Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA

Replication by Escherichia coli DNA polymerase III is disrupted on encountering DNA damage. Consequently, specialized Y-family DNA polymerases are used to bypass DNA damage. The protein UmuD is extensively involved in modulating cellular responses to DNA damage and may play a role in DNA polymerase exchange for damage tolerance. In the absence of DNA, UmuD interacts with the α subunit of DNA polymerase III at two distinct binding sites, one of which is adjacent to the single-stranded DNA-binding site of α. Here, we use single molecule DNA stretching experiments to demonstrate that UmuD specifically inhibits binding of α to ssDNA. We predict using molecular modeling that UmuD residues D91 and G92 are involved in this interaction and demonstrate that mutation of these residues disrupts the interaction. Our results suggest that competition between UmuD and ssDNA for α binding is a new mechanism for polymerase exchange.     

Simulation of biological growth

Researchers concerned with the growth of biological tissue often use models that predict the growth as a function of a mechanical stimulus such as stress, strain or elastic energy. However, a general theory for bulk growth should consider that the mechanical stimulus may only be one of many factors contributing to growth. Another important factor could be time, as living tissues can be assumed to have a pre-programmed directional biological growth that is independent of mechanical stimuli. This paper has two objectives: the first is to introduce the concept of directional biological growth within a well developed growth theory, the second is to present the computational methods by which three-dimensional growth that encompasses time and stress effects can be simulated using commercially available finite element analysis software.     

The Synechocystis PCC6803 MerA-Like Enzyme Operates in the Reduction of Both Mercury and Uranium under the Control of the Glutaredoxin 1 Enzyme

In a continuing effort to analyze the selectivity/redundancy of the three glutaredoxin (Grx) enzymes of the model cyanobacterium Synechocystis PCC6803, we have characterized an enzyme system that plays a crucial role in protection against two toxic metal pollutants, mercury and uranium. The present data show that Grx1 (Slr1562 in CyanoBase) selectively interacts with the presumptive mercuric reductase protein (Slr1849). This MerA enzyme plays a crucial role in cell defense against both mercuric and uranyl ions, in catalyzing their NADPH-driven reduction. Like MerA, Grx1 operates in cell protection against both mercury and uranium. The Grx1-MerA interaction requires cysteine 86 (C86) of Grx1 and C78 of MerA, which is critical for its reductase activity. MerA can be inhibited by glutathionylation and subsequently reactivated by Grx1, likely through deglutathionylation. The two Grx1 residues C31, which belongs to the redox active site (CX₂C), and C86, which operates in MerA interactions, are both required for reactivation of MerA. These novel findings emphasize the role of glutaredoxins in tolerance to metal stress as well as the evolutionary conservation of the glutathionylation process, so far described mostly for eukaryotes.     

Spatio-Temporal Distribution of Injured Elephants in Masai Mara and the Putative Negative and Positive Roles of the Local Community

Background

Very few studies have ever focused on the elephants that are wounded or killed as local communities attempt to scare these animals away from their settlements and farms, or on the cases in which local people take revenge after elephants have killed or injured humans. On the other hand, local communities live in close proximity to elephants and hence can play a positive role in elephant conservation by informing the authorities of the presence of injured elephants.

Methodology/Principal Findings

Between 2007 and 2011, 129 elephants were monitored in Masai Mara (Kenya), of which 54 had various types of active (intentionally caused) or passive (non-intentionally caused) injuries. Also studied were 75 random control samples of apparently unaffected animals. The observed active injuries were as expected biased by age, with adults suffering more harm; on the other hand, no such bias was observed in the case of passive injuries. Bias was also observed in elephant sex since more males than females were passively and actively injured. Cases of passive and active injuries in elephants were negatively related to the proximity to roads and farms; the distribution of injured elephants was not affected by the presence of either human settlements or water sources. Overall more elephants were actively injured during the dry season than the wet season as expected. Local communities play a positive role by informing KWS authorities of the presence of injured elephants and reported 43% of all cases of injured elephants.

Conclusions

Our results suggest that the negative effect of local communities on elephants could be predicted by elephant proximity to farms and roads. In addition, local communities may be able to play a more positive role in elephant conservation given that they are key informants in the early detection of injured elephants.     

Biostimulation of anaerobic digestion using nanomaterials for increasing biogas production

Reviews in Environmental Science and Bio/Technology - Biomass energy, especially biogas production, is a renewable and sustainable form of energy. Biogas is becoming more important due to its...     

Isolation of progenitor cells from cord blood using adhesion matrices

The aim of this study was to develop optimal conditions for selective adhesion and isolation of mesenchymal progenitor cells (PCs) from cord blood and to determine their potential for osteogenic differentiation. Mononuclear cells (MNCs) were isolated by Ficoll-Paque gradient and plated onto 48-well culture plates precoated with: human or bovine collagen type I, human collagen type IV, fibronectin or matrigel. Cultures were incubated in αMEM containing fetal calf serum. Viability of the adherent cells was determined by alamarBlue® assay after 2, 3, and 4 weeks. After 4 weeks in culture, cells were typsinized and replated. Primary cultures were analyzed by histochemistry and third passage cells by FACS. Isolated fibroblast-like cells were cultured in the presence of osteogenic factors and differentiation determined by Alizarin Red S staining, RT-PCR and electron dispersive spectroscopy (EDS). MNCs adhered to all types of matrices with the greatest adhesion rates on fibronectin. These cells were CD45⁺, CD105⁺, CD14⁺, CD49a⁺, CD49f⁺, CD44⁺ and CD34⁻. The highest incidence of PCs was observed on fibronectin and polystyrene. Passages were CD45⁻, CD14⁻, CD34⁻ and weakly CD105⁺. Primary cultures expressed endothelial/macrophage RNA markers whether cultured on fibronectin or polystyrene and these markers decreased upon passage. The best osteogenic differentiation was observed in MPCs cultured in osteogenic medium containing Vit D₃ and FGF9. These cells expressed the bone-related mRNA, collagen type I, core binding factor I (Cbfa I), osteocalcin and osteopontin. EDS of deposits produced by these cells demonstrated a calcium/phosphate ratio parallel to hydroxyapatite. It was concluded that fibronectin increased adhesion rates and isolation potential of cord blood mesenchymal progenitor cells.     

A randomized controlled trial to assess the safety and efficacy of silymarin on symptoms,signs and biomarkers of acute hepatitis

PurposeMilk thistle or its purified extract, silymarin (Silybum marianum), is widely used in treating acute or chronic hepatitis. Although silymarin is hepatoprotective in animal experiments and some human hepatotoxic exposures, its efficacy in ameliorating the symptoms of acute clinical hepatitis remains inconclusive. In this study, our purpose was to determine whether silymarin improves symptoms, signs and laboratory test results in patients with acute clinical hepatitis, regardless of etiology.MethodsThis is a randomized, placebo-controlled trial in which participants, treating physicians and data management staff were blinded to treatment group. The study was conducted at two fever hospitals in Tanta and Banha, Egypt where patients with symptoms compatible with acute clinical hepatitis and serum alanine aminotransferase (ALT) levels >2.5 times the upper limit of normal were enrolled. The intervention consisted of three times daily ingestion of either a standard recommended dose of 140 mg of silymarin (Legalon^®, MADAUS GmbH, Cologne, Germany), or a vitamin placebo for four weeks with an additional four-week follow-up. The primary outcomes were symptoms and signs of acute hepatitis and results of liver function tests on days 2, 4 and 7 and weeks 2, 4, and 8. Side-effects and adverse events were ascertained by self-report.ResultsFrom July 2003 through October 2005, 105 eligible patients were enrolled after providing informed consent. No adverse events were noted and both silymarin and placebo were well tolerated. Patients randomized to the silymarin group had quicker resolution of symptoms related to biliary retention: dark urine (p=0.013), jaundice (p=0.02) and scleral icterus (p=0.043). There was a reduction in indirect bilirubin among those assigned to silymarin (p=0.012), but other variables including direct bilirubin, ALT and aspartate aminotransferase (AST) were not significantly reduced.ConclusionsPatients receiving silymarin had earlier improvement in subjective and clinical markers of biliary excretion. Despite a modest sample size and multiple etiologies for acute clinical hepatitis, our results suggest that standard recommended doses of silymarin are safe and may be potentially effective in improving symptoms of acute clinical hepatitis despite lack of a detectable effect on biomarkers of the underlying hepatocellular inflammatory process.