Genetic diversity of Garra rufa Heckel, 1843 (Teleostei: Cyprinidae) in Anatolia

In the present study, mitochondrial DNA polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) and nuclear DNA inter-simple sequence repeat (ISSR) assays were used to assess the phylogenetic and phylogeographic relationships among Garra rufa samples from Anatolia. The complete mtDNA NADH 3/4 dehydrogenase (ND-3/4) gene amplified by PCR was digested with eight restriction enzymes. These enzymes produced 20 composite haplotypes for G. rufa populations. All the mtDNA haplotypes detected were highly diverged from each other and each lineage had a unique genetic profile. The evaluation of mtDNA PCR-RFLP data coupled with geological history of Anatolia indicated a deep genetic divergence among the mtDNA haplotypes of G. rufa populations from drainages of the Mediterranean and Persian Gulf, suggesting an early isolation of Tigris-Euphrates with Orontes river and other rivers draining into the Mediterranean Sea. In general, data from both mtDNA and nDNA were congruent.     

TAP1 and TAP2 gene polymorphisms in childhood cystic echinococcosis

The incidence of cystic echinococcosis (CE) due to Echinococcus granulosus is as high as 2000–2500 patients per year in Turkey. Whether genetic characteristics of the Turkish population cause a tendency to the disease is currently unknown. We aimed at studying the role of TAP gene polymorphisms in Turkish children with cystic echinococcosis. For an overview of allelic distribution of TAP1 and TAP2 genes, genotypes of 85 patients with CE and 100 controls were studied. To determine the genotype–phenotype correlation, 81 of the patients whose clinical data were available were analyzed. For TAP1-637, Asp/Gly heterozygosity was significantly more prevalent in CE patients than in controls (20 vs. 4%, odds ratio 6.0), while Gly/Gly homozygosity was less frequent (5 vs. 14%). For TAP2-379, Ile/Val heterozygosity was significantly more prevalent in CE patients than in controls (14 vs. 1%, odds ratio 16.27), while Ile/Ile homozygosity was less frequent (13 vs. 25%). TAP1-637 and TAP2-379 polymorphisms may have a role in causing genetic tendency for CE in children. The data may reflect the genetic properties of the Turkish population or may reveal the minor role of TAP gene polymorphisms in CE.     

Identification of a potent and selective non-basic cathepsin K inhibitor

Based on our previous study with trifluoroethylamine as a P2-P3 amide isostere of cathepsin K inhibitor, further optimization led to identification of compound 22 (L-873724) as a potent and selective non-basic cathepsin K inhibitor. This compound showed excellent pharmacokinetics and efficacy in an ovariectomized (OVX) rhesus monkey model. The volumes of distribution close to unity were consistent with this compound not being lysosomotropic, which is a characteristic of basic cathepsin K inhibitors.     

A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets

Well-defined relationships between oligonucleotide properties and hybridization signal intensities (HSI) can aid chip design, data normalization and true biological knowledge discovery. We clarify these relationships using the data from two microarray experiments containing over three million probes from 48 high-density chips. We find that melting temperature (T_m) has the most significant effect on HSI while length for the long oligonucleotides studied has very little effect. Analysis of positional effect using a linear model provides evidence that the protruding ends of probes contribute more than tethered ends to HSI, which is further validated by specifically designed match fragment sliding and extension experiments. The impact of sequence similarity (SeqS) on HSI is not significant in comparison with other oligonucleotide properties. Using regression and regression tree analysis, we prioritize these oligonucleotide properties based on their effects on HSI. The implications of our discoveries for the design of unbiased oligonucleotides are discussed. We propose that isothermal probes designed by varying the length is a viable strategy to reduce sequence bias, though imposing selection constraints on other oligonucleotide properties is also essential.     

Treatment of dye-rich wastewater by an immobilized thermophilic cyanobacterial strain: Phormidium sp.

The removal of Remazol Blue and Reactive Black B by the immobilized thermophilic cyanobacterial strain Phormidium sp. was investigated under thermophilic conditions in a batch system, in order to determine the optimal conditions required for the highest dye removal. In the experiments, performed at pH 8.5, with different initial dye concentrations between 9.1 mg l⁻¹ and 82.1 mg l⁻¹ and at 45 °C, calcium alginate immobilized Phormidium sp. showed high dye decolorization, with maximum uptake yields ranging from 50% to 88% at all dye concentrations tested. When the effects of high dye concentrations on dye removal were investigated, the highest uptake yield in the beads was 50.3% for 82.1 mg l⁻¹ Remazol Blue and 60.0% for 79.5 mg l⁻¹ Reactive Black B. The highest color removal was detected at 45 °C and 50 °C incubation temperatures for all dye concentrations. As the temperature decreased, the removal yield of immobilized Phormidium sp. also decreased. At about 75 mg l⁻¹ initial dye concentrations, the highest specific dye uptake measured was 41.29–41.17 mg g⁻¹ for Remazol Blue and 47.69–43.82 mg g⁻¹ for Reactive Black B at 45 °C and 50 °C incubation temperatures, respectively, after 8 days incubation.     

Pyrolysis of safflower (Charthamus tinctorius L.) seed press cake: part 1. The effects of pyrolysis parameters on the product yields

Safflower (Charthamus tinctorius L.) seed press cake was pyrolysed in a fixed-bed reactor. The effects of pyrolysis temperature, heating rate and sweep gas flow rates on the yields of the products were investigated. Pyrolysis runs were performed using pyrolysis temperatures between 400 and 600 °C with heating rates of 10, 30 and 50 °C min⁻¹. The obtained bio-char, gas and bio-oil yields ranged between 25 and 34 wt%, 19 and 25 wt%, and 28 and 36 wt%, respectively, at different pyrolysis conditions. The highest liquid yield was obtained at 500 °C pyrolysis temperature with a heating rate of 50 °C min⁻¹ under the sweep gas of N₂ with a flow rate of 100 cm³ min⁻¹. Employing the higher heating rate of 50 °C min⁻¹ results in maximum bio-oil yield, probably due to the decrease in mass transfer limitations. According to the results obtained under the conditions of this study, the effects of pyrolysis temperature and sweep gas flow rate are more significant than the effect of heating rate on the yields.     

Epileptic seizures induce structural and functional alterations on brain tissue membranes

Epilepsy is characterized by disruption of balance between cerebral excitation and inhibition, leading to recurrent and unprovoked convulsions. Studies are still underway to understand mechanisms lying epileptic seizures with the aim of improving treatment strategies. In this context, the research on brain tissue membranes gains importance for generation of epileptic activities. In order to provide additional information for this field, we have investigated the effects of pentylenetetrazol-induced and audiogenetically susceptible epileptic seizures on structure, content and function of rat brain membrane components using Fourier transform infrared (FT-IR) spectroscopy.     

Biomolecular Structure and Composition Changes in the Root System of Long-Lipped Serapias (Serapias vomeracea) After In Vitro Chitosan and Plant Growth Regulator Treatments

In the current study, effects of chitosan oligomers (CHI-OM) with different polymerization degrees (DP) between 2 and 15, and polymeric chitosan (CHI-P) with a DP of 70 were compared with kinetin (KIN), 6-benzylaminopurine (BAP), indole-3-butyric acid (IBA), indole-3-acetic acid (IAA), and jasmonic acid (JAS) on the structure and composition of several biomolecules in the root system of Serapias vomeracea. Evaluation of molecular alterations in the root system of S. vomeracea through an infrared spectroscopic approach provided insight into the differentiation between action mechanisms of chitosan and commonly used plant growth regulators. The results revealed that CHI-P and JAS treatments at low concentrations might enhance the lignin content in the cell walls. Also, JAS, CHI-OM, and CHI-P treatments enhanced cell wall lignification. The water-associated cellulose content of the cell walls was affected by the DP of chitosan. Membrane lipid stabilization and protein content were enhanced after CHI-P, JAS, and KIN treatments, while BAP and CHI-OM treatments triggered lipid, protein, and cell wall polysaccharide synthesis. In particular, CHI-OM treatment also enhanced rhamnogalacturonan and β-galactan content as well as xyloglucans and glucomannans, while the auxin treatments had a similar impact only on glucomannan content. These findings suggest that chitosan may show either purine-based cytokinin-like or lipid-based jasmonic acid-like activity in the root system of S. vomeracea. Additionally, depending on its degree of polymerization, the effects of chitosan may vary on root system development in S. vomeracea.

     

The role of the PTEN/mTOR axis in clinical response of rectal cancer patients

Background

Preoperative chemoradiotherapy has long been accepted as a method to improve survival and lifetime quality of rectal cancer patients. However, physiologic effects of these therapies largely depend on the resistance of cells to the radiation, type of chemotherapeutic agents and individual responses. As one of the signaling cascades involved in chemo- or radiation- resistance, the present study focused on several proteins involved in pTEN/Akt/mTOR pathway to explore their prognostic significance.

Materials and methods

Samples from advanced stage rectal cancer patients were analyzed to detect expression levels of pTEN/Akt/mTOR pathway related proteins pTEN, mLST8, REDD1, BNIP3, SAG and NOXA, together with p53, by RT-qPCR. Kaplan–Meier analysis was used to assess expression-survival relation and correlations among all proteins and clinicopathological features were statistically analyzed.

Results.

Except p53, none of the proteins showed prognostic significance. High p53 expression presented clear impact on overall survival and disease free survival. It was also significantly related to pathologic complete response. p53 showed high correlation to local recurrence as well. On the other hand, strong correlation was observed with PTEN expression and tumor response, but not with survival. High associations were also observed between mLST8/REDD1, PTEN and NOXA, confirming their role in the same cascade.

Conclusion

The contentious role of p53 as a prognostic biomarker in colorectal cancer was further affirmed, while PTEN and REDD1 could be suggested as potential candidates. Additionally, NOXA emerges as a conjunctive element for different signaling pathways.