U (VI) tolerance affects Shewanella sp. RCRI7 biological responses: growth, morphology and bioreduction ability.

Native Shewanella sp. RCRI7 is recently counted as an operative bacterium in the uranium bio-reduction. The aim of this study was to investigate the effects of uranium tolerance on the morphology and population of RCRI7, following its potential removal capacity in different time intervals. In this research, the bacterial growth and uranium removal kinetic were evaluated in aerobic TSB medium, uranium-reducing condition (URC), aerobic uranium-containing (AUC) and anaerobic uranium-free (AUF) solution, following evaluations of omcAB gene expressions. In addition, spectrophotometry analyses were performed in URC confirming the bio-reduction mechanism. It was found that the bacteria can grow efficiently in the presence of 0.5 mM uranium anaerobically, unlike AUC and AUF solutions. Since the bacterium's adsorption capacity is quickly saturated, it can be deduced that uranium reduction should be dominant as incubation times proceed up to 84 h in URC. In 92 h incubation, the adsorbed uranium containing unreduced and reduced (U (IV) monomeric), was released to the solution due to either increased pH or bacterial death. In AUC and AUF, improper conditions lead to the reduced bacterial size (coccus-shape formation) and increased bacterial aggregations; however, membrane vesicles produced by the bacteria avoid the uranium incrustation in AUC. In overall, this study implies that Shewanella sp. RCRI7 are well tolerated by uranium under anaerobic conditions and the amount of regenerated uranium increases over time in the reduced form.

Evaluation of mtr cluster expression in Shewanella RCRI7 during uranium removal.

In recent years, bioremediation is considered as an efficient method to remove the pollutants from the industrial wastewater. In this study, quantitative gene expressions (Real-time RT-PCR) of mtr gene cluster (mtrA, mtrB, mtrC, mtrD, mtrE, mtrF and omcA) in five different uranium concentrations (0.1, 0.25, 0.5, 1 and 2 mM) were performed with ICP and microscopic live cell counting analysis under anaerobic condition, by Shewanella RCRI7 as a native bacterium. The results indicated that the amount of uranium removal and live-cell counting were decreased in the higher uranium concentrations (1 and 2 mM), due to the uranium toxicity, suggesting 0.5 mM as the optimum uranium concentration for Shewanella RCRI7 resistance. The expression of mtrCED and omcA genes presented increasing trend in the lower uranium concentrations (0.1, 0.25 and 0.5 mM) and a decreasing trend in 1 and 2 mM, while mtrABF, presented an inverse pattern, proving the alternative role of mtrF for mtrC and omcA, as the substantial multiheme cytochromes in Extracellular Electron Transfer (EET) pathway. These data are a proof of these gene vital roles in the EET pathway, proposing them for genetic engineering toward EET optimization, as the certain pathway in heavy metal bioremediation process.

Computational insights into pH-dependence of structure and dynamics of pyrazinamidase: A comparison of wild type and mutants.

The mycobacterial enzyme pyrazinamidase (PZase) is the target of key tuberculosis drug, pyrazinamide. Mutations in PZase cause drug resistance. Herein, three point mutations, W68G, L85P, and V155G, were investigated through over 8 µs of molecular dynamics simulations coupled with essential dynamics and binding pocket analysis at neutral (pH = 7) and acidic (pH = 4) ambient conditions. The 51-71 flap region exhibited drastic displacement leading to enlargement of binding cavity, especially at the lower pH. Accessibility of solvent to the active site of the mutant enzymes was also reduced. The protonation of key surface residues at low pH results in more contribution of these residues to structural stability and integrity of the enzyme and reduced interactions with solvent molecules, which acts as a cage, keeping the enzyme together. The observed results suggest a pattern of structural alterations due to point mutations in PZase, which is consistent with other experimental and theoretical investigations and, can be harnessed for drug design purposes.

Expression of the circulating and the tissue microRNAs after surgery, chemotherapy, and radiotherapy in mice mammary tumor.

The expression of microRNAs (miRNAs), as novel biomarkers, is subject to change in many cancers. Therefore, the overall profile of miRNAs can be used for detection of cancer type, response to therapies, pathological variables, and other factors related to the disease. In this study, to evaluate miRNA expression associated with the tumor progression and response to treatment, 60 BALB/c mice received subcutaneous injections of 4T1 cells. The study includes ten groups: one group as control, six groups were euthanized at different time points to assess the role of miRNA expression in the tumor progression, and three groups received chemotherapy, radiotherapy, and surgery to evaluate miRNA expression in response to treatment. MicroRNAs were extracted from the breast tumor and the plasma samples, and their relative expressions were quantified using qRT-PCR. MiR-155 expression was increased in the plasma in the early weeks after the cell injection but decreased in the plasma after surgery and radiotherapy and also in tumor samples after chemotherapy and radiotherapy. MiR-10b expression was increased in the late weeks both in the plasma and the tumor and was decreased in the plasma after radiotherapy and surgery and in the tumor after radiotherapy. MiR-21 expression was increased in the plasma and the tumor tissue during the disease progression at the third and the fourth weeks following tumor induction but was decreased in the plasma in all the therapy groups. Interestingly, miR-125a showed a significant decrease during the tumor progression, and its expression was increased after the treatment. Our results showed that the candidate miRNAs could be divided into two groups of oncomiRs and tumor suppressor miR based on their deregulation after tumor growth and treatments. It seems that the oncomiRs in the plasma can be an ideal noninvasive candidate biomarker for the early detection of breast cancer and also for following the response of the common therapies.

The effect of not-anaerobicization and discolored bacteria on uranium reduction by Shewanella sp. RCRI7.

Shewanella sp. RCRI7 is a native strain capable of reducing uranium in anaerobic conditions. In order to employ this bacterium for the bioremediation, the mutual effects of uranium and the bacteria are studied in two different approaches. The optimal settings for the bacterial proliferation capacity and uranium reduction without anaerobicization of the environment, as well as the related effects of bioremediation and bacterial color under uranium-reducing conditions, have been investigated in this study. Uranium reduction procedure was analyzed using XRD, spectrophotometry and ICP-AES. In addition, the uranium's effect on the population of the first-generation of the bacteria as well as the color and growth of the second-generation were investigated using neobar lam and CFU (Colony Forming Unit), respectively. Uranium toxicity reduced the population of non-anaerobicized bacteria more than the anaerobicized bacteria after one day of incubation, while the amount of uranium extracted by the bacteria was almost the same. In both situations, the bacteria were able to reduce uranium after two weeks of incubation. In addition to the cell counts, uranium toxicity disrupts the growth and development of healthy second-generation anaerobicized bacteria, as created creamy-colored colonies grow slower than red-colored colonies. Furthermore, due to malfunctioning cytochromes, unlike red bacteria, creamy-colored bacteria were unable to extract the optimum amount of uranium. This study reveals that reduced uranium can be produced in a deprived environment without anaerobicization. Creamy-colored Shewanella can remove soluble uranium, however the most effective bacteria have red cytochromes. These findings represent a big step forward in the industrialization of uranium bioremediation.

Effect of nanoparticle treatment on expression of a key gene involved in thymoquinone biosynthetic pathway in Nigella sativa L.

Thymoquinone is the most important secondary metabolite in black Cumin, which has several pharmaceutical applications. In this study, effect of TiO2 and SiO2 nanoparticles as new elicitors, on expression of Geranyl diphosphate synthase gene (GPPS gene), as a key gene involved in thymoquione biosynthesis pathway was investigated in two Iranian accessions. Plants were treatment in the early flowering stage and after 24 h of 50 and 100 mg/L of each nanoparticle, separately. After RNA extraction, GPPS gene expression was analysed by qRT-PCR method. The results showed that the TiO2 and SiO2 nanoparticles, generally stimulates the GPPS expression. The TiO2 nanoparticles were more effective than SiO2 for the induction of GPPS expression. Also, 100 mg/L treatment of nanoparticles raised gene expression more than 50 mg/L concentration. It can be concluded these nanoparticles can be used as robust elicitors to enhance the production of Thymoquinone in black cumin through up-regulation of related metabolic pathway genes.

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.

Study of orientation and penetration of LAH4 into lipid bilayer membranes: pH and composition dependence.

LAH4 is an antimicrobial peptide that is believed to possess both antibiotic and DNA delivery capabilities. It is one of a number of membrane-active peptides that show increased affinity toward anionic lipids. Herein, we have performed molecular dynamics simulations to compare LAH4 effects on anionic palmitoyl-oleoyl-phosphatidylglycerol bilayer, which approximate a prokaryotic membrane environment and zwitterionic palmitoyl-oleoyl-phosphatidylcholine bilayer, which approximate a eukaryotic membrane environment. One particular interest in this work is to study how different kinds of lipid bilayers respond to the attraction of LAH4. Remarkably, our data have shown that the depth of peptide penetration strongly depends on membrane composition and pH. At acidic pH, LAH4 has exhibited a high tendency to interact strongly with and be adsorbed on anionic membrane. We have also shown that electrostatic interactions between His11 and the phosphor atoms of bilayers should have a significant impact on the penetration of LAH4. These results provide insights into the interactions of LAH4 and lipid bilayers at the atomic level, which is useful to understand cell selectivity and mechanism of the peptide action.

Redirection of the phenylpropanoid pathway to feruloyl malate in Arabidopsis mutants deficient for cinnamoyl-CoA reductase 1.

Cinnamoyl-CoA reductase 1 (CCR1, gene At1g15950) is the main CCR isoform implied in the constitutive lignification of Arabidopsis thaliana. In this work, we have identified and characterized two new knockout mutants for CCR1. Both have a dwarf phenotype and a delayed senescence. At complete maturity, their inflorescence stems display a 25-35% decreased lignin level, some alterations in lignin structure with a higher frequency of resistant interunit bonds and a higher content in cell wall-bound ferulic esters. Ferulic acid-coniferyl alcohol ether dimers were found for the first time in dicot cell walls and in similar levels in wild-type and mutant plants. The expression of CCR2, a CCR gene usually involved in plant defense, was increased in the mutants and could account for the biosynthesis of lignins in the CCR1-knockout plants. Mutant plantlets have three to four-times less sinapoyl malate (SM) than controls and accumulate some feruloyl malate. The same compositional changes occurred in the rosette leaves of greenhouse-grown plants. By contrast and relative to the control, their stems accumulated unusually high levels of both SM and feruloyl malate as well as more kaempferol glycosides. These findings suggest that, in their hypolignified stems, the mutant plants would avoid the feruloyl-CoA accumulation by its redirection to cell wall-bound ferulate esters, to feruloyl malate and to SM. The formation of feruloyl malate to an extent far exceeding the levels reported so far indicates that ferulic acid is a potential substrate for the enzymes involved in SM biosynthesis and emphasizes the remarkable plasticity of Arabidopsis phenylpropanoid metabolism.