Exploration,antifungal and antiaflatoxigenic activity of halophilic bacteria communities from saline soils of Howze-Soltan playa in Iran

In the present study, halophilic bacteria communities were explored in saline soils of Howze-Soltan playa in Iran with special attention to their biological activity against an aflatoxigenic Aspergillus parasiticus NRRL 2999. Halophilic bacteria were isolated from a total of 20 saline soils using specific culture media and identified by 16S rRNA sequencing in neighbor-joining tree analysis. Antifungal and antiaflatoxigenic activities of the bacteria were screened by a nor-mutant A. parasiticus NRRL 2999 using visual agar plate assay and confirmed by high-performance liquid chromatography. Among a total of 177 halophilic bacteria belonging to 11 genera, 121 isolates (68.3%) inhibited A. parasiticus growth and/or aflatoxin production. The most potent inhibitory bacteria of the genera Bacillus, Paenibacillus and Staphylococcus were distributed in three main phylogenetic clusters as evidenced by 16S rRNA sequence analysis. A. parasiticus growth was inhibited by 0.7–92.7%, while AFB₁ and AFG₁ productions were suppressed by 15.1–98.9 and 57.0–99.6%, respectively. Taken together, halophilic bacteria identified in this study may be considered as potential sources of novel bioactive metabolites as well as promising candidates to develop new biocontrol agents for managing toxigenic fungi growth and subsequent aflatoxin contamination of food and feed in practice.

     

A systematic survey of centrality measures for protein-protein interaction networks

Background

Numerous centrality measures have been introduced to identify “central” nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measure may best suit the analysis of a given network. The choice of a suitable measure is furthermore complicated by the impact of the network topology on ranking influential nodes by centrality measures. To approach this problem systematically, we examined the centrality profile of nodes of yeast protein-protein interaction networks (PPINs) in order to detect which centrality measure is succeeding in predicting influential proteins. We studied how different topological network features are reflected in a large set of commonly used centrality measures.

Results

We used yeast PPINs to compare 27 common of centrality measures. The measures characterize and assort influential nodes of the networks. We applied principal component analysis (PCA) and hierarchical clustering and found that the most informative measures depend on the network’s topology. Interestingly, some measures had a high level of contribution in comparison to others in all PPINs, namely Latora closeness, Decay, Lin, Freeman closeness, Diffusion, Residual closeness and Average distance centralities.

Conclusions

The choice of a suitable set of centrality measures is crucial for inferring important functional properties of a network. We concluded that undertaking data reduction using unsupervised machine learning methods helps to choose appropriate variables (centrality measures). Hence, we proposed identifying the contribution proportions of the centrality measures with PCA as a prerequisite step of network analysis before inferring functional consequences, e.g., essentiality of a node.

     

Fucosylated protein of retinal cone photoreceptor outer segments: morphological and biochemical analyses

Cone outer segments (OS) of the goldfish retina are diffusely labeled after intravitreal injection of [(3)H]fucose while rod OS remain unlabeled. By electron microscopic radioautography, the OS of red- and blue-sensitive cones are heavily labeled while green- sensitive cone OS are lightly labeled. The time-course and pattern of OS labeling in all cone types from 30 min to 24 h resemble that of incorporation of other sugars into rhodopsin in rod OS. The nature of the cone OS-specific fucosylated component(s) was examined using biochemical techniques. Cone OS were prelabeled by intravitreal injection of [(3)H]fucose 24 h before sacrifice. Photoreceptor OS were isolated using a discontinuous sucrose density gradient and it was verified by electron microscopic radioautography that the only source of radioactivity in the preparations was cone OS. The different cone types could be recognized by the heaviness of labeling, characteristic membrane spacing, and 'staining' of green cone OS in vitro with horseradish peroxidase. After acid hydrolysis of prelabeled photoreceptor membranes, 90 percent of the counts were in the neutral sugar fraction which was analyzed by thin-layer chromatography. Approximately 70 percent of the radioactivity co-chromatographed with authentic fucose. SDS-PAGE/fluorography of prelabeled photoreceptor membranes revealed a single radioactive component that was lightly stained with coomassie blue and showed an apparent molecular weight of 33,000. This cone-derived band was separated from unlabeled rod opsin which was well stained and showed an apparent mol wt of 38,000. Isoelectric focusing under denaturing conditions produced two major and one minor band of radioactivity with isoelectric points of 8.2, 8.6, and 8.8 respectively. No radioactivity was found in association with a stained band corresponding in isoelectric point to that of bovine opsin (pl, 6.2). The fucosylated component was readily digested by pronase, indicating its protein nature. Washing of the isolated OS with isotonic and hypotonic buffers failed to extract major amounts of the radioactivity, suggesting that the fucosylated component is an integral membrane protein. The presence of a fucosylated protein thus represents a major difference between cone and rod OS in the goldfish and has enabled us to identify cone OS in preparations of isolated photoreceptor membranes and to demonstrate the separation of a cone-derived glycoprotein from rod opsin.     

Phenotypic and genotypic variation in Iranian sour and duke cherries

Phenotypic and genotypic variation and structure of 29 sour cherry (P. cerasus) and duke cherry (P. x gondouinii) genotypes from different regions of Iran were identified using random amplified polymorphic DNA (RAPD) markers and morphological characters. Furthermore, one Prunus mahaleb genotype was used as an outgroup for molecular analysis. For morphological analysis, 23 variables were recorded to detect similarities between and among studied sour and duke cherries. Most studied characteristics were showing a high degree of variability. Principal component analysis showed that the first three components explained a total of 73.87 % of the whole phenotypic variability. Based on the morphological cluster analysis, studied sour and duke cherry genotypes were placed into three main clusters. The first main cluster included 16 sour cherry genotypes. The second main cluster contained all duke cherry genotypes and eight sour cherry genotypes, while, only one sour cherry genotype was placed in third main cluster. For RAPD analysis, 17 primers generated a total of 233 discernible and reproducible bands across genotypes analyzed, out of which 214 (91.51 %) were polymorphic with varied band size from 300 to 3000 bp. According to the similarity matrix, the lowest similarity was obtained between P. mahaleb, as an outgroup, and sour cherry. Dendrogram based on molecular data separated genotypes according to their species and geographic origin. Low correlation was observed between the similarity matrices obtained based on morphological and RAPD data. The information obtained here could be valuable for devising strategies for conservation of Iranian sour and duke cherries.     

Application of zeolite and geohumus superabsorbent on establishment and some growth indices of Nitraria schoberi L.

Using Superabsorbent is one of the solutions to water shortages in arid and semi-arid regions. In order to evaluate the effect of zeolite and geohumus on the growth of Nitraria schoberi L. species, a factorial experiment in a completely randomized design was conducted with nine replications in Kashan city. The treatments consisted of various zeolite levels (0, 10 and 15 wt%) and geohumus (0, 100, 150, 250 gr for hole) and irrigation (normal irrigation, low irrigation). This study showed that superabsorbent application has a positive effect on establishment and other indices such as plant height, large and small canopy diameter and collar diameter. The highest survival percentage was observed in superabsorbent application (100%) and the lowest was measured in control treatment of low irrigation (the soil free of modifying substances) (78%). Also, the most growth indices of the plant are related to the treatment of 250 g geohumus with low irrigation treatment. Based on the results, it was found that adding superabsorbent on soil causes more establishment and improves vegetative growth traits. Also, considering the economical price of zeolite superabsorbent compared to geohumus as well as its abundance in Iran, it is recommended to use in order to increase irrigation intervals and reduce costs in desertification projects.     

Rheum neyshabourense sp. nov. (Polygonaceae) from Iran

Rheum neyshabourense Baradaran & Jafari from northeastern Iran (Khorassan Razavi Province) is newly described. It is similar to R. ribes but differs in the number of prominent leaf veins, the position of the joint on the pedicle, fruit shape, epidermal cell shape and the type of stele in the inflorescence axis. A key to Rheum species in Iran is also provided.     

Improving Cathodes with a Polymer Interlayer in Reversed Organic Solar Cells

The effects of cathode modification by a conjugated polymer interlayer PFPA1 on the performance of reversed organic solar cells (substrate/cathode/active layer/transparent anode) based on different active material systems and different substrate electrodes are systematically investigated. A reduction of the work function irrespective of the substrate cathode used is observed upon the deposition of the PFPA1 interlayer, which is further related to an improved built‐in electric field and open‐circuit voltage. The amphiphilic character of the PFPA1 interlayer alters the surface energy of the substrate cathode, leading to the formation of a better active layer morphology aiding efficient exciton dissociation and photocurrent extraction in the modified solar cells. Hence, internal quantum efficiency is found to be significantly higher than that of their unmodified counterparts, while optically, the modified and unmodified solar cells are identical. Moreover, the deep highest occupied molecular orbital (HOMO) of the PFPA1 interlayer improves the selectivity for all investigated substrate cathodes, thus enhancing the fill factor.     

Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a member of the phospholipase D superfamily that hydrolyzes 3'-phospho-DNA adducts via two conserved catalytic histidines-one acting as the lead nucleophile and the second acting as a general acid/base. Substitution of the second histidine specifically to arginine contributes to the neurodegenerative disease spinocerebellar ataxia with axonal neuropathy (SCAN1). We investigated the catalytic role of this histidine in the yeast protein (His432) using a combination of X-ray crystallography, biochemistry, yeast genetics, and theoretical chemistry. The structures of wild-type Tdp1 and His432Arg both show a phosphorylated form of the nucleophilic histidine that is not observed in the structure of His432Asn. The phosphohistidine is stabilized in the His432Arg structure by the guanidinium group that also restricts the access of nucleophilic water molecule to the Tdp1-DNA intermediate. Biochemical analyses confirm that His432Arg forms an observable and unique Tdp1-DNA adduct during catalysis. Substitution of His432 by Lys does not affect catalytic activity or yeast phenotype, but substitutions with Asn, Gln, Leu, Ala, Ser, and Thr all result in severely compromised enzymes and DNA topoisomerase I-camptothecin dependent lethality. Surprisingly, His432Asn did not show a stable covalent Tdp1-DNA intermediate that suggests another catalytic defect. Theoretical calculations revealed that the defect resides in the nucleophilic histidine and that the pK(a) of this histidine is crucially dependent on the second histidine and on the incoming phosphate of the substrate. This represents a unique example of substrate-activated catalysis that applies to the entire phospholipase D superfamily.     

Effects of age and leg length upon central loop of the Gastrocnemius-soleus H-reflex latency

Background  

central loop of the gastrocnemius-soleus H-reflex latency (T_c) that looks promising in the diagnosis of S1 radiculopathy; has been investigated in a few studies and only two of them have focused on the constitutional factors affecting it. Although leg length has been shown to contribute to the T_c, the role of age is controversial. More confusing, none of the previously performed studies have used strict criteria to rule out subclinical neuropathy, so the results could be misleading. This study has been performed to determine the influence of leg length and age on T_c among a carefully selected group of healthy volunteers.