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31.
MAGIC Tool: integrated microarray data analysis 总被引:5,自引:1,他引:4
Heyer LJ Moskowitz DZ Abele JA Karnik P Choi D Campbell AM Oldham EE Akin BK 《Bioinformatics (Oxford, England)》2005,21(9):2114-2115
Summary: Several programs are now available for analyzing thelarge datasets arising from cDNA microarray experiments. Mostprograms are expensive commercial packages or require expensivethird party software. Some are freely available to academicresearchers, but are limited to one operating system. MicroArrayGenome Imaging and Clustering Tool (MAGIC Tool) is an open sourceprogram that works on all major platforms, and takes users fromtiff to gif. Several unique features of MAGIC Tool areparticularly useful for research and teaching. Availability: http://www.bio.davidson.edu/MAGIC Contact: laheyer{at}davidson.edu 相似文献
32.
Glutathione S-Transferase M1, T1, P1 Genotypes and Risk for Development of Colorectal Cancer 总被引:3,自引:0,他引:3
Ateş NA Tamer L Ateş C Ercan B Elipek T Ocal K Camdeviren H 《Biochemical genetics》2005,43(3-4):149-163
The glutathione S-transferase (GST) supergene family is an important part of cellular enzyme defense against endogenous and exogenous chemicals, many of which have carcinogenic potential. The present investigation was conducted to detect a possible association between polymorphisms at the GSTM1, GSTT1, and GSTP1 genes and the interaction with cigarette smoking and colorectal cancer incidence. We examined 181 patients with colorectal cancer and 204 controls. DNA was extracted from whole blood, and the GSTM1, GSTT1, and GSTP1 polymorphisms were determined using a real-time polymerase chain reaction and fluorescence resonance energy transfer with a Light-Cycler instrument. Associations between specific genotypes and the development of colorectal cancer were examined by use of logistic regression analysis to calculate odds ratios (OR) and 95% confidence intervals (CI). The GSTM1 polymorphism was associated with an increased risk of developing colorectal cancer (OR = 1.62, 95% CI: 1.06–2.46). Also the risk of colorectal cancer associated with the GSTT1 null genotype was 1.64 (95% CI: 1.10–2.59). Statistically no differences were found between patients with colorectal cancer and control groups for the GSTP1 Ile/Ile, Ile/Val and Val/Val genotypes. In addition, the frequencies of the GSTM1 and GSTT1 deletion genotypes differed significantly between the cases and controls for current smokers; the GSTT1 null genotype especially is associated with a greater risk of colorectal cancer (OR = 2.44, 95% CI: 1.24–4.81). The GSTM1 and GSTT1 deletions were associated with an increased risk of developing a transverse or rectal tumor (OR = 1.86, 95% CI: 1.15–3.00; OR = 1.70, 95% CI: 1.02–2.84; respectively). The glutathione S-transferase polymorphisms were not associated with risk in patients stratified by age. The risk of colorectal cancer increased as putative high-risk genotypes increased for the combined genotypes of GSTM1 null, GSTT1 null, and either GSTP1 valine heterozygosity or GSTP1 valine homozygosity (OR = 2.69, 95% CI: 1.02–7.11). In conclusion, the results obtained in this study clearly suggest that those susceptibility factors related to different GST polymorphic enzymes are predisposing for colorectal cancer. 相似文献
33.
The aim of this study was to determine the consistency of spouses' declarations about contraceptive use and child desire in Turkey. Husbands eligible for the study were currently married to eligible women, i.e. those who generally lived in the same household or who stayed in the household the night before the interview. Husband questionnaires were completed by 1971 men. It was found that 88.9% of the couples had not talked about family planning with each other in the last two months. The percentage of answers on current contraceptive use for all methods that were consistent for husbands and wives was 70.2%. The consistency among partners who stated they would like to have children in the future was found to be 94.8%, and that among partners who were planning to use a contraceptive method was found to be 88.3%. 相似文献
34.
Karabay O Kocoglu E Ince N Sahan T Ozdemir D 《Journal of microbiology (Seoul, Korea)》2006,44(1):129-131
The antimicrobial effects of sodium benzoate against Enterococcus faecalis and Enterococcus faecium were investigated. The MIC(90) of sodium benzoate were 64 mg/L for E. faecalis and 32 mg/L for E. faecium, while the MBC(90) were 128 mg/L and 64 mg/L, respectively. Although further studies are required for clinical evidence, sodium benzoate seems to be effective against Enterococcus spp. 相似文献
35.
Bulbul Ahmed Bin Cao Jeffrey S. McLean Tuba Ica Alice Dohnalkova Ozlem Istanbullu Akin Paksoy Jim K. Fredrickson Haluk Beyenal 《Applied and environmental microbiology》2012,78(22):8001-8009
A facultative iron-reducing [Fe(III)-reducing] Paenibacillus sp. strain was isolated from Hanford 300A subsurface sediment biofilms that was capable of reducing soluble Fe(III) complexes [Fe(III)-nitrilotriacetic acid and Fe(III)-citrate] but unable to reduce poorly crystalline ferrihydrite (Fh). However, Paenibacillus sp. 300A was capable of reducing Fh in the presence of low concentrations (2 μM) of either of the electron transfer mediators (ETMs) flavin mononucleotide (FMN) or anthraquinone-2,6-disulfonate (AQDS). Maximum initial Fh reduction rates were observed at catalytic concentrations (<10 μM) of either FMN or AQDS. Higher FMN concentrations inhibited Fh reduction, while increased AQDS concentrations did not. We also found that Paenibacillus sp. 300A could reduce Fh in the presence of natural ETMs from Hanford 300A subsurface sediments. In the absence of ETMs, Paenibacillus sp. 300A was capable of immobilizing U(VI) through both reduction and adsorption. The relative contributions of adsorption and microbial reduction to U(VI) removal from the aqueous phase were ∼7:3 in PIPES [piperazine-N,N′-bis(2-ethanesulfonic acid)] and ∼1:4 in bicarbonate buffer. Our study demonstrated that Paenibacillus sp. 300A catalyzes Fe(III) reduction and U(VI) immobilization and that these reactions benefit from externally added or naturally existing ETMs in 300A subsurface sediments. 相似文献
36.
Cronin M Akin AR Collins SA Meganck J Kim JB Baban CK Joyce SA van Dam GM Zhang N van Sinderen D O'Sullivan GC Kasahara N Gahan CG Francis KP Tangney M 《PloS one》2012,7(1):e30940
The ability to track microbes in real time in vivo is of enormous value for preclinical investigations in infectious disease or gene therapy research. Bacteria present an attractive class of vector for cancer therapy, possessing a natural ability to grow preferentially within tumours following systemic administration. Bioluminescent Imaging (BLI) represents a powerful tool for use with bacteria engineered to express reporter genes such as lux. BLI is traditionally used as a 2D modality resulting in images that are limited in their ability to anatomically locate cell populations. Use of 3D diffuse optical tomography can localize the signals but still need to be combined with an anatomical imaging modality like micro-Computed Tomography (μCT) for interpretation.In this study, the non-pathogenic commensal bacteria E. coli K-12 MG1655 and Bifidobacterium breve UCC2003, or Salmonella Typhimurium SL7207 each expressing the luxABCDE operon were intravenously (i.v.) administered to mice bearing subcutaneous (s.c) FLuc-expressing xenograft tumours. Bacterial lux signal was detected specifically in tumours of mice post i.v.-administration and bioluminescence correlated with the numbers of bacteria recovered from tissue. Through whole body imaging for both lux and FLuc, bacteria and tumour cells were co-localised. 3D BLI and μCT image analysis revealed a pattern of multiple clusters of bacteria within tumours. Investigation of spatial resolution of 3D optical imaging was supported by ex vivo histological analyses. In vivo imaging of orally-administered commensal bacteria in the gastrointestinal tract (GIT) was also achieved using 3D BLI. This study demonstrates for the first time the potential to simultaneously image multiple BLI reporter genes three dimensionally in vivo using approaches that provide unique information on spatial locations. 相似文献
37.
M Serdar E Sertoglu M Uyanik S Tapan K Akin C Bilgi I Kurt 《Free radical research》2012,46(10):1291-1295
Abstract Background. Measurement of urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG) has recently become more popular as a means of assessing oxidative stress in the human body. The aim of this study is to compare the levels of urine 8-OHdG in patients with type 2 diabetes with and without nephropathy and to evaluate its role as a biochemical marker for distinguishing these patients from healthy and patients without complications. Methods. For this purpose, 52 patients with type 2 diabetes mellitus (32 with nephropathy (DMN), 20 without nephropathy (DM)) and 20 healthy control subjects (C) were included in this study. The urine concentrations of 8-OHdG were measured by modified LC-MS/MS method and compared with the first morning voiding urine albumin/creatinine ratio (UACR) and HbA1c values of the same patients. Results. The concentrations of urine 8-OHdG in DMN and DM patients were higher than those of the control subjects (3.47?±?0.94, 2.92?±?1.73, 2.1?±?0.93 nmol/mol creatinine, respectively). But there was no statistical difference between DMN and DM (p =?0.115). There is significant correlation between urinary 8-OHdG and UACR (r =?0.501, p 0.001). According to ROC analysis, the AUC value of HbA1c was higher than the value of the AUC of 8-OHdG (0.882 and 0.771, respectively). Conclusions. This study shows that the urine 8-OHdG levels increase in diabetic patients. However, urinary 8-OHdG is not a useful clinical marker, compared with UACR, to predict the development of diabetic nephropathy in diabetic patients. 相似文献
38.
Erdogan Kocamaz Duygu Gok Ayse Cetinkaya A. Cevik Tufan 《Journal of molecular histology》2012,43(5):497-508
This study investigated the involvement of CNP-3, chick homologue for human C-type natriuretic peptide (CNP), in TGF-β1 induced chondrogenic differentiation of chicken bone marrow-derived mesenchymal stem cells (MSCs). Chondrogenic differentiation of MSCs in pellet cultures was induced by TGF-β1. Chondrogenic differentiation and glycosaminoglycan synthesis were analyzed on the basis of basic histology, collagen type II expression, and Alcian blue staining. Antibodies against CNP and NPR-B were used to block their function during these processes. Results revealed that expression of CNP-3 and NPR-B in MSCs were regulated by TGF-β1 in monolayer cultures at mRNA level. In pellet cultures of MSCs, TGF-β1 successfully induced chondrogenic differentiation and glycosaminoglycan synthesis. Addition of CNP into the TGF-β1 supplemented chondrogenic differentiation medium further induced the glycosaminoglycan synthesis and hypertrophy of differentiated chondrocytes in these pellets. Pellets induced with TGF-β1 and treated with antibodies against CNP and NPR-B, did show collagen type II expression, however, Alcian blue staining showing glycosaminoglycan synthesis was significantly suppressed. In conclusion, CNP-3/NPR-B signaling may strongly be involved in synthesis of glycosaminoglycans of the chondrogenic matrix and hypertrophy of differentiated chondrocytes during TGF-β1 induced chondrogenic differentiation of MSCs. 相似文献
39.
Ogura Y Naito H Akin S Ichinoseki-Sekine N Kurosaka M Kakigi R Sugiura T Powers SK Katamoto S Demirel HA 《American journal of physiology. Regulatory, integrative and comparative physiology》2008,294(5):R1600-R1607
This study examined whether the exercise-increased extracellular heat shock protein 72 (eHsp72) levels in rats was associated with body temperature elevation during exercise. In all, 26 female Sprague-Dawley rats (3 mo old) were assigned randomly to control (CON; n = 8), exercise under warm temperature (WEx; n = 9), or exercise under cold temperature (CEx; n = 9). The WEx and CEx were trained at 25 degrees C or 4 degrees C, respectively, for nine days using a treadmill. Before and immediately after the final exercise bout, the colonic temperatures were measured as an index of body temperature. The animals were subsequently anesthetized, and blood samples were collected and centrifuged. Plasma samples were obtained to assess their eHsp72 levels. Only the colonic temperature in WEx was increased significantly (P < 0.05) by exercise. The eHsp72 level in WEx was significantly higher (P < 0.05) than that of either the CON or CEx. However, no significant difference was found between CON and CEx. Regression analyses revealed that the eHsp72 level increased as a function of the body temperature. In another experiment, the eHsp72 level of animals with body temperature that was passively elevated through similar kinetics to those of the exercise was studied. Results of this experiment showed that mere body temperature elevation was insufficient to induce eHsp72 responses. Collectively, our results suggest that body temperature elevation during exercise is important for induction of exercise-increased eHsp72. In addition, the possible role of body temperature elevation is displayed when the exercise stressor is combined with it. 相似文献
40.
Effect of Strontium Ranelate on Hydrogen Peroxide-Induced Apoptosis of CRL-11372 Cells 总被引:2,自引:0,他引:2
Senkoylu A Yilmaz A Ergun MA Ilhan MN Simsek A Altun N Bolukbasi S Menevse S 《Biochemical genetics》2008,46(3-4):197-205
In vitro and in vivo studies have proven strontium to be an osteoinductive trace element. The effect of strontium ranelate
(SR) on H2O2-induced apoptosis of CRL-11372 cells and optimization of its anti-apoptotic dose were the aims of this study. After 1 h of
pretreatment with SR 1 μM, 50 μM, 100 μM, 500 μM, and 1,000 μM concentrations, CRL-11372 osteoblasts were exposed to 100 μM H2O2 for periods of 6–12 h. The same experiments were repeated without H2O2. The apoptotic index and viability of cells were assessed quantitatively with a fluorescent dye and qualitatively with agarose
gel electrophoresis. Concentrations of 1–100 μM of SR with a 6-h treatment and only 1 μM concentration with a 12-h treatment
inhibited the apoptotic effect of H2O2 on cultured osteoblasts significantly (P < 0.05). SR was shown to inhibit H2O2-induced apoptosis of CRL-11372 cells in a dose-dependent manner. 相似文献