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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 highfat- 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. [ABSTRACT FROM AUTHOR]

Background: Masticatory stimulation during the healing period may promote periodontal ligament healing. The aim of the present study is to investigate the effect of orthodontic force on the periodontal healing of autotransplanted teeth. Methods: A total of 30 teeth from four dogs were endodontically treated to prevent subsequent inflammatory root resorption. The teeth were atraumatically extracted and autotransplanted to the other side of the same jaw. A continuous 50-g orthodontic force was applied during the first, second, and fourth weeks after autotransplantation. After 8 weeks, the animals were sacrificed using vital perfusion fixation, and the teeth were histologically prepared and evaluated following the Andreasen method. Results: The application of force in the first, second, and fourth weeks after autotransplantation resulted in a lower occurrence of ankylosis. The first- and second-week loading groups differed significantly from the control group (P <0.05); however, significantly more resorption and less complete healing were observed in the first-week loading group than in the other groups (P<0.05). Conclusion: The results of this study demonstrate that orthodontic force promotes periodontal ligament healing and that early force loading may prevent dentoalveolar ankylosis; however, a period of rest of ≥2 weeks is recommended for the autotransplants before loading. J Periodontol 2012;83:235-241. [ABSTRACT FROM AUTHOR]

Cell-to-cell heterogeneity in gene transcription plays a central role in a variety of vital cell processes. To quantify gene expression heterogeneity patterns among cells and to determine their biological significance, methods to measure gene expression levels at the single-cell level are highly needed. We report an experimental technique based on the DNA-intercalating fluorescent dye SYBR green for quantitative expression level analysis of up to ten selected genes in single mammalian cells. The method features a two-step procedure consisting of a step to isolate RNA from a single mammalian cell, synthesize cDNA from it, and a qPCR step. We applied the method to cell populations exposed to hypoxia, quantifying expression levels of seven different genes spanning a wide dynamic range of expression in randomly picked single cells. In the experiment, 72 single Barrett's esophageal epithelial (CP-A) cells, 36 grown under normal physiological conditions (controls) and 36 exposed to hypoxia for 30 min, were randomly collected and used for measuring the expression levels of 28S rRNA, PRKAA1, GAPDH, Angptl4, MT3, PTGES, and VEGFA genes. The results demonstrate that the method is sensitive enough to measure alterations in gene expression at the single-cell level, clearly showing heterogeneity within a cell population. We present technical details of the method development and implementation, and experimental results obtained by use of the procedure. We expect the advantages of this technique will facilitate further developments and advances in the field of single-cell gene expression profiling on a nanotechnological scale, and eventually as a tool for future point-of-care medical applications. [ABSTRACT FROM AUTHOR]

Curcumin, a polyphenolic compound, is the active component of Curcuma longa and has been extensively investigated as an anticancer drug that modulates multiple pathways. Eukaryotic initiation factors (eIFs) have been known to play important roles in translation initiation, which controls cell growth and proliferation. Little is known about the effects of curcumin on eIFs in lung cancer. The objective of this study was to exam the curcumin cytotoxic effect and modulation of two major rate-limiting translation initiation factors, including eIF2α and eIF4E protein expression levels in lung adenocarcinoma epithelial cell line A549. Cytotoxicity was measured by MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay and protein changes were determined by Western blot. A549 cells were treated with 0-240 μM curcumin for 4-96 h. The inhibitory effects of curcumin on cytotoxicity were dose- and time-dependent ( P < 0.001). The 50% inhibitory curcumin concentrations (IC50s) at 24, 48, 72, and 96 h were 93, 65, 40, and 24 μM, respectively. Protein expressions of eIF2α, eIF4E, Phospho-4E-BP1 were down-regulated, while Phospho-eIF2α and Phospho-eIF4E were up-regulated after A549 cells were treated with 20 and 40 μM curcumin for 24 h. In addition, the effects of curcumin on these protein expression changes followed a significant dose-response ( P < 0.05, trend test). These findings suggest that curcumin could reduce cell viability through prohibiting the initiation of protein synthesis by modulating eIF2α and eIF4E. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

By removing the symmetry of a free plate configuration, fluid loading significantly modifies the nature of acoustic waves travelling along a plate, and it even gives existence to new acoustic modes. We present theoretical predictions for the existence, dispersive behavior, and spatial distribution of leaky Lamb waves in a fluid-loaded film. Although Lamb modes are often investigated by studying the radiated fluid waves resulting from their leakage, here their properties are assessed by detecting the wave displacements directly using laser beam deflection. By using crossed laser beam excitation, the detection and analysis of the different modes is done at a fixed wavelength, allowing one to verify the existence, the velocity, and the damping of each predicted mode in a simple and unambiguous way. Our theoretical predictions for the nature of the modes in a waterloaded Plexiglas film, including parts of looping modes, are experimentally confirmed. [ABSTRACT FROM AUTHOR]

To evaluate the efficacy of green tea polyphenols (GTPs) in modulating aflatoxin B1 (AFB1) biomarkers, a total of 352 serum samples and 352 urine samples collected from a 3 month chemoprevention trial with 500 mg GTPs, 1000 mg GTPs and a placebo were measured for AFB1–albumin adducts (AFB–AA), aflatoxin M1 (AFM1) and aflatoxin B1–mercapturic acid (AFB–NAC). Levels of AFB–AA at baseline were comparable for all three dose groups (P = 0.506). No significant differences were observed in AFB–AA levels in the placebo group over the 3 month period (P = 0.252). However, a significant reduction in AFB–AA levels was observed in the 500 mg group (P = 0.002). A marginally significant reduction in AFB–AA levels was also found in the 1000 mg group over the 3 month intervention period (P = 0.051). An analysis using a mixed-effects model indicated that the reduction in AFB–AA levels over time was dose and time dependent (dose–time interaction P = 0.049). There were no significant differences in median AFM1 levels among the three study groups at the baseline (P = 0.832), 1 month (P = 0.188) and 3 months (P = 0.132) of the GTP intervention; however, reduction of 42 and 43% in median AFM1 levels, as compared with the placebo, were found in 500 mg (P = 0.096) and 1000 mg (P = 0.072) groups at 3 months of the intervention. Significant elevations in median AFB–NAC levels and the ratio of AFB–NAC:AFM1 were found in both 500 and 1000 mg groups compared with the placebo group at both 1 month (P P 1 metabolism and metabolic activation. [ABSTRACT FROM AUTHOR]

Vacuum fluidised beds have a distinct advantage of being operated with reduced mass consumption of the fluidising media. However, a low quality of fluidisation reduces the opportunity to utilise the bubbling regime in vacuum fluidised beds. Fluidisation maps are often used to depict the interface between the quiescent, bubbling and slugging regimes inside a fluidised bed. Such maps have been obtained by visual observations of the fluidisation interface in transparent fluidised beds. For beds which are visually inaccessible fluidisation maps are difficult to obtain. The present work therefore attempts to model the interface travel in a vacuum fluidised bed. The pressure gradient due to the bed weight has been determined to be a main contributor for fluidisation/defluidisation under vacuum. A simple analytical model based on the pressure gradient (PG model) is developed to predict the interface location in a vacuum fluidised bed. For a segregated bed, the Gibilaro-Rowe (GR) model is modified and used to predict the jetsam layer growth along with the fluidisation interface. The predictions are compared with the experimental data for minimally and highly segregated particles and it is seen that for non-segregated powders the predictions are quite accurate. Lack of sufficient knowledge of bubble characteristics, however, impeded accurate prediction of the jetsam growth especially at high flow rates. However, an approximate complete fluidisation interface is successfully predicted using the GR-PG model. [ABSTRACT FROM AUTHOR]

The structure, energy and bonding property of TixCy clusters formed in iron matrix were studied through molecular dynamics (MD) simulation method. The initial clusters with 1D-linear, 2D-ring, and 3D-tetrahedral structures were determined and their stability was calculated. The effect of temperature on the stability of the clusters was also discussed. In addition, the dissociation path of TiC clusters in iron matrix and the corresponding energy variation were analyzed. [ABSTRACT FROM AUTHOR]

The beneficial effects on meat quality of adding vitamin E to diets have been extensively studied in cattle and lamb. However, how supplemental vit E affects the performance and meat quality of 'Tan' sheep has not been reported. Thirty-five male lambs of 'Tan' sheep (20-30 after weaning) with similar body weight were randomly divided into five groups of seven each to receive a basal diet plus five levels of vit E supplementation: 0 (control group, CG), 20, 100, 200, and 2000 IU d-1 lamb-1. The results showed: 1) no differences were observed in animal growth performance between CG and vit E treated groups (VG) (P > 0.05); 2) vit E supplementation levels over 200 IU d-1 lamb-dramatically suppressed subcutaneous fat deposition and similarly that above 100 IU d-1 lamb-1 considerably reduced drip loss and pH 24 h of Longissimus dorsi (LD) muscle in VG lambs compared to those of CG (P < 0.01), but with no significant effect on other carcass characteristics (P > 0.05); 3) although vit E supplementation generally did not affect the fatty acid composition of intramuscular lipids in LD muscle, the percentage of n-6 polyunsaturated fatty acids (PUFA) and the ratio of n-6/n-3 PUFA were significantly enhanced (P < 0.05) and an increasing tendency (P < 0.1) for both total PUFA proportion and the ratio of PUFA/saturated fatty acids (SFA) was also observed in 'Tan' sheep lambs treated with vit E. In conclusion, vit E supplementation of male 'Tan' sheep lambs did not influence growth performance, significantly reduced subcutaneous fat deposition, drip loss, pH 24 h and tended to improve fatty acid profile of LD muscle. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]