Use of in silico tools for classification of novel missense mutations identified in dystrophin gene in developing countries

DMD gene which is composed of 79 exons is the largest known gene located on X chromosome (Xp21). Point mutations in the dystrophin gene are responsible for 30–35% of cases with DMD/BMD. Mutation analysis of all the exons of the DMD gene is costly in developing countries, therefore, a few of the exons are selected to be analyzed routinely in clinical laboratories. In this study, direct sequencing was used for detection of point mutations in 10 exons of dystrophin gene in patients affected with DMD without detectable large rearrangements. Freely available programs were used to predict the damaging effects of the mutations. Point mutations were successfully detected in three patients. Three novel mutations, two missense mutations located on nonconservative domains and a single nucleotide deletion, were detected. Missense mutations were predicted to change splicing efficiency. Detection of point mutations by DNA analysis followed by prediction of the pathogenecity by using bioinformatic tool might be an asset to provide proper diagnosis or genetic counseling to patients and their family.     

A new aqueous biphasic system containing polypropylene glycol and a water-miscible ionic liquid

In this work, we proposed a novel aqueous biphasic system (ABS) composed of polypropylene glycol P400 (PPG P400) and hydrophilic ionic liquids (IL), 1-alkyl-3-methylimidazolium bromide (alkyl = ethyl or butyl), forming an upper polymer-rich phase and a lower IL-rich phase at ambient temperature. This new ABS can present interesting characteristics shared by ILs and polymers such as low volatility, good solvation ability, tunable physical properties, and high design capacity for achieving task-specific phase components to enhance the partitioning of target species. Ternary phase diagram of the novel ABS formed by PPG 400 and [C(2) mim]Br in water was measured at T = 298.15 K. Factors affecting the binodal curves such as the cation side alkyl chain length and the temperature were also evaluated. The results were successfully interpreted in terms of the kosmotropic/chaotropic nature of ILs. Furthermore, the phase behavior of the PPG-[C(2) mim]Br ABS is described by the NRTL model. Finally, the extraction potential of the proposed ABS was evaluated through its application to the extraction of the essential amino acids such as L-tryptophan and L-tyrosine. The partition coefficients here obtained demonstrated the fine potential of the proposed ABS for biomolecules separation.     

Altered tubulin assembly dynamics with N-homocysteinylated human 4R/1N tau in vitro

Tau isoforms promote neuronal integrity through binding and stabilization of microtubule proteins (MTP). It has been shown that hyperphosphorylation of tau contributes to Alzheimer’s disease (AD) pathology and related tauopathies. However, other pathogenic modifications of tau have not been well characterized. It is well accepted that elevated level of homocysteine (Hcy) is associated with neurodegenerative diseases such as AD. As a result of N-homocysteinylation of lysine residues, Hcy becomes a component of proteins, as a protein–homocystamide adduct, which affects protein structure and function. Here we demonstrate that N-homocysteinylation of human tau (4R/1N isoform) inhibits its function via impaired tau–tubulin specific binding and MTP assembly dynamics in vitro.     

The Effects of Synbiotic Supplementation on Pregnancy Outcomes in Gestational Diabetes

Synbiotics are known to exert multiple beneficial effects, including anti-inflammatory and antioxidative actions. This study was designed to evaluate the effects of synbiotic administration on biomarkers of inflammation, oxidative stress, and pregnancy outcomes among gestational diabetic (GDM) women. This randomized, double-blind, placebo-controlled clinical trial was carried out among 60 subjects with GDM who were not on oral hypoglycemic agents. Patients were randomly assigned to consume either one synbiotic capsule containing Lactobacillus acidophilus strain T16 (IBRC-M10785), L. casei strain T2 (IBRC-M10783), and Bifidobacterium bifidum strain T1 (IBRC-M10771) (2 × 10⁹ CFU/g each) plus 800 mg inulin (HPX) (n = 30) or placebo (n = 30) for 6 weeks. Compared with the placebo, synbiotic supplementation significantly decreased serum high-sensitivity C-reactive protein (hs-CRP) (? 1.9 ± 4.2 vs. +1.1 ± 3.5 mg/L, P = 0.004), plasma malondialdehyde (MDA) (? 0.1 ± 0.6 vs. + 0.3 ± 0.7 μmol/L, P = 0.02), and significantly increased total antioxidant capacity (TAC) (+ 70.1 ± 130.9 vs. ? 19.7 ± 124.6 mmol/L, P = 0.009) and total glutathione (GSH) levels (+ 28.7 ± 61.5 vs. ? 14.9 ± 85.3 μmol/L, P = 0.02). Supplementation with synbiotic had a significant decrease in cesarean section rate (16.7 vs. 40.0%, P = 0.04), lower incidence of hyperbilirubinemic newborns (3.3 vs. 30.0%, P = 0.006), and newborns’ hospitalization (3.3 vs. 30.0%, P = 0.006) compared with the placebo. Synbiotic supplementation did not affect plasma nitric oxide (NO) levels and other pregnancy outcomes. Overall, synbiotic supplementation among GDM women for 6 weeks had beneficial effects on serum hs-CRP, plasma TAC, GSH, and MDA; cesarean section; incidence of newborn’s hyperbilirubinemia; and newborns’ hospitalization but did not affect plasma NO levels and other pregnancy outcomes. http://www.irct.ir: www.irct.ir: IRCT201704205623N108     

Serological and Ecological Characteristics of a Nodule-Dominant Serotype from an Indigenous Soil Population of Rhizobium leguminosarum bv. trifolii

Although at least 13 antigenically distinct serotypes of Rhizobium leguminosarum bv. trifolii exist in an Abiqua silty clay loam soil, one serotype, AS6, occupies ≥50% of the root nodules formed on field-grown subclover and between 33 and 78% of the nodules formed on five annual clover species grown in the same soil under laboratory conditions. The dominance of subclover nodules by serotype AS6 was reproducible over a 4-year sampling period and throughout the entire 200- by 100-m pasture examined. Serotype AS6 was composed of three antigenically distinct subtypes (AS6-a, AS6-b, and AS6-c). Each subtype contributed about one-third of the AS6 isolates recovered from nodules of field-grown subclover plants and maintained similar population densities in nonrhizosphere and rhizosphere soil. Rhizobia with the AS6 antigenic signature accounted for from 20 to 100% of the soil populations of R. leguminosarum in arable and pasture soils under legumes throughout the state of Oregon. Over a 12-month period, the population densities of the serotype AS6 complex and three minor nodule-occupying serotypes (AG4, AP17, and AS21) were measured in the rhizospheres of field-grown subclover and orchard grass and in nonrhizosphere Abiqua soil. Regardless of season or serotype, the orchard grass rhizosphere effect was minimal, with the ratio between rhizosphere and nonrhizosphere serotype population densities ranging between 2.5 (midsummer) and 10.5 (spring). In contrast, the magnitude of the subclover rhizosphere effect varied seasonally and among serotypes. Between October and December the ratios for all serotypes were similar (12.5 to 25.5). However, in the spring (April and May), the magnitude of the rhizosphere effect varied among the indigenous serotypes (ratios, 10.5 to 442) and for minor nodule-occupying serotypes AS21 (ratio, 442) and AP17 (ratio, 47) was as great as, or even greater than, the magnitude of the rhizosphere effect observed with the AS6 complex (ratio, 65.5).     

Genetic Variation and Association Analysis of the SSR Markers Linked to the Major Drought-Yield QTLs of Rice

Drought is one of the major abiotic stresses, which hampers the production of rice worldwide. Informative molecular markers are valuable tools for improving the drought tolerance in various varieties of rice. The present study was conducted to evaluate the informative simple sequence repeat (SSR) markers in a diverse set of rice genotypes. The genetic diversity analyses of the 83 studied rice genotypes were performed using 34 SSR markers closely linked to the major quantitative trait loci (QTLs) of grain yield under drought stress (qDTYs). In general, our results indicated high levels of polymorphism. In addition, we screened these rice genotypes at the reproductive stage under both drought stress and nonstressful conditions. The results of the regression analysis demonstrated a significant relationship between 11 SSR marker alleles and the plant paddy weight under stressful conditions. Under the nonstressful conditions, 16 SSR marker alleles showed a significant correlation with the plant paddy weight. Finally, four markers (RM279, RM231, RM166, and RM231) demonstrated a significant association with the plant paddy weight under both stressful and nonstressful conditions. These informative-associated alleles may be useful for improving the crop yield under both drought stress and nonstressful conditions in breeding programs.     

Genetic Diversity of Persian Ecotypes of Indian Walnut (<Emphasis Type="Italic">Aeluropus littoralis</Emphasis> (Gouan) Pari.) by AFLP and ISSR Markers

Indian walnut Aeluropus littoralis (Gouan) Pari, well known for its salt tolerance and forage quality, is a perennial monocot grass from Chlorideae tribe that shows a high potential to become an important genetic model. Although, Aeluropus germplasm is very rich in Iran; but is still unexplored. In this study, 20 ecotypes of A. littoralis were gathered from different geographic zones and a set 16 primers (ISSRs-AFLPs combined) was used for genetic diversity evaluation. A total of 635 fragments and 594 polymorphic fragments were produced (93.5%) and modest levels of genetic similarity were found (ranging from 0.38 to 0.71) among ecotypes. The results showed an equal competition between the two markers on polymorphism detection, so both molecular techniques were able to distinguish the A. littoralis ecotypes. Furthermore, Dendrogram based on both the Bayesian and PCoA analysis showed a clear discrimination and significant variation among ecotypes; however, molecular clustering indicated a weak concordance with geographical grouping. The amount of molecular diversity revealed by molecular markers for A. littoralis in this study can be exploited for pasture conservation programs and new forage crop development.     

Robust Sub‐Monolayers of Co3O4 Nano‐Islands: A Highly Transparent Morphology for Efficient Water Oxidation Catalysis

The scalable synthesis of highly transparent and robust sub‐monolayers of Co₃O₄ nano‐islands, which efficiently catalyze water oxidation, is reported. Rapid aerosol deposition of Co₃O₄ nanoparticles and thermally induced self‐organization lead to an ultra‐fine nano‐island morphology with more than 94% light transmission at a wavelength of 500 nm. These transparent sub‐monolayers demonstrate a remarkable mass‐weighted water oxidation activity of 2070–2350 A g_Co3O4^?1 and per‐metal turnover frequency of 0.38–0.62 s^?1 at an overpotential of 400 mV in 1 m NaOH aqueous solution. This mixed valent cobalt oxide structure exhibits excellent long‐term electrochemical and mechanical stability preserving the initial catalytic activity over more than 12 h of constant current electrolysis and 1000 consecutive voltammetric cycles. The potential of the Co₃O₄ nano‐islands for photoelectrochemical water splitting has been demonstrated by incorporation of co‐catalysts in GaN nanowire photoanodes. The Co₃O₄‐GaN photoanodes reveal significantly reduced onset overpotentials, improved photoresponse and photostability compared to the bare GaN ones. These findings provide a highly performing catalyst structure and a scalable synthesis method for the engineering of efficient photoanodes for integrated solar water‐splitting cells.     

Dynamics of bacterial populations during bench‐scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats

This study describes a bench‐scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture‐independent analysis of seawater from continuous cultures revealed high‐bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate.