Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations

Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biology. However, these methods have been less frequently used with empirical population genetics data. In this study, we developed a new combined approach of data analysis using microsatellite marker data from our previous studies of olive populations using machine learning algorithms. Herein, 267 olive accessions of various origins including 21 reference cultivars, 132 local ecotypes, and 37 wild olive specimens from the Iranian plateau, together with 77 of the most represented Mediterranean varieties were investigated using a finely selected panel of 11 microsatellite markers. We organized data in two ‘4-targeted’ and ‘16-targeted’ experiments. A strategy of assaying different machine based analyses (i.e. data cleaning, feature selection, and machine learning classification) was devised to identify the most informative loci and the most diagnostic alleles to represent the population and the geography of each olive accession. These analyses revealed microsatellite markers with the highest differentiating capacity and proved efficiency for our method of clustering olive accessions to reflect upon their regions of origin. A distinguished highlight of this study was the discovery of the best combination of markers for better differentiating of populations via machine learning models, which can be exploited to distinguish among other biological populations.     

Effect of salinity and waterlogging on growth,anatomical and antioxidative responses in <Emphasis Type="Italic">Mentha aquatica</Emphasis> L.

Salinity and waterlogging are two stresses which in nature often occur simultaneously. In this work, effects of combined waterlogging and salinity stresses are studied on the anatomical alteration, changes of enzymatic antioxidant system and lipid peroxidation in Mentha aquatica L. plants. Seedlings were cultured in half-strength Hoagland medium 50 days after sowing, and were treated under combination of three waterlogging levels (well drained, moderately drained and waterlogging) and NaCl (0, 50, 100, 150 mM) for 30 days. Moderately drained and waterlogging conditions induced differently aerenchyma formation in roots of M. aquatica salt-treated and untreated plants. Moreover, stele diameter and endodermis layer were also affected by salt stress and waterlogging. Salt stress significantly decreased growth, relative water content (RWC), protein level, catalase (CAT) and polyphenol oxidase (PPO) activities, and increased proline content, MDA content, H₂O₂ level and activities of superoxide dismutase (SOD), peroxidase (POX), and ascorbate peroxidase (APX). Waterlogging in salt-untreated plants increased significantly growth parameters, RWC, protein content, antioxidant enzyme activity, and decreased proline content, H₂O₂ and MDA levels. In salt-treated plant, waterlogging caused strong induction of antioxidant enzymes activities especially at severe stress condition. These results suggest M. aquatica is a waterlogging tolerant plant due to significant increase of antioxidant activity, membrane stability and growth under water stress. High antioxidant capacity under waterlogging can be a protective strategy against oxidative damage, and help to salt stress alleviation.     

Toxicity of abamectin and imidacloprid on different life stages of Trialeurodes vaporariorum (Westwood) reared on two different host plants under greenhouse conditions

Chemical application is the common control technique of the pest Trialeurodes vaporariorum (Westwood) (Hom.: Aleyrodidae). Toxicity of two insecticides abamectin and imidacloprid in 2009 was evaluated on different life stages of the pest. Bioassay tests were carried out under controlled environmental conditions (25?±?2?°C 50?±?5% RH and a photoperiod of 18:6 L/D) on different stages of whitefly (1-,3- and 5-day-old ages of eggs, first, second and third nymphal instars, pupa and adult). Both insecticides showed their best efficacy on the primary stages; though, with increasing the age, the susceptibility of all stages to chemicals was decreased. It was shown that sensitivity of eggs and first nymphal stage to abamectin in each host was different. But in imidacloprid treatment, only the eggs showed different sensitivity on both host plants. It seems that application of abamectin in primary stages induce higher mortality rates than of imidacloprid.     

Molecular docking based screening of predicted potential inhibitors for VP40 from Ebola virus

Ebola virus is a member of Filoviridae and cause severe human disease with 90 percent mortality. The life cycle of Ebola contains an assembly stage which is mediated by VP40 proteins. VP40 subunits oligomerize and form ring-structures which are either octamers or hexamers. Prevention of VP40 matrix protein assembly prevents virus particle formation as well as virus budding. In the present study we simulated the biological condition for a single VP40 subunit. Then a library containing 120.000 drugs like chemicals was used as the virtual screening database. Top 10 successive hits were then analyzed regarding absorption, distribution, metabolism, and excretion properties. Moreover probable accessorial human protein targets and toxicity properties of successive hits were analyzed by in silico tools. We found 4 chemicals that could bind VP40 subunits in a manner that by making an interfering steric condense prevents matrix protein oligomerization. The pharmacokinetic and toxicity studies also validated the potential of 4 finlay successive hits to be considered as a new anti-Ebola drugs.     

Determination of clarithromycin in human serum by high-performance liquid chromatography after pre-column derivatization with 9-fluorenylmethyl chloroformate: application to a bioequivalence study

A sensitive liquid chromatographic method for the analysis of clarithromycin, a macrolide antibiotic, in human serum using pre-column derivatization with 9-fluorenylmethyl chloroformate (FMOC-Cl) is described. The method involved liquid-liquid extraction of the drug and an internal standard (amantadine) followed by pre-column derivatization of the analytes with FMOC-Cl. A mixture of 0.05 M phosphate buffer containing triethylamine (2 mL L(-1); pH 3.8) and methanol (17:83, v/v) was used as mobile phase and chromatographic separation was achieved on a Shimpack CLC-ODS column. The eluate was monitored by a fluorescence detector with respective excitation and emission wavelengths of 265 and 315 nm. The analytical method was linear over the concentration range of 0.025-10 microg mL(-1) of clarithromycin in human serum with a limit of quantification of 0.025 microg mL(-1). The assay is sensitive enough to measure drug levels obtained in human single dose studies. In the present method, sensitivity and run time of analysis have been improved, and successfully applied in a bioequivalence study of three different clarithromycin preparations in 12 healthy volunteers.     

In silico structural, functional and pathogenicity evaluation of a novel mutation: an overview of HSD3B2 gene mutations

Mutations of 3 beta hydroxysteroid dehydrogenase type II (HSD3B2) gene result in different clinical consequences. We explain a patient who demonstrated a salt wasting form of 3βHSD deficiency in infancy. Signs of hyponatremia and hyperkalemia were recognized in the infant with ambiguous genitalia and perineal hypospadias. The 46,XY male was genotyped by direct sequencing of HSD3B2 gene. Steroid profiles showed elevated concentration of 17 hydroxyprogesterone, and decrease in concentration of cortisol, and testosterone. Dehydroepiandrotone (DHEA) to androstenedione ratio had 6 fold increases. Direct sequencing of the patient revealed homozygous missense A82P mutation in exon 3. This mutation was confirmed by segregation analysis of the parents. Bioinformatic tools were used for in silico structural and functional analyses. Also, the pathological effect of the mutation was validated by different software. Alanine is a conserved amino acid in the membrane binding domain of the enzyme and proline substitution was predicted to destabilize the protein. This report may highlight the importance of the screening programs of the disorder in Iran.     

Stabilization of transcription factor Nrf2 by tBHQ prevents oxidative stress-induced amyloid β formation in NT2N neurons

Alzheimer's disease (AD) a progressive neurodegenerative disorder of later life, is characterized by brain deposition of amyloid β-protein (Aβ) plaques, accumulation of intracellular neurofibrillatory tangles, synaptic loss and neuronal cell death. There is significant evidence that oxidative stress is a critical event in the pathogenesis of AD.     

The Role of 5-HT1A Receptors and Neuronal Nitric Oxide Synthase in a Seizur Induced Kindling Model in Rats

Neurochemical Research - Dentate gyrus (DG) has a high density of 5-HT1A receptors. It has neural nitric oxide synthase (nNOS), which is involved in neural excitability. The purpose of this study...