell cycle and apoptosis by flow cytometry further confirmed the cytotoxic data. To investigate molecular mechanisms for this drug combination effects, p53 pathways were analyzed by Western blot, and nuclear proteome was evaluated by two dimensional-difference gel electrophoresis (2D-DIGE) and mass spectrometry. In comparison with control groups, the levels of p53, phospho-p53 (ser15), and p21 proteins were significantly increased while phospho-p53 (Thr55) and survivin were significantly decreased after treatments of pre-DOX and LMB (P<0.05). The 2D-DIGE/MS analysis identified that sequestosome 1 (SQSTM1/p62) had a significant increase in pre-DOX and LMB-treated cells (P<0.05). In conclusion, our results suggest that drug-resistant lung cancer cells with p53 wild type could be sensitized to cell death by scheduled combination treatment of DOX and LMB through activating and restoring p53 as well as potentially other signaling pathway(s) involving sequestosome 1.
doi:10.1371/journal.pone.0032895
PMCID: PMC3296751  PMID: 22412944
13.  Influence of Matrices on Oxygen Sensing of Three Sensing Films with Chemically Conjugated Platinum Porphyrin Probes and Preliminary Application for Monitoring of Oxygen Consumption of Escherichia coli (E. coli) 
Sensors and actuators. B, Chemical  2010;150(2):579-587.
Oxygen sensing films were synthesized by a chemical conjugation of functional platinum porphyrin probes in silica gel, polystyrene (PS), and poly(2-hydroxyethyl methacrylate) (PHEMA) matrices. Responses of the sensing films to gaseous oxygen and dissolved oxygen were studied and the influence of the matrices on the sensing behaviors was investigated. Silica gel films had the highest fluorescence intensity ratio from deoxygenated to oxygenated environments and the fastest response time to oxygen. PHEMA films had no response to gaseous oxygen, but had greater sensitivity and a faster response time for dissolved oxygen than those of PS films. The influence of matrices on oxygen response, sensitivity and response time was discussed. The influence is most likely attributed to the oxygen diffusion abilities of the matrices. Since the probes were chemically immobilized in the matrices, no leaching of the probes was observed from the sensing films when applied in aqueous environment. One sensing film made from the PHEMA matrix was used to preliminarily monitor the oxygen consumption of Escherichia coli (E. coli) bacteria. E. coli cell density and antibiotics ampicillin concentration dependent oxygen consumption was observed, indicating the potential application of the oxygen sensing film for biological application.
doi:10.1016/j.snb.2010.08.036
PMCID: PMC2976577  PMID: 21076638
Oxygen sensor; chemical conjugation; platinum porphyrin; matrix influence; E. coli
14.  Validation of Green Tea Polyphenol Biomarkers in a Phase II Human Intervention Trial 
Health benefits of green tea polyphenols (GTPs) have been reported in many animal models, but human studies are inconclusive. This is partly due to a lack of biomarkers representing green tea consumption. In this study, GTP components and metabolites were analyzed in plasma and urine samples collected from a phase II intervention trial carried out in 124 healthy adults who received 500- or 1,000-mg GTPs or placebo for 3 months. A significant dose-dependent elevation was found for (-)-epicatechin-3-gallate (ECG) (p<0.001, trend test) and (-)-epigallocatechin-3-gallate (EGCG) (p<0.05, trend test) concentrations in plasma at both 1-month and 3-months after intervention with GTP. No significant increase of (-)-epicatechin (EC) or (-)-epigallocatechin (EGC) was observed in plasma after GTP intervention. A mixed-effects model indicated significant effects of dose (EGCG) and dose by time interaction (ECG), but not for EC and EGC. Analysis of phase 2 metabolic conjugates revealed a predominance of free GTPs in plasma, up to 85% for EGCG, while a majority of GTPs in urine were sulfated and glucuronidated conjugates (up to 100% for EC and 89% for EGC). These results suggest that plasma ECG and EGCG concentrations are reliable biomarkers for green tea consumption at the population level.
doi:10.1016/j.fct.2007.08.007
PMCID: PMC2253676  PMID: 17888558
Green Tea Polyphenols; Biomarker; Intervention; Glucuronidation; Sulfation
15.  Reduction of Uranium(VI) to Uranium(IV) by Clostridia▿  
Applied and Environmental Microbiology  2008;74(14):4580-4584.
Several different species of clostridia reduced U(VI) to U(IV) to various degrees. The optimal pH for U(VI) reduction is 5 to 6 in most cases; a Clostridium sp. showed the highest rate at pH 4. Nitrate did not affect U(VI) reduction, indicating that this process in clostridia is nitrate independent.
doi:10.1128/AEM.00239-08
PMCID: PMC2493151  PMID: 18515477
16.  Promoter methylation of RASSF1A and DAPK and mutations of K-ras, p53, and EGFR in lung tumors from smokers and never-smokers 
BMC Cancer  2007;7:74.
Background
Epidemiological studies indicate that some characteristics of lung cancer among never-smokers significantly differ from those of smokers. Aberrant promoter methylation and mutations in some oncogenes and tumor suppressor genes are frequent in lung tumors from smokers but rare in those from never-smokers. In this study, we analyzed promoter methylation in the ras-association domain isoform A (RASSF1A) and the death-associated protein kinase (DAPK) genes in lung tumors from patients with primarily non-small cell lung cancer (NSCLC) from the Western Pennsylvania region. We compare the results with the smoking status of the patients and the mutation status of the K-ras, p53, and EGFR genes determined previously on these same lung tumors.
Methods
Promoter methylation of the RASSF1A and DAPK genes was analyzed by using a modified two-stage methylation-specific PCR. Data on mutations of K-ras, p53, and EGFR were obtained from our previous studies.
Results
The RASSF1A gene promoter methylation was found in tumors from 46.7% (57/122) of the patients and was not significantly different between smokers and never-smokers, but was associated significantly in multiple variable analysis with tumor histology (p = 0.031) and marginally with tumor stage (p = 0.063). The DAPK gene promoter methylation frequency in these tumors was 32.8% (40/122) and did not differ according to the patients' smoking status, tumor histology, or tumor stage. Multivariate analysis adjusted for age, gender, smoking status, tumor histology and stage showed that the frequency of promoter methylation of the RASSF1A or DAPK genes did not correlate with the frequency of mutations of the K-ras, p53, and EGFR gene.
Conclusion
Our results showed that RASSF1A and DAPK genes' promoter methylation occurred frequently in lung tumors, although the prevalence of this alteration in these genes was not associated with the smoking status of the patients or the occurrence of mutations in the K-ras, p53 and EGFR genes, suggesting each of these events may represent independent event in non-small lung tumorigenesis.
doi:10.1186/1471-2407-7-74
PMCID: PMC1877812  PMID: 17477876
17.  Etiological study of esophageal squamous cell carcinoma in an endemic region: a population-based case control study in Huaian, China 
BMC Cancer  2006;6:287.
Background
Continuous exposure to various environmental carcinogens and genetic polymorphisms of xenobiotic-metabolizing enzymes (XME) are associated with many types of human cancers, including esophageal squamous cell carcinoma (ESCC). Huaian, China, is one of the endemic regions of ESCC, but fewer studies have been done in characterizing the risk factors of ESCC in this area. The aims of this study is to evaluate the etiological roles of demographic parameters, environmental and food-borne carcinogens exposure, and XME polymorphisms in formation of ESCC, and to investigate possible gene-gene and gene-environment interactions associated with ESCC in Huaian, China.
Methods
A population based case-control study was conducted in 107 ESCC newly diagnosed cases and 107 residency- age-, and sex-matched controls in 5 townships of Huaian. In addition to regular epidemiological and food frequency questionnaire analyses, genetic polymorphisms of phase I enzymes CYP1A1, CYP1B1, CYP2A6, and CYP2E1, and phase II enzymes GSTM1, GSTT1, GSTP1, and microsomal epoxide hydrolase (EPHX) were assessed from genomic DNA using PCR based techniques.
Results
Consuming acrid food, fatty meat, moldy food, salted and pickled vegetables, eating fast, introverted personality, passive smoking, a family history of cancer, esophageal lesion, and infection with Helicobacter pylori were significant risk factors for ESCC (P < 0.05). Regular clean up of food storage utensils, green tea consumption, and alcohol abstinence were protective factors for ESCC (P < 0.01). The frequency of the GSTT1 null genotype was higher in cases (59.4%) compared to controls (47.2%) with an odds ratio (OR) of 1.68 and 95% confidence interval (CI) from 0.96 to 2.97 (P = 0.07), especially in males (OR = 2.78; 95% CI = 1.22–6.25; P = 0.01). No associations were found between polymorphisms of CYP1A1, CYP1B1, CYP2A6, CYP2E1, GSTM1, GSTP1, and EPHX and ESCC (P > 0.05).
Conclusion
Our results demonstrated that dietary and environmental exposures, some demographic parameters and genetic polymorphism of GSTT1 may play important roles in the development of ESCC in Huaian area, China.
doi:10.1186/1471-2407-6-287
PMCID: PMC1774575  PMID: 17173682
18.  Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium, Shewanella sp. Strain PV-4 
A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium, Shewanella sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. Growth during iron reduction occurred over the pH range of 7.0 to 8.9, a sodium chloride range of 0.05 to 5%, and a temperature range of 0 to 37°C, with an optimum growth temperature of 18°C. Unlike mesophilic dissimilatory Fe(III)-reducing bacteria, which produce mostly superparamagnetic magnetite (<35 nm), this psychrotolerant bacterium produces well-formed single-domain magnetite (>35 nm) at temperatures from 18 to 37°C. The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation.
doi:10.1128/AEM.72.5.3236-3244.2006
PMCID: PMC1472395  PMID: 16672462
19.  Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1 
BMC Genomics  2006;7:76.
Background
Shewanella oneidensis MR-1 is a facultative, gram-negative bacterium capable of coupling the oxidation of organic carbon to a wide range of electron acceptors such as oxygen, nitrate and metals, and has potential for bioremediation of heavy metal contaminated sites. The complete 5-Mb genome of S. oneidensis MR-1 was sequenced and standard sequence-comparison methods revealed approximately 42% of the MR-1 genome encodes proteins of unknown function. Defining the functions of hypothetical proteins is a great challenge and may need a systems approach. In this study, by using integrated approaches including whole genomic microarray and proteomics, we examined knockout effects of the gene encoding SO1377 (gi24372955), a member of the conserved, hypothetical, bacterial protein family COG2268 (Clusters of Orthologous Group) in bacterium Shewanella oneidensis MR-1, under various physiological conditions.
Results
Compared with the wild-type strain, growth assays showed that the deletion mutant had a decreased growth rate when cultured aerobically, but not affected under anaerobic conditions. Whole-genome expression (RNA and protein) profiles revealed numerous gene and protein expression changes relative to the wild-type control, including some involved in iron metabolism, oxidative damage protection and respiratory electron transfer, e. g. complex IV of the respiration chain. Although total intracellular iron levels remained unchanged, whole-cell electron paramagnetic resonance (EPR) demonstrated that the level of free iron in mutant cells was 3 times less than that of the wild-type strain. Siderophore excretion in the mutant also decreased in iron-depleted medium. The mutant was more sensitive to hydrogen peroxide and gave rise to 100 times more colonies resistant to gentamicin or kanamycin.
Conclusion
Our results showed that the knock-out of SO1377 gene had pleiotropic effects and suggested that SO1377 may play a role in iron homeostasis and oxidative damage protection in S. oneidensis MR-1.
doi:10.1186/1471-2164-7-76
PMCID: PMC1468410  PMID: 16600046
20.  Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions 
Journal of Bacteriology  2005;187(7):2501-2507.
Whole-genomic expression patterns were examined in Shewanella oneidensis cells exposed to elevated sodium chloride. Genes involved in Na+ extrusion and glutamate biosynthesis were significantly up-regulated, and the majority of chemotaxis/motility-related genes were significantly down-regulated. The data also suggested an important role for metabolic adjustment in salt stress adaptation in S. oneidensis.
doi:10.1128/JB.187.7.2501-2507.2005
PMCID: PMC1065217  PMID: 15774893

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