Strategies for optimizing DNA hybridization on surfaces

Specific and predictable hybridization of the polynucleotide sequences to their complementary counterparts plays a fundamental role in the rational design of new nucleic acid nanodevices. Generally, nucleic acid hybridization can be performed using two major strategies, namely hybridization of DNA or RNA targets to surface-tethered oligonucleotide probes (solid-phase hybridization) and hybridization of the target nucleic acids to randomly distributed probes in solution (solution-phase hybridization). Investigations into thermodynamic and kinetic parameters of these two strategies showed that hybridization on surfaces is less favorable than that of the same sequence in solution. Indeed, the efficiency of DNA hybridization on surfaces suffers from three constraints: (1) electrostatic repulsion between DNA strands on the surface, (2) steric hindrance between tethered DNA probes, and (3) nonspecific adsorption of the attached oligonucleotides to the solid surface. During recent years, several strategies have been developed to overcome the problems associated with DNA hybridization on surfaces. Optimizing the probe surface density, application of a linker between the solid surface and the DNA-recognizing sequence, optimizing the pH of DNA hybridization solutions, application of thiol reagents, and incorporation of a polyadenine block into the terminal end of the recognizing sequence are among the most important strategies for enhancing DNA hybridization on surfaces.     

Development of an indirect sandwich ELISA for detection of urinary antigen,using Legionella pneumophila PAL protein

Legionella pneumophila peptidoglycan-associated lipoprotein (PAL) protein is an extremely conserved antigen among Legionella species. In this study, rabbit and rat anti-PAL immunoglobulin G antibodies were produced by immunization with purified, recombinant PAL (r-PAL) protein of L. pneumophila serogroup 1 and used as capture and detection antibodies in the PAL antigen-based enzyme-linked immunosorbent assay (ELISA) to detect urinary PAL antigen. Urine samples were obtained from rats experimentally infected with L. pneumophila serogroup 1. The PAL antigen was measured in urine samples of 40 infected and 40 uninfected rats. After choosing the cut-off value of 0.192, the sensitivity and specificity of the PAL antigen-based ELISA were 87.5 and 97.5 %, respectively. The results obtained by PAL antigen base ELISA were compared with those obtained by Biotest. The PAL antigen was detected efficiently by both of the assays and all of the control human urine samples were negative by the ELISA test. The PAL antigen-based ELISA assay was relatively simple to perform, precise, highly sensitive and specific, and reproducible. Based on our data the PAL antigen-based ELISA described here is the first indirect sandwich ELISA for urinary antigen detection which could easily be applied for diagnosis of Legionnaires disease.     

Environmental variables and their interaction effects on chlorophyll-a in coastal waters of the southern Caspian Sea: assessment by multiple regression grey models

Main and interaction effects of environmental parameters on variations of chlorophyll-a along the coast of the southern Caspian Sea were determined. Parameters such as temperature, conductivity, turbidity salinity, dissolved oxygen (DO), pH, chlorophyll-a and nutrients were evaluated monthly in four transects and different depths (0, 5, 10, 20, 35 and 50 m), using multiple regression and grey relational analysis. Additionally, the long-term data (1994–2009) on the seasonal phytoplanktonic variation were included in our discussion. There was a good agreement between the observed and predicted values in the models that included the interaction effects during spring, summer, autumn and winter, with the adjusted R ² of 0.64, 0.63, 0.60 and 0.54, respectively. Temperature and its interactions were found to be the most important factor on chlorophyll-a throughout the year. Overall, the most effective factors were seasonally categorized as: organic phosphorus, ammonium and their interactions (spring); organic phosphorus, nitrate, DO, silica and their interactions (summer); organic phosphorus, pH, DO and their interactions (autumn); pH, ammonium, DO and their interactions (winter). Thermocline, riverine transport, nitrification and the presence of Mnemiopsis leidyi and Cyanophyta were found to be the most important phenomena affecting the dynamics of nutrients and phytoplanktonic biomass in the area. In the distribution of chlorophyll-a, the interaction effects of different environmental parameters proved to be more important than their individual effects. The multiple regression and grey analyses were also found to be useful tools to understand the interactions between phytoplankton and environmental factors.     

Expression analysis of dehydrin multigene family across tolerant and susceptible barley (Hordeum vulgare L.) genotypes in response to terminal drought stress

Dehydrins are one of the characteristic families of plant proteins that usually accumulate in response to drought. In the present study, gene expressions of dehydrin multigene family (13 genes) were examined in flag leaves of tolerant (Yousef) and susceptible (Moroco) barley varieties under terminal drought to characterize the involvement of dehydrins in the adaptive processes. The stomatal conductance, RWC, and Chl a, b contents had more reduction in Moroco than the Yousef which has more elevated osmotic adjustment. Drought stress increased significantly MDA and electrolyte leakage levels, but greater in Moroco, indicating a poor protection of cell and cytoplasmic membrane in this variety. Yousef variety had no reduction in grain yield under drought condition. Five genes (Dhn1, Dhn3, Dhn5, Dhn7 and Dhn9) were exclusively induced in Yousef under drought stress. In the stress condition, relative gene expression of Dhn3, Dhn9 had the direct correlations (P < 0.05) with Chl a, b contents, osmotic adjustment, stomatal conductance, plant biomass and grain yield, and the negative correlations (P < 0.05) with MDA and electrolyte leakage levels. The results supported the impending functional roles of dehydrin K_n and particularly Y_nSK_n types in dehydration tolerance of barley during the reproductive stage.     

Identification of Phytochemicals Targeting c-Met Kinase Domain using Consensus Docking and Molecular Dynamics Simulation Studies

c-Met receptor tyrosine kinase is a proto-oncogene whose aberrant activation is attributed to a lower rate of survival in most cancers. Natural product-derived inhibitors known as “fourth generation inhibitors” constitute more than 60% of anticancer drugs. Furthermore, consensus docking approach has recently been introduced to augment docking accuracy and reduce false positives during a virtual screening. In order to obtain novel small-molecule Met inhibitors, consensus docking approach was performed using Autodock Vina and Autodock 4.2 to virtual screen Naturally Occurring Plant-based Anti-cancer Compound–Activity–Target database against active and inactive conformation of c-Met kinase domain structure. Two hit molecules that were in line with drug-likeness criteria, desired docking score, and binding pose were subjected to molecular dynamics simulations to elucidate intermolecular contacts in protein–ligand complexes. Analysis of molecular dynamics simulations and molecular mechanics Poisson–Boltzmann surface area studies showed that ZINC08234189 is a plausible inhibitor for the active state of c-Met, whereas ZINC03871891 may be more effective toward active c-Met kinase domain compared to the inactive form due to higher binding energy. Our analysis showed that both the hit molecules formed hydrogen bonds with key residues of the hinge region (P1158, M1160) in the active form, which is a hallmark of kinase domain inhibitors. Considering the pivotal role of HGF/c-Met signaling in carcinogenesis, our results propose ZINC08234189 and ZINC03871891 as the therapeutic options to surmount Met-dependent cancers.     

Erratum to: Effects of Supplemental Feeding of Common Carp (Cyprinus carpio) with Iron Nanoparticles and Probiotic Lactobacillus on Blood Biochemical Factors

Biology Bulletin - An Erratum to this paper has been published: https://doi.org/10.1134/S1062359021060078     

IL-1β (−511T/C) gene polymorphism not IL-1β (+3953T/C) and LT-α (+252A/G) gene variants confers susceptibility to visceral leishmaniasis

Lymphotoxin-α (LT-α) and interleukin-1beta (IL-1β) are proinflammatory cytokines playing important roles in immunity against Leishmania infection and the outcome of the disease. As cytokine productions are under the genetic control, this study tried to find any probable relationship between these cytokine gene polymorphisms and the susceptibility to visceral leishmaniasis in Iranian pediatric patients. Ninety-five pediatric patients involved with visceral leishmaniasis and 128 non-relative healthy people, from the same area as the patients, were genotyped for LT-α (+252A/G) and IL-1β (+3953T/C and −511T/C) gene polymorphisms using polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP). There was not found any significant differences in allele and genotype frequencies of LT-α (+252A/G) and IL-1β (+3953) among the study groups. However, the frequency of IL-1β −511TT genotype was higher in the controls (P = 0.0004) while the frequency of IL-1β −511CC genotype and C allele were higher in the patients (P = 0.008 and P = 0.00006, respectively). Furthermore, IL-1β CC (−511/+3953) haplotype was more frequent in VL patients compared with the controls (P = 0.0002) and the distribution of TT haplotype was higher in the controls compared with the patients (P = 0.003). In conclusion, based on the results, IL-1β −511C allele, CC genotype and CC (−511/+3953) haplotype could be considered as the susceptibility factors for visceral leishmaniasis while IL-1β −511TT genotype, T allele and TT haplotype (−511/+3953) might be counted as the influential factors for resistance to the disease.     

Synthesis, characterization and the thermodynamic study of intermediate sitting-atop (i-SAT) complexes of free base meso-tetraarylporphyrins with InCl3

The reaction of free base para-substituted meso-tetraarylporphyrins (H₂T(p-X)PP, X = H, OMe, Me, and Cl) with indium(III) chloride in CHCl₃ and mild conditions produced intermediate sitting-atop (i-SAT) complexes, [InCl₂(H₂T(p-X)PP)]InCl₄, as sole products. In the proposed structures of these complexes, four pyrrole rings are tilted alternatively up and down the porphyrin plane. This distortion makes suitable orientation of lone pairs of two pyrrolenine nitrogens for electron donation to an indium center of cation. The 1:2 (porphyrin:indium) formation constant of resulting i-SAT complexes were calculated by the computer fitting of the complexes absorbance versus mole ratio data based on appropriate equations. Thermodynamic parameters, ΔG⁰, ΔH⁰, and ΔS⁰, have been determined and the influence of electron donation of the para-substituted aryl groups in the free base porphyrins on the stability of the complexes is discussed.     

Biosorption of Baftkar textile effluent

Decolourization of wastewater from a textile plant by a marine Aspergillus niger was studied. The fungus was previously isolated from Gorgan Bay in the Caspian Sea. The kinetics of decolourization was studied by varying energy sources. The best decolourization was achieved when sucrose was used as source of carbon and energy. NH4+ ion was demonstrated to be the best nitrogen source. Color reduction was found to increase from 80-97% as inoculum concentration increased from 0.04-1.0 g/L. A minimum inoculum of 0.2 g/L is necessary to achieve decolourization. The optimal temperature for the growth of A. niger on Baftkar wastewater is found to be 30 degrees C. 90-96% colour reduction is achieved in 19-20 hr of contact of mycelium cell with the wastewater. Colour reduction in a continuous column reactor of 70% was obtained using treated mycelium (NaOH, 90 degrees C) after 1 hr.     

A novel nanobiosensor for the detection of paraoxon using chitosan-embedded organophosphorus hydrolase immobilized on Au nanoparticles

Organophosphorus (OP) compounds are one of the most hazardous chemicals used as insecticides/pesticide in agricultural practices. A large variety of OP compounds are hydrolyzed by organophosphorus hydrolases (OPH; EC 3.1.8.1). Therefore, OPHs are among the most suitable candidates that could be used in designing enzyme-based sensors for detecting OP compounds. In this work, a novel nanobiosensor for the detection of paraoxon was designed and fabricated. More specifically, OPH was covalently embedded onto chitosan and the enzyme–chitosan bioconjugate was then immobilized on negatively charged gold nanoparticles (AuNPs) electrostatically. The enzyme was immobilized on AuNPs without chitosan as well, to compare the two systems in terms of detection limit and enzyme stability under different pH and temperature conditions. Coumarin 1, a competitive inhibitor of the enzyme, was used as a fluorogenic probe. The emission of coumarin 1 was effectively quenched by the immobilized Au-NPs when bound to the developed nanobioconjugates. However, in the presence of paraoxon, coumarin 1 left the nanobioconjugate, leading to enhanced fluorescence intensity. Moreover, compared to the immobilized enzyme without chitosan, the chitosan-immobilized enzyme was found to possess decreased K_m value by more than 50%, and increased V_max and K_cat values by around 15% and 74%, respectively. Higher stability within a wider range of pH (2–12) and temperature (25–90°C) was also achieved. The method worked in the 0 to 1050?nM concentration ranges, and had a detection limit as low as 5?×?10^?11 M.