The role of Wnt pathway antagonists in early-stage lung adenocarcinoma

Molecular Biology Reports - We aimed to examine the expression levels of the genes encoding adenomatous polyposis coli (APC) 1, APC-2, Dickkopf related protein (DKK)-1, DKK-3, secreted...     

Coat Polymorphism in Eurasian Lynx: Adaptation to Environment or Phylogeographic Legacy?

Journal of Mammalian Evolution - We studied the relationship between the variability and contemporary distribution of pelage phenotypes in one of most widely distributed felid species and an array...     

The effects of inter-annual fluctuations in precipitation,lake surface area,and wind speed on phytoplankton structure in three shallow Mediterranean lakes (Sakarya,Turkey)

Aquatic Ecology - Phytoplankton biomass, diversity, functional groups (FGs), and environmental parameters in three shallow lakes were evaluated to show the inter-annual fluctuations in...     

Assessing significance of connectivity and conservation in protein interaction networks.

Comparative analyses of cellular interaction networks enable understanding of the cell's modular organization through identification of functional modules and complexes. These techniques often rely on topological features such as connectedness and density, based on the premise that functionally related proteins are likely to interact densely and that these interactions follow similar evolutionary trajectories. Significant recent work has focused on efficient algorithms for identification of such functional modules and their conservation. In spite of algorithmic advances, development of a comprehensive infrastructure for interaction databases is in relative infancy compared to corresponding sequence analysis tools. One critical, and as yet unresolved aspect of this infrastructure is a measure of the statistical significance of a match, or a dense subcomponent. In the absence of analytical measures, conventional methods rely on computationally expensive simulations based on ad-hoc models for quantifying significance. In this paper, we present techniques for analytically quantifying statistical significance of dense components in reference model graphs. We consider two reference models--a G(n, p) model in which each pair of nodes in a graph has an identical likelihood, p, of sharing an edge, and a two-level G(n, p) model, which accounts for high-degree hub nodes generally observed in interaction networks. Experiments performed on a rich collection of protein interaction (PPI) networks show that the proposed model provides a reliable means of evaluating statistical significance of dense patterns in these networks. We also adapt existing state-of-the-art network clustering algorithms by using our statistical significance measure as an optimization criterion. Comparison of the resulting module identification algorithm, SIDES, with existing methods shows that SIDES outperforms existing algorithms in terms of sensitivity and specificity of identified clusters with respect to available GO annotations.     

Efficacy and safety of Saccharomyces boulardii in the 14-day triple anti-Helicobacter pylori therapy: a prospective randomized placebo-controlled double-blind study

Background: Recent studies indicate a potential role of Saccharomyces boulardii in the prevention of Helicobacter pylori treatment‐related side‐effects and also in improvement of eradication rate. Our aim is to investigate the efficacy and safety of S. boulardii in the prevention of side‐effects related to H. pylori eradication. The secondary aim of the study was to define the effect of S. boulardii on the eradication success of anti‐H. pylori therapy. Materials and methods: One hundred and twenty‐four patients with H. pylori infection (male/female: 44/80, mean age: 48 ± 14.25 year) receiving 14 days of triple therapy (clarithromycin 500 mg b.i.d., amoxicillin 1000 mg b.i.d., and lansoprazole 30 mg b.i.d.) were randomly assigned to S. boulardii or placebo. Dyspeptic symptoms were recorded by using modified Glasgow Dyspepsia Questionnaire (GDQ). Side‐effect profile and tolerability were assessed using a symptom‐based questionnaire. H. pylori status was rechecked after 6 weeks after completion of eradication therapy. Results: H. pylori eradication rate, although higher in the treatment group, was statistically similar in treatment and control groups: 71% (44/62) versus 59.7% (37/62), respectively (p > .05). Nine (14.5%) patients in the treatment group and 19 (30.6%) patients in the placebo group experienced diarrhea (p < .05). Epigastric discomfort was more frequent in the control group [9 (14.5%) versus 27 (43.5%), respectively (p < .01)]. Diffuse abdominal pain, abdominal gas, taste disturbance, urticaria, nausea symptoms were similar in both groups. GDQ scores after treatment were significantly better for treatment group (mean ± SD, range: 1.38 ± 1.25 (0–5) vs. 2.22 ± 1.44 (0–6), respectively; p < .01). Conclusion: S. boulardii improved anti‐H. pylori antibiotherapy‐associated diarrhea, epigastric discomfort, and treatment tolerability. In addition, S. boulardii supplement decreased post‐treatment dyspepsia symptoms independent of H. pylori status. However, S. boulardii had no significant affect on the rate of H. pylori eradication.     

Combination of Hb Knossos [Cod 27 (G-T)] and IVSII-745 (C-G) in a Turkish patient with beta-thalassemia major

Beta-thalassemia is the most common disease among hemoglobinopathies in Antalya, Turkey, as well as world-wide. Mutations found in Turkish beta-thalassemia patients constitute a heterogeneous group, consisting mostly of point mutations. Only in very rare cases did deletions or insertions cause affected or carrier phenotypes. Hb Knossos [beta 27 (B9) Ala-Ser] is a rare variant with a normal HbA2 level. In this study, we aimed to investigate the effect of compound heterozygosity for Hb Knossos [Cod 27 (G-T)] and IVSII-745 (C-G). To our knowledge, this is the first report of such a combination related with beta-thalassemia major phenotype in a Turkish family, where reverse dot blot hybridization (RDBH) and DNA sequencing analysis were used. Heterozygous inheritance of the mutation results in mild beta-thalassemia phenotype, whereas homozygous inheritance leads to intermediate beta-thalassemia. As a result, the compound heterozygosity of Hb Knossos with IVSII-745 appears as the cause of the beta-thalassemia major phenotype in our case. The combination of these mutations [Hb Knossos, Cod 27 (G-T), and IVSII-745, C-G] causes the beta-thalassemia major phenotype, and this is important for genetic counseling.     

Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus

Background

Two component lantibiotics, such as the plasmid-encoded lacticin 3147 produced by Lactococcus lactis DPC3147 and staphylococcin C55 produced by Staphylococcus aureus C55, represent an emerging subgroup of bacteriocins. These two bacteriocins are particularly closely related, exhibiting 86% (LtnA1 and C55α) and 55% (LtnA2 and C55β) identity in their component peptides. The aim of this study was to investigate, for the first time for any two component bacteriocins, the significance of the relatedness between these two systems.

Results

So close is this relatedness that the hybrid peptide pairs LtnA1:C55β and C55α:LtnA2 were found to have activities in the single nanomolar range, comparing well with the native pairings. To determine whether this flexibility extended to the associated post-translational modification/processing machinery, the staphylococcin C55 structural genes were directly substituted for their lacticin 3147 counterparts in the ltn operon on the large conjugative lactococcal plasmid pMRC01. It was established that the lacticin LtnA1 post-translational and processing machinery could produce functionally active C55α, but not C55β. In order to investigate in closer detail the significance of the differences between LtnA1 and C55α, three residues in LtnA1 were replaced with the equivalent residues in C55α. Surprisingly, one such mutant LtnA1-Leu21Ala was not produced. This may be significant given the positioning of this residue in a putative lipid II binding loop.

Conclusion

It is apparent, despite sharing striking similarities in terms of structure and activity, that these two complex bacteriocins display some highly dedicated features particular to either system.     

Effects of some drugs on human erythrocyte 6-phosphogluconate dehydrogenase: an in vitro study

Inhibitory effects of some drugs were investigated on human erythrocyte 6-phosphogluconate dehydrogenase obtained with a 6552-fold purification in a yield of 78% using 2', 5'-ADP Separose 4B affinity gel. Which on SDS polyacrylamide gel electrophoresis showed a single band. Larnoxicam, metronidazole, imipenem, ornidazole, vancomycin, clindamycin, and amoxicillin exhibited inhibitory effects on the enzyme in vitro with IC50 values of 0.17, 0.23, 0.43, 21.79, 46.39, 117.43 and 287.35 mM, and the Ki constants 0.40 +/- 0.04, 0.57 +/- 0.06, 0.77 +/- 0.11, 42.40 +/- 2.89, 65.60 +/- 4.03, 130.22 +/- 9.21, and 287.58 +/- 10.56 mM, respectively. While vancomycin, clindamycin and amoxicillin showed competitive inhibition the other drugs displayed noncompetitive inhibition.     

Determinants of adolescent pregnancy in an urban area in Turkey: a population-based case-control study

The aim of this study was to determine the degree to which socioeconomic status is a risk factor for first birth at age 19 or younger in married women in an urban area of Turkey. The research was a population-based case-control study. The study group comprised all married and pregnant women aged 15-19 (adolescent pregnancies) attending primary care centres (144 subjects). Married women between 20 and 29 years of age, experiencing their first pregnancy (adult pregnancies), were determined as the control group (144 subjects). A questionnaire was completed for each subject during face-to-face interviews. Adolescent pregnancy was more frequent in women from families with a low socioeconomic status, as determined by occupation (class) and income; both were associated with adolescent pregnancy. Multiple logistic regression analysis identified seven factors associated with adolescent pregnancy: exposure to violence within the family prior to marriage; families partially opposed or unopposed to adolescent marriage; secondary school or lower education level; lack of social security; living in houses in which the number of persons per room was over 1; unemployed women; and having sisters with a history of adolescent pregnancy.     

Mutations in the <Emphasis Type="Italic">S</Emphasis> gene region of hepatitis B virus genotype <Emphasis Type="Italic">D</Emphasis> in Turkish patients

The S gene region of the hepatitis B virus (HBV) is responsible for the expression of surface antigens and includes the ‘a’-determinant region. Thus, mutation(s) in this region would afford HBV variants a distinct survival advantage, permitting the mutant virus to escape from the immune system. The aim of this study was to search for mutations of the S gene region in different patient groups infected with genotype D variants of HBV, and to analyse the biological significance of these mutations. Moreover, we investigated S gene mutation inductance among family members. Forty HBV-DNA-positive patients were determined among 132 hepatitis B surface antigen (HbsAg) carriers by the first stage of seminested PCR. Genotypes and subtypes were established by sequencing of the amplified S gene regions. Variants were compared with original sequences of these serotypes, and mutations were identified. All variants were designated as genotype D and subtype ayw3. Ten kinds of point mutations were identified within the S region. The highest rates of mutation were found in chronic hepatitis patients and their family members. The amino acid mutations 125 (M → T) and 127 (T → P) were found on the first loop of ‘a’-determinant. The other consequence was mutation inductance in a family member. We found some mutations in the S gene region known to be stable and observed that some of these mutations affected S gene expression.