Cancer Detection with Surface Plasmon Resonance-Based Photonic Crystal Fiber Biosensor

Plasmonics - In this study, early cancer detection of a single living cell is investigated by employing a surface plasmon resonance (SPR)-based photonic crystal fiber (PCF) biosensor structure. The...     

Molecular dynamics investigation of Helicobacter pylori chemotactic protein CheY1 and two mutants

The Michael-Claisen domino (MCD) cyclization used in the lycopodine synthesis by Stork, was evaluated mechanistically using DFT calculations. Calculations suggest that a dianion is not formed, which conforms to classical dianion formation normally requiring strong kinetic bases. Instead ethoxide in ethanol produces a monoanionic species driving the MCD cyclization. This endeavor has opened up potential to expand the scope of this unique reaction and provide educational clarity.     

The Effects of Chronomodulated Therapy with 5-Fluorouracil (5-Fu) and Folinic Acid (Fa) on the Toxicity and Quality of Life in Patients with Advanced Gastric Cancer

This study was designed to assess the tolerability of chronomodulated infusion chemotherapy, individualized by the rhythm of peripheral blood cells. Twenty patients with metastatic gastric cancer were randomized to chronotherapy or day-time arms of 5-fluorouracil (FU) (600 mg/m², 8 h inf.d1-5) and folinic acid (FA) (20 mg/m², iv, d1-5) in the first cycle and crossed-over to the other arm in the following cycles. Ten of 18 evaluable patients were assigned to chronotherapy arm and eight to day-time in the first cycle. Although there was no significant difference between two arms on enrollment, chronotherapy arm yielded an improvement of 45% of QLQ-C30 scores (p = 0.021) and the day-time arm had 11% improvement (p = 0.575). After the crossing-over, chronotherapy arm, again, had a significant improvement in QLQ-C30 scores, compared to the day-time arm (14% vs. -18%, p = 0.001, respectively). Mucositis/diarrhea was significantly higher in the day-time arm compared to chronotherapy arm (p = 0.015). In conclusion, chronomodulated infusion of 5-FU might improve the quality of life.     

Differences in shape and size of skull and mandible in Talpa species (Mammalia: Eulipotyphla) from Turkey

We analysed with landmark-based images morphological differences between four species of Talpa which resemble each other morphologically and are all highly adapted to underground life. Subtle shape differences of the skull and mandibular bones were found between all species. However, there is also broad overlap between all species. Talpa caucasica had the largest skull and mandibles, and Talpa levantis the smallest.     

Phytochemical Profiling,in Vitro Biological Activities and in Silico Molecular Docking Studies of the Crude Extract of Crambe orientalis,an Endemic Plant in Turkey

In this study, total phenolic and flavonoid analyses of flower, leaf, and stem aqueous extracts of C. orientalis were performed. Total phenolic contents of C. orientalis extracts ranged from 12.2±0.06 to 19.0±0.07 mg GAE/g extract. Total flavonoid values range between 2.0±0.11 and 6.6±0.19 mg CE/g extract. Urease, collagenase, tyrosinase, and α-glucosidase inhibition activities were determined in vitro and the relationship between them was examined. IC₅₀ results for all enzymes were obtained between 0.18 and 3.53 μg/mL. The aqueous extract of the plant C. orientalis showed potent cytotoxic effects against the human colon cancer cell lines DLD-1. As the extract concentration increases, cell death increases. The main fatty acid composition by GC/MS analysis is erucic acid (36.5 %). The potential binding modes of the fatty acids in the plant extract to the enzymes and possible inhibition mechanisms were determined by molecular docking calculation.     

Complete mitochondrial genomes of Chionomys roberti and Chionomys nivalis (Mammalia: Rodentia) from Turkey: Insight into their phylogenetic position within Arvicolinae

Organisms Diversity & Evolution - The complete mitochondrial DNA (mitogenome) sequences of Chionomys nivalis and C. roberti were first presented as reference mitogenomes by the current study...     

In vitro conservation and cryopreservation of mature pistachio (Pistacia vera L.) germplasm

As genetic erosion of pistachio (Pistacia vera L.) has been occurring in the Mediterranean, Central and West Asia and North Africa, experiments were conducted to conserve two cultivars (‘Atl?’ and ‘Siirt’) of mature pistachio germplasm by assessing both medium- and long-term conservation techniques. In medium-term conservation, our results showed that it was feasible to conserve both cultivars in the form of either microshoots or encapsulated shoot apices up to 12 months at 4°C in the dark. As regards long-term conservation, encapsulation-dehydration and droplet-vitrification techniques were assessed for cryopreservation of cold-hardened and osmoprotected shoot apices of mature ‘Atl?’ cultivar. Among the methods tested, 13.6% of regrowth was achieved with incubation of explants in the droplets of vitrification solution for 150 min at 0°C followed by direct immersion in liquid nitrogen (LN), rapidly thawed and then cultured on Murashige and Skoog’s (MS) medium containing 1 mg L^?1 BA and 0.5 mg L^?1 GA_3. The developed droplet-vitrification technique appeared as a promising procedure for long-term preservation of shoot apices of mature pistachio germplasm. Moreover, assesment of genetic fidelity by Random Amplified Polymorphic DNA analysis (RAPD) revealed out high levels of genetic stability between donor plant and cryopreserved plants (similarity indexes between 0.959 and 0.973) after they were subcultured for at least 3 months. The detected low level of genetic instability could be due to the toxic effect of PVS2 and regeneration phase. The optimized conservation techniques, especially slow growth storage, could be applied to preserve other Pistacia species.     

Sinus Node Dysfunction as the First Manifestation of Left Ventricular Noncompaction with Multiple Cardiac Abnormalities

Left ventricular noncompaction (LVNC) is a genetically heterogenous form of cardiomyopathy which may remain undiagnosed till adulthood due to the late presentation of typical symptoms such as dyspnea, congestion, ventricular arrhythmias and thromboembolism. Symptomatic bradycardia secondary to persistent sinus node dysfunction is very rare. Coexistent cardiac defects are common in children however in adults the disease is usually in isolated form. Here, we present a case of twenty-three year-old female LVNC patient with patent ductus arteriosus, bicuspid aortic valve and persistent sinus node dysfunction who presented with dizziness as the first manifestation of the disease.     

OETMAP: a new feature encoding scheme for MHC class I binding prediction

Deciphering the understanding of T cell epitopes is critical for vaccine development. As recognition of specific peptides bound to Major histocompatibility complex (MHC) class I molecules, cytotoxic T cells are activated. This is the major step to initiate of immune system response. Knowledge of the MHC specificity will enlighten the way of diagnosis, treatment of pathogens as well as peptide vaccine development. So far, a number of methods have been developed to predict MHC/peptide binding. In this article, a novel feature amino acid encoding scheme is proposed to predict MHC/peptide complexes. In the proposed method, we have combined orthonormal encoding (OE) and Taylor’s Venn-diagram, and have used Linear support vector machines as the classifier in the tests. We also have compared our method to current feature encoding scheme techniques. The tests have been carried out on comparatively large Human leukocyte antigen (HLA)-A and HLA-B allele peptide three binding datasets extracted from the Immune epitope database and analysis resource. On three datasets experimented, the IC50 cutoff a criteria is used to select the binders and non-binders peptides. Experimental results show that our amino acid encoding scheme leads to better classification performance than other amino acid encoding schemes on a standalone classifier.