The importance of antioxidant status in gastric intestinal metaplasia

BackgroundOxidative stress status in different cancer types was investigated before, but not studied in gastric intestinal metaplasia to the best of our knowledge. Purpose of this study is to examine whether there is a difference between oxidative stress status in patients with intestinal metaplasia (IM) compared to individuals without IM, we compared the serum levels of disulfide (SS), total thiol (TT) and native thiol (NT).MethodsThis was a prospective, non-randomized casecontrol study including 67 patients with histopathologically confirmed IM and 60 individuals demographically matched in terms of age, gender, BMI, smoking status, and chronic diseases as control group.ResultsThe mean NT, TT and NT to TT (NT/TT) ratios were statistically significantly higher in IM group compared to controls ((351.71 ± 81.9 mol/L vs. 271.82 ± 54.13 mol/L, p=0.000), (391.5 ± 92.69 mol/L vs. 308.59 ± 55.53 mol/L, p=0.000) and (0.89 ± 0.6 vs. 0.87 ± 0.29, p=0.022), respectively). The mean SS to TT (SS/TT) ratio was significantly lower in IM group than control group (0.050 ± 0.31 vs. 0.060 ± 0.014, P=0.022). Median SS and mean SS/NT ratio was similar in both groups (16.3 (3.3-78) vs. 18.3 (10-32.7), p=0.271 and 0.055 ± 0.041 vs. 0.070 ± 0.019, p=0.068, respectively). In ROC analysis, cut off value of SS/NT for IM was found 0.062, in regression analysis, SS/NT <0.062 was found as an independently prognostic marker for IM (OR, 2.38; 95%CI: 1.168-4.865, P=0.017).ConclusionsSS/NT ratio lower than 0.062 was found as an independently prognostic marker for IM. This ratio could help to distinguish which patients should be followed closely for gastric cancer.     

smyRNA: A Novel Ab Initio ncRNA Gene Finder

Background

Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs.

Methodology/Principal Findings

We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences.

Conclusions/Significance

Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown) ncRNA families. Availability: http://compbio.cs.sfu.ca/taverna/smyrna     

No association between polymorphism in the vascular endothelial growth factor gene at position−460 and sporadic prostate cancer in the Turkish population

The development and progression of prostate cancer (PCa) has biologically and genetically remained a mystery. A man’s risk of developing PCa is influenced by both genetic and environmental factors. Angiogenic cytokines like vascular endothelial growth factor (VEGF) play a pivotal role in tumor angiogenesis. Single nucleotide polymorphisms in angiogenesis-dependent genes affect the sensibility of cancer development and progression. Therefore, we hypothesized a potential association between DNA sequence variations in VEGF −460 gene region and sporadic PCa patients in the Turkish population. 133 sporadic PCa patients and 157 healthy controls were studied. Genotypes were determined by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. The distribution of genotype and allele frequencies of the polymorphism did not yield a statistically significant difference between patients and controls (P > 0.05). Furthermore, classification of patients by tumor-lymph nodes-metastasis (TNM), Gleason Scores (GS) and serum prostate-specific antigen (PSA) levels did not show significant differences among the VEGF −460 C>T genotypes (P > 0.05). This is the first demonstration showing that the VEGF −460 C>T polymorphism in men is not associated with sporadic PCa in the Turkish population.     

Absence of typical diel vertical migration in Daphnia: varying role of water clarity, food, and dissolved oxygen in Lake Eymir, Turkey

Diel vertical migration (DVM) is a complex and dynamic behaviour against predation because the reaction of migrating organisms to light intensity plays a primary role, but is modified by other factors. In the relatively shallow but thermally stratified Lake Eymir, Daphnia pulex de Geers utilized vertical refugia afforded by the hypolimnion during both day and night. Differences in general vulnerability to fish predation determined the differences in their mean residence depths (MRDs) of different population categories such as most conspicuous and vulnerable individuals of adult with eggs inhabited the deepest depth, whereas juveniles stayed close the thermocline. In late spring, profoundly high amplitude of displacement within the hypolimnion, probably due to the hypolimnion being well-lit and relatively well-oxygenated for the fish and rather unsafe for the large-sized daphnids, was recorded. Therefore, the large-sized daphnids daytime refuge was close to the bottom whereas at night they moved upward to benefit from warmer water temperature along with food availability in the presence of fish predation but still remained below the thermocline. In summer, the insignificant amplitude of the hypolimnetic, which later became epilimnetic, displacements were probably due to the near-anoxic condition found below the thermocline. This might have deterred the fish, thus providing a safer refuge for daphnids in the below thermocline, which afterwards became the above thermocline. Low oxygen availability was regarded as the summer proximate factor. The abundant food and warmer water conditions found in the below/above thermocline also accounted for absence of DVM in summer. Consequently, this study suggests that DVM by Daphnia is an adaptation that is plastic to changing environmental conditions.     

The activation loop phosphorylation of protein kinase D is an early marker of neuronal DNA damage

In neurons, DNA damage induces protein synthesis-dependent apoptosis mediated by the mitochondrial intrinsic cell-death pathway. Signal transduction cascades activated by genotoxic stress upstream of the mitochondria are largely unknown. We identified protein kinase D (PKD) as one of the earliest markers of neuronal DNA damage. Phosphorylation of the PKD-activation domain could be detected within 15 min of genotoxic stress and was concurrent with ataxia telangiectasia-mutated (ATM) activation. PKD stimulation was selective to DNA damage and did not occur with other stress stimuli examined. In vivo, both young and adult rats showed increased levels of phosphorylated PKD in neuronal tissues after injection of DNA-toxin etoposide. These results indicate that PKD activation is an early neuronal response to DNA damage, suggesting that signaling downstream of PKD may be critical for neuronal survival after genotoxic stress.     

Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains

A systems approach to biology requires a principled approach to pathway identification. In this study, the two nuclear petite yeast mutants K1Deltapet191a and K1Deltapet191ab and their parental industrial strain K1 were cultured in glucose-containing microaerobic chemostats. Exometabolomic profiles were used to infer the differences in the fermentation characteristics and respiration capacity of the strains. The ability of the metabolite measurement information to describe genetically different strains was investigated using a genome-scale yeast model. Flux balance analysis (FBA) of the model reveals that the objective function of minimal oxygen consumption enables the identification of the effect of genotypic differences when combined with the knowledge of the extracellular state of metabolism. The predicted decrease in oxygen consumption flux of K1Deltapet191a and K1Deltapet191ab strains with respect to the parental strain is about 80% and 100%, respectively, which coincides with the respiratory deficiencies of the strains. The expected increase in ethanol production rates in response to the decrease in the respiratory capacity was also predicted to be very close to the experimental values. This study shows the predictive power of the integrated analysis of genome-scale models with exometabolomic profiles, since accurate predictions could be made without any information about the respiration capacity of the strains. The FBA approach thereby enables identification of responsive pathways and so permits the elucidation of the genetic characteristics of strains in terms of expressed metabolite profiles.     

Health risk perspectives of metal(loid) exposure via consumption of striped venus clam (Chamelea gallina Linnaeus, 1758)

The metal(loid)s are mainly transported to the Black Sea via rivers and affect the coastal area where fisheries are intensive. Chamelea gallina (striped venus clam) is the most abundant mollusk species in the Black Sea and used as a bioindicator for monitoring of metal(loid) pollution. In this respect, the concentrations of As, Cd, Cr, Cu, Pb, and Zn in C. gallina collected from 16 different locations along the Black Sea coast (Turkey, Bulgaria, and Russia) were determined and evaluated for the potential human health risk. The results obtained were found to be below the maximum permissible limits indicated in the food safety guidelines. Similarly, the analyzed metal(loid)s did not pose a potential hazard to humans for consumption of the C. gallina, regarding provisional tolerable weekly intake described by the Joint FAO/WHO Expert Committee on Food Additives (JECFA). Moreover, target hazard quotient and hazard index were found to be lower than 1 for not only average consumer but also the consumer who consumed a portion (160 g) once a week. In contrast, consumption of C. gallina could cause health risks for Cd and As in case of increasing portion sizes.