Mining Tamarix ramosissima roots for endophytic growth promoting fungi to improve wheat root growth.

Endophytic fungi are commonly found in the root endosphere and can enhance plant growth through various mechanisms. The aim of this study was to isolate cultivable endophytic fungi associated with the roots of Tamarix ramosissima and to evaluate their plant growth promoting properties. About 35 isolated fungal endophytes belonging to the Ascomycota from four different genera were isolated from the endosphere of T. ramosissima: Alternaria, Aspergillus, Fusarium and Talaromyces. These fungal endophytes showed different abilities to solubilize phosphate and produce indole-3-acetic acid (IAA). The fungal isolates of T. allahabadensis (T3) and A. niger (T4) showed different efficiency in solubilizing phosphate. Almost all fungal isolates were able to produce IAA, and the highest value (0.699 µg/ml) was found in the isolate of F. solani (T11). Inoculation of wheat seeds with endophytic fungi significantly increased the initial growth of wheat roots. The results showed that inoculation with the endophytic fungus A. fumigatus T15 significantly increased root length by 75%. The extensive root system of T. ramosissima may be due to symbiosis with IAA-producing endophytic fungi, which enhance root development and water uptake in dry conditions. These fungi can also boost soil phosphorus levels, promoting plant growth.

Halomonas urmiana sp. nov., a moderately halophilic bacterium isolated from Urmia Lake in Iran.

In the course of screening halophilic bacteria in Urmia Lake in Iran, which is being threatened by dryness, a novel Gram-negative, moderately halophilic, heterotrophic and short rod-shaped bacteria was isolated and characterized. The bacterium was isolated from a water specimen and designated as TBZ3T. Colonies were found to be creamy yellow, with catalase- and oxidase-positive activities. The growth of strain TBZ3T was observed to be at 10-45 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0.5-20 % (w/v) NaCl (optimum, 7.5 %). Strain TBZ3T contained C16 : 0, cyclo-C19 : 0 ω8c, summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) as major fatty acids and ubiquinone-9 as the only respiratory isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid, unidentified phospholipid and unidentified polar lipids were detected as the major polar lipids. Strain TBZ3T was found to be most closely related to Halomonas saccharevitans AJ275T , Halomonas denitrificans M29T and Halomonas sediminicola CPS11T with the 16S rRNA gene sequence similarities of 98.93, 98.15 and 97.60 % respectively and in phylogenetic analysis strain TBZ3T grouped with Halomonas saccharevitans AJ275T contained within a large cluster within the genus Halomonas. Based on phenotypic, chemotaxonomic and molecular properties, strain TBZ3T represents a novel species of the Halomonas genus, for which the name Halomonas urmiana sp. nov. is proposed. The type strain is TBZ3T (=DSM 22871T=LMG 25416T).

Identification of Minimum Set of Master Regulatory Genes in Gene Regulatory Networks.

Identification of master regulatory genes is one of the primary challenges in systems biology. The minimum dominating set problem is a powerful paradigm in analyzing such complex networks. In these models, genes stand as nodes and their interactions are assumed as edges. Here, members of a minimal dominating set could be regarded as master genes. As finitely many minimum dominating sets may exist in a network, it is difficult to identify which one represents the most appropriate set of master genes. In this paper, we develop a weighted gene regulatory network problem with two objectives as a version of the dominating set problem. Collective influence of each gene is considered as its weight. The first objective aims to find a master regulatory genes set with minimum cardinality, and the second objective identifies the one with maximum weight. The model is converted to a single objective using a parameter varying between zero and one. The model is implemented on three human networks, and the results are reported and compared with the existing model of weighted network. Parametric programming in linear optimization and logistic regression are also implemented on the arisen relaxed problem to provide a deeper understanding of the results. Learned from computational results in parametric analysis, for some ranges of priorities in objectives, the identified master regulatory genes are invariant, while some of them are identified for all priorities. This would be an indication that such genes have higher degree of being master regulatory ones, specially on the noisy networks.

Optimization of the Four Most Effective Factors on ß-Carotene Production by Dunaliella salina Using Response Surface Methodology.

During recent years, there was growing demand in using microalga valuable products such as ß-carotene in health care. ß-Carotene has anti-cancer and anti-aging properties for human. In Dunaliella salina cells, ß-carotene has a major protecting role for biomolecules, when the production of reactive oxygen species is elevated. In the present study, we investigated the influence of the four most effective factors (light intensity, temperature, nitrate and salinity concentration) and their interactions on the ß-carotene production and the total chlorophyll/ß-carotene ratio in low light adapted D. salina cells. Box-Benken design and response surface methodology (RSM) were used for this purpose and optimization of the factor levels. Two models were developed to explain how ß-carotene productivity and the total chlorophyll/ß-carotene ratio may depend on the stress factors. Among the four stress variables for ß-carotene production, light intensity was stronger than the others. Meanwhile, interaction between light intensity and salt concentration exhibited the most important effect on the total chlorophyll/ ß-carotene ratio. The predicted optimal conditions for maximum ß-carotene productivity and minimum total chlorophyll/ß-carotene ratio were derived from the fitted model in 200 µmol photons m-2s-1 light intensity, 25 ºC, 0.9 mM nitrate and 3.8 M NaCl. When the predicted condition was tested experimentally, the expected results were observed. This suggests that overproduction of ß-carotene in D. salina under certain conditions depends on used light intensity for preadaptation. The step-wise manner applying of stresses may act as a beneficial strategy to ß-carotene overproduction.

Halomonas tabrizica sp. nov., a novel moderately halophilic bacterium isolated from Urmia Lake in Iran.

A novel moderately halophilic, Gram-stain negative and aerobic bacterium, designated strain TBZ21T, was isolated from a water sample of Urmia Lake, Iran. Cells were observed to be non-motile rods with no flagellum, showing positive catalase and oxidase reactions. Strain TBZ21T was found to grow at 10-40 °C (optimum, 30 °C), at pH 7-10 (optimum, pH 8) and in the presence of 1-22% (optimum, 10%). The major fatty acids were identified as C19:0 cyclo ω8c, C16:0, Summed features 3 (C13:0 3-OH and/or iso-C15:1 H) and 8 (C18:1 ω7c and/or C18:1 ω6c) and C12:0 3-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phosphoaminolipid. The genomic DNA G+C content of strain TBZ21T was determined to be 63.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain TBZ21T belongs to the genus Halomonas, and shows high sequence similarities to Halomonas fontilapidosi 5CRT (99.43%), Halomonas ventosae AL12T (98.64%), Halomonas sediminicola CPS11T (98.63%) and Halomonas aestuarii Hb3T (98.08%), and has low similarities (below 98.0%) with other members of the genus. The values of DNA-DNA relatedness between strain TBZ21T and the closely related strains H. fontilapidosi LMG 24455T and H. ventosae LMG 26187T were 42 ± 11% and 54 ± 16%, respectively. On the basis of phenotypic, chemotaxonomic and molecular characteristics, strain TBZ21T is concluded to represent a novel species of the genus Halomonas, for which the name Halomonas tabrizica sp. nov. is proposed. The type strain is TBZ21T (=LMG 25445T=DSM 23018T).

The combinatorial effects of osmolytes and alcohols on the stability of pyrazinamidase: Methanol affects the enzyme stability through hydrophobic interactions and hydrogen bonds.

Inside the cells, proteins are surrounded by mixtures of different osmolytes. However, our current understanding of the combinatorial effects of such mixtures on the stability of proteins remains elusive. In the present study, the stability and structure of recombinant pyrazinamidase (PZase) from Mycobacterium tuberculosis were analyzed in the presence of stabilizing osmolytes (sorbitol, sucrose and glycerol) and alcohols (methanol, ethanol, isopropanol and n-propanol). The far-UV and near-UV circular dichroism (CD), intrinsic fluorescence and thermostability results indicated that methanol, unexpectedly, has stronger effect on destabilization of the enzyme compared to ethanol which has larger log P. Interestingly, the relative half-life of PZase was longer in mixtures methanol with the osmolytes, sorbitol or sucrose (expectedly), or glycerol (unexpectedly), compared to other alcohols. Molecular dynamics simulation results showed that methanol increases the flexibility of region 5-40 and loop 51-71 in the PZase, which are potentially crucial for the stability and activity of the enzyme, respectively. Our results indicated that methanol can interact with PZase via hydrophobic interactions and hydrogen bonds, and therefore resulting in destabilization of the structure of the enzyme. In addition, glycerol probably increases the stability of the enzyme in methanol by disrupting the unfavorable hydrophobic interactions and hydrogen bonds.

Identification of the Crucial Residues in the Early Insertion of Pardaxin into Different Phospholipid Bilayers.

Antimicrobial peptides (AMPs) are part of the innate host defense system, and they are produced by living organisms to defend themselves against infections. Pardaxin is a cationic AMP with antimicrobial and antitumor activities that has potential to be used as a novel antibiotic or for drug delivery in cancer therapy. This peptide acts on the membrane of target cells and can lead to lysis using different mechanisms of action. Here, we conducted 4.5 µs all-atom molecular dynamics (MD) simulations to determine the critical fragments and residues of Pardaxin for early insertion into different lipid bilayers. Our results revealed that the N-terminal domain of the peptide, particularly the Phe 2 and (/or) Phe 3 residues, has a crucial role in early insertion, independent of the type of lipid bilayers.

Effect of sorbitol and glycerol on the stability of trypsin and difference between their stabilization effects in the various solvents.

The effect of glycerol and sorbitol on the stability of porcine pancreas trypsin was investigated in this work. Molecular dynamics simulation and thermostability results showed that trypsin has two flexible regions, and polyols (sorbitol and glycerol) stabilize the enzyme by decreasing the flexibility of these regions. Radial distribution function results exhibited that sorbitol and glycerol were excluded from the first water layer of the enzyme, therefore decrease the flexibility of the regions by preferential exclusion. Also, results showed that the stabilization effect of sorbitol is more than glycerol. This observation could be because of the larger decrease in the fluctuations of trypsin in the presence of sorbitol. We also examined the role of solvent's hydrophobicity in enzyme stabilization by sorbitol and glycerol. To do so, the thermostability of trypsin was evaluated in the presence of solvents with different hydrophobicity (methanol, ethanol, isopropanol and n-propanol) in addition to the polyols. Our results depicted that glycerol is a better stabilizer than sorbitol in the presence of hydrophobic solvents (n-propanol), whereas sorbitol is a better stabilizer than glycerol in the presence of hydrophilic solvents (methanol).

Biochemical Characterization and Computational Identification of Mycobacterium tuberculosis Pyrazinamidase in Some Pyrazinamide-Resistant Isolates of Iran.

Pyrazinamide (PZA) is one the first line anti-tuberculosis drugs that require activation by the pyrazinamidase (PZase). Most PZA-resistant Mycobacterium tuberculosis strains have mutations in the pncA gene which encoding PZase that result in the reduction or loss of the enzyme activity. Herein, we have examined how various mutations, which have been found from the PZA-resistant M. tuberculosis strains in Iran, modify the PZase activity. To elucidate the possible role of these mutations, namely A143T (MUT1), L151S (MUT2), A143T/T168A/E173K (MUT3), in the bioactivity of the enzyme, the PZase and mutant genes were cloned, functionally expressed and biochemically and computationally characterized. In comparison to the PZase enzyme, the enzymatic efficiency of mutant enzymes was decreased, with MUT2 indicating the largest enzymatic efficiency reduction. Homology models of mutants were constructed based on the PZase X-ray crystal structure. Molecular modeling and substrate docking revealed that the wild-type has much stronger binding affinity to PZA than the mutants whereas MUT2 has the weakest binding affinity. In addition, the molecular dynamics simulations and the essential dynamics results illustrated that the positions of the 51st to 71st residues were more dynamics in MUT2 as compared to the other atoms in PZase, MUT1 and MUT3 which could decrease the K(m) and k(cat) values of the enzymes.

The association between thrombophilic gene mutations and recurrent pregnancy loss.

PURPOSE: To determine whether the Factor V (1691G/A), Factor V HR2 (4070A/G), Prothrombin (20210G/A), PAI-1 (-675 I/D, 5G/4G), ACE (intron 16 I/D), Factor VII (Gln353Arg), Factor XIII (Val34Leu), ß-fibrinogen (-455G/A), Glycoprotein Ia (807C/T), tPA (intron 8 D/I) gene mutations could be risk factors for recurrent pregnancy loss (RPL). METHODS: Genotyping of thrombophilic gene mutations were carried out by amplification Refractory Mutation System-PCR (ARMS-PCR) method after DNA extraction. RESULTS: We found that the mutant allele frequencies of Factor V (1691G/A), Factor V HR2 (4070A/G), Prothrombin (20210G/A), PAI-1 (-675 I/D, 5G/4G), Factor XIII (Val34Leu) and ß-fibrinogen (-455G/A) were more seen in the case group compared with the healthy control; However, the difference between the two group is not statistically significant (p > 0.05). Whilst the mutant allele frequencies of other studied genes were lower in the case in comparison to the fertile control women (p > 0.05). CONCLUSION: Taken together, our data has shown that the prevalence of thrombophilic gene mutations was similar in women with RPL and healthy controls. Therefore, it appears that further studies on large-scale population and other genetic variants will be needed to conclusively find candidate genes for RPL unknown etiology in the future.

Methylenetetrahydrofolate Reductase C677T and A1298C Mutations in Women with Recurrent Spontaneous Abortions in the Northwest of Iran.

Introduction. Recurrent spontaneous abortion (RSA) is a significant obstetrical complication that may occur during pregnancy. Various studies in recent years have indicated that two common mutations (C677T and A1298C) of the methylenetetrahydrofolate reductase (MTHFR) gene are risk factor for RSA. This study was carried out to determine the influence of (C677T and A1298C) of the methylenetetrahydrofolate reductase (MTHFR) gene mutations with RSA. Materials and Methods. A total of 139 women were included in this study: 89 women with two or more consecutive miscarriages and 50 healthy controls. Total genomic DNA was isolated from blood leukocytes. To determine the frequency of the two common C677T and A1298C MTHFR gene mutations in the patients and controls, we used two methods, amplification refractory mutation system-PCR and PCR-restriction fragment length polymorphism. Results. There is no significant difference in the prevalence of 677T/T genotype among women with RSA and healthy controls (P = 0.285). Also no statistically significant difference in the frequency of A1298C MTHFR gene mutation was detected between the two groups (P = 0.175 ). Conclusion. In conclusion, the results indicate that the Amplification Refractory Mutation System-PCR method was in complete concordance with the results obtained by standard PCR-restriction fragment length polymorphism method. The results also show no significant difference in MTHFR C677T/A1298C genotype distribution among the two groups; therefore, further studies on larger population and other genetic variants to better understand the pathobiology of RSA are needed.

Structural and dynamical studies of Humanin in water and TFE/water mixture: a molecular dynamics simulation.

The structural and dynamical properties of Humanin, a small peptide with neuroprotective activity against the insults of the Alzheimer's disease-related genes and the neurotoxic amyloid peptide, are studied in two different environments by molecular dynamics simulation. In this study, we have performed comparative molecular dynamics simulations in the absence and in the presence of TFE. The resulting trajectories were analyzed in terms of structural and dynamical properties of peptide and compared to the available NMR data. In water humanin is observed to partly unfold. The peptide is readily stabilized in an ordered helical conformation in the TFE/water mixture. Our simulations show that the peptide is flexible with definite turn point in its structure in water environment. It is free to interact with receptors that mediate its action in polar environment. Humanin may also find an alpha helix structure necessary for passage through biomembranes and/or specific interactions.

Effects of mycorrhizal colonization on growth parameters of onion under different irrigation and soil conditions.

The effects of three Arbuscular Mycorrhizal Fungi (AMF), Glomus versiforme, G. intraradices and G. etonicatum) and three irrigation intervals (7, 9 and 11 days) on growth of onion (Allium cepa L.) cv. Red Azar Shahr were studied under two soil conditions (sterilized and non-sterilized). The results indicated that, AMF colonization improved plant height, Leaf Area Index (LAI), total biomass, bulb dry mass and diameter, Harvest Index (HI) and chlorophyll content (p < 0.001). Bulbing occurred 10-15 days earlier in mycorrhizal plants. Irrigation interval decreased biomass, LAI, Leaf Area Ratio (LAR), bulb diameter and dry mass and chlorophyll content (b and total) at 11 day irrigation interval. In term of interaction, G. versiforme at 9 day and non-mycorrhizal plants at 11 day produced the greatest and the lowest LAI (8.56 vs. 1.57), respectively. Mycorrhizal onions in contrary to non-mycorrhizal ones produced more LAI and biomass in sterilized soil and inoculation with G. etonicatum and the non-mycorrhizal onions in sterilized soil had the highest and the lowest biomass, respectively.

Antioxidative responses of Calendula officinalis under salinity conditions.

To gain a better insight into long-term salt-induced oxidative stress, some physiological parameters in marigold (Calendula officinalis L.) under 0, 50 and 100 mM NaCl were investigated. Salinity affected most of the considered parameters. High salinity caused reduction in growth parameters, lipid peroxidation and hydrogen peroxide accumulation. Under high salinity stress, a decrease in total glutathione and an increase in total ascorbate (AsA + DHA), accompanied with enhanced glutathione reductase (GR, EC 1.6.4.2) and ascorbate peroxidase (APX, EC 1.11.1.11) activities, were observed in leaves. In addition, salinity induced a decrease in superoxide dismutase (SOD, EC 1.15.1.1) and peroxidase (POX, EC 1.11.1.7) activities. The decrease in dehydroascorbate reductase (DHAR, EC 1.8.5.1) and monodehydroascorbate reductase (MDHAR, EC 1.6.5.4) activities suggests that other mechanisms play a major role in the regeneration of reduced ascorbate. The changes in catalase (CAT, EC 1.11.1.6) activities, both in roots and in leaves, may be important in H2O2 homeostasis.