Key criteria for engineering mycotoxin binding aptamers via computational simulations: Aflatoxin B1 as a case study.

Due to the difficulties in monoclonal antibody production specific to mycotoxins, aptameric probes have been considered as suitable alternatives. The low efficiency of the SELEX procedure in screening high affinity aptamers for binding mycotoxins as small molecules can be significantly improved through computational techniques. Previously, we designed five new aptamers to aflatoxin B (AFB1) based on a known aptamer sequence (Patent: PCT/CA2010/001 292, Apt1) through a genetic algorithm-based in silico maturation strategy and experimentally measured their affinity to the target toxin.

In silico maturation of affinity and selectivity of DNA aptamers against aflatoxin B for biosensor development.

A high affinity and selectivity DNA aptamer for aflatoxin B (AFB) was designed through Genetic Algorithm (GA) based in silico maturation (ISM) strategy. The sequence of a known AFB aptamer (Patent: PCT/CA2010/001292, Apt1) applied as a probe in many aptasensors was modified using seven GA rounds to generate an initial library and three different generations of ss DNA oligonucleotides as new candidate aptamers. Molecular docking methodology was used to screen and analyze the best aptamer-AFB complexes.

A computational method for prediction of xylanase enzymes activity in strains of Bacillus subtilis based on pseudo amino acid composition features.

Xylanases are hydrolytic enzymes which based on physicochemical properties, structure, mode of action and substrate specificities are classified into various glycoside hydrolase (GH) families. The purpose of this study is to show that the activity of the members of the xylanase family in the specified pH and temperature conditions can be computationally predicted. The proposed computational regression model was trained and tested with the Pseudo Amino Acid Composition (PseAAC) features extracted solely from the amino acid sequences of enzymes.

A novel phytase characterized by thermostability and high pH tolerance from rice phyllosphere isolated Bacillus subtilis B.S.46.

In this study, an extracellular alkali-thermostable phytase producing bacteria, Bacillus subtilis B.S.46, were isolated and molecularly identified using 16S rRNA sequencing.

Valorisation of untreated cane molasses for enhanced phytase production by Bacillus subtilis K46b and its potential role in dephytinisation.

Background: The high cost of phytase production is the most limiting factor in its application in animal feeds. The present study aimed to develop a low-cost medium for production of a novel phytase in submerged fermentation using inexpensive agro-industrial by-products. The applicability of phytase in dephytinisation of commonly used food/feed ingredients, i.

Evaluation of anti-phytoplasma properties of surfactin and tetracycline towards lime witches' broom disease using real-time PCR.

The anti-phytoplasma activities of surfactin (derived from Iranian native Bacillus subtilis isolates) and tetracycline towards Candidatus "Phytoplasma aurantifolia", the agent of lime Witches' broom disease, were investigated. HPLC was used to quantify the surfactin production in four previously characterized native surfactin-producing strains, and the one producing the highest amount of surfactin (about 1,500 mg/l) was selected and cultivated following optimized production and extraction protocols. Different combinations of purified surfactin and commercial tetracycline were injected into artificially phytoplasmainfected Mexican lime seedlings using a syringe injection system.

Molecular detection of nematicidal crystalliferous Bacillus thuringiensis strains of Iran and evaluation of their toxicity on free-living and plant-parasitic nematodes.

The characterization of nematode-effective strains and cry genes in the Iranian Bacillus thuringiensis (Bt) collection (70 isolates) is presented. Characterization was based on PCR analysis using 12 specific primers for cry5, cry6, cry12, cry13, cry14, and cry21 genes encoding proteins active against nematodes, crystal morphology, and protein band patterns as well as their nematicidal activity on root-knot nematode (Meloidogyne incognita) and two free-living nematodes (Chiloplacus tenuis and Acrobeloides enoplus). PCR results with primers for these genes showed that 22 isolates (31.