Investigation of Oxidative Status of the 2-Furan-2-yl-1H-Benzimidazole in Rats

We investigated the influence of 2-furan-2-yl-1H-benzimidazole regarding vitamins A, E, C, selenium (Se), malondialdehyde (MDA), and glutathione peroxidase (GSH-Px) levels on rats. 2-Furan-2-yl-1H-benzimidazole was given to rats by subcutaneous injection every other day for a total of 22 injections. At the end of the experiment, Se levels were determined by using a fluorimetric method. Serum levels of vitamins A, E, C, and malondialdehyde (MDA) were determined by high-performance liquid chromatography. Glutathione peroxidase (GSH-Px) levels of erythrocytes were spectrophotometrically determined. Our experimental results showed that vitamins A, E, C, and Se levels were found generally lower than the control groups, while serum MDA level and GSH-Px activity flexibly increased, which is dependent on injection days. The observed decreases in vitamins A, E, C, and Se levels in the blood might be causally related to the increased amount of free radicals that are generated with 2-furan-2-yl-1H-benzimidazole injection. However, further investigations are needed to clarify the significance of this observation in respect with the 2-furan-2-yl-1H-benzimidazole injection.     

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes

Conformational transitions between open/closed or free/bound states in proteins possess functional importance. We propose a technique in which the collective modes obtained from an anisotropic network model (ANM) are used in conjunction with a Monte Carlo (MC) simulation approach, to investigate conformational transition pathways and pathway intermediates. The ANM-MC technique is applied to adenylate kinase (AK) and hemoglobin. The iterative method, in which normal modes are continuously updated during the simulation, proves successful in accomplishing the transition between open-closed conformations of AK and tense-relaxed forms of hemoglobin (C^α− root mean square deviations between two end structures of 7.13 Å and 3.55 Å, respectively). Target conformations are reached by root mean-square deviations of 2.27 Å and 1.90 Å for AK and hemoglobin, respectively. The intermediate conformations overlap with crystal structures from the AK family within a 3.0-Å root mean-square deviation. In the case of hemoglobin, the transition of tense-to-relaxed passes through the relaxed state. In both cases, the lowest-frequency modes are effective during transitions. The targeted Monte Carlo approach is used without the application of collective modes. Both the ANM-MC and targeted Monte Carlo techniques can explore sequences of events in transition pathways with an efficient yet realistic conformational search.     

Building Resilience in Lagoon Social–Ecological Systems: A Local-level Perspective

Building resilience in integrated human and nature systems or social–ecological systems (SES) is key for sustainability. Therefore, developing ways of assessing resilience is of practical as well as theoretical significance. We approached the issue by focusing on the local level and using five lagoon systems from various parts of the world for illustration. We used a framework based on four categories of factors for building resilience: (1) learning to live with change and uncertainty; (2) nurturing diversity for reorganization and renewal; (3) combining different kinds of knowledge; and (4) creating opportunity for self-organization. Under each category, the cases generated a number of items for building resilience, and potential surrogates of resilience, that is, variables through which the persistence of SES emerging through change can be assessed. The following factors were robust across all five lagoon SES cases: learning from crisis, responding to change, nurturing ecological memory, monitoring the environment, and building capacity for self-organization and conflict management.     

Essential roles of lipoyl domains in the activated function and control of pyruvate dehydrogenase kinases and phosphatase isoform 1.

Four pyruvate dehydrogenase kinase and two pyruvate dehydrogenase phosphatase isoforms function in adjusting the activation state of the pyruvate dehydrogenase complex (PDC) through determining the fraction of active (nonphosphorylated) pyruvate dehydrogenase component. Necessary adaptations of PDC activity with varying metabolic requirements in different tissues and cell types are met by the selective expression and pronounced variation in the inherent functional properties and effector sensitivities of these regulatory enzymes. This review emphasizes how the foremost changes in the kinase and phosphatase activities issue from the dynamic, effector-modified interactions of these regulatory enzymes with the flexibly held outer domains of the core-forming dihydrolipoyl acetyl transferase component.     

Enhanced biological treatment of saline wastewater by using halophilic bacteria

Biological treatment of saline wastewater by conventional activated sludge culture usually results in low removal of chemical oxygen demand (COD) because of plasmolysis of the organisms at high salt concentrations. Since salt removal operations by physicochemical processes before biological treatment are costly, a salt-tolerant organism (Halobacter halobium) was used for effective biological treatment of saline wastewater in this study. Halobacter halobium was used in activated sludge culture for COD removal from saline wastewater (1–5% salt) by fed-batch operation of an aeration tank. Inclusion of Halobacter halobium into activated sludge culture improved the rate and extent of COD removals especially with salt above 2% (w/v).     

Enhancement of YD spin relaxation by the CaMn4 cluster in photosystem II detected at room temperature: a new probe for the S-cycle

One of the major conceptual advances in the understanding of the pathogenesis of heart failure has been the insight that myocardial dysfunction and heart failure may progress as the result of the sustained over-expression of nitric oxide (NO) metabolites locally and in blood modulated by inducible nitric oxide synthase (iNOS). This by virtue of their deleterious effects is sufficient to contribute to disease progression by provoking left ventricular (LV) remodeling, hypertrophy and progressive LV dysfunction. Recently, tumor necrosis factor-alpha (TNF-alpha) has also been identified in this setting of heart failure. Analogous to the situation with NO, the over-expression of TNF-alpha is sufficient to contribute to disease progression in heart failure phenotype. Although important interactions between TNF-alpha and the NO have been recognized in the cardiovascular system for over a decade, the nature and importance of the interactions between these biologically active molecules in cardiac hypertrophy has become apparent only in the recent times. Therefore, we focused on the prevailing updated evidence which suggests that there is a functionally significant cross-regulation between NO and TNF-alpha signaling in blood thus playing a part in cardiac hypertrophy and failure. The discussions presented here will have a bearing on the therapeutic potential via inhibitors of these pathways in reducing cardiomyocyte hypertrophy and the LV dysfunction.     

Relative growth and size at onset of sexual maturity of the brown crab,Cancer pagurus in the Isle of Man,Irish Sea

In this study, the relative growth, size–weight relationships and size at onset of maturity of the brown crab Cancer pagurus were investigated in the Isle of Man. For the analyses of relative growth and size at onset of maturity, the samples were collected seasonally between autumn 2012 and spring 2013 using several methods: pot surveys, dredge and trawl surveys, market surveys and shore surveys. Results showed that allometric growth occurred in the chelipeds of males (n?=?87) and in the abdomen of females (n?=?222). Four different measures of maturity (behavioural, functional, morphometric and physiological) were examined. With respect to the behavioural maturity, the smallest female crab found with a sperm plug measured 110?mm CW, whereas in terms of functional maturity the smallest ovigerous female had a CW of 134?mm. Based on direct observations of gonad maturity, 50% of females were mature at 108?mm CW, whereas 50% of males were mature at 89?mm CW. The size at the onset of maturity measurements of female and male C. pagurus based on gonad development is smaller than the current minimum landing size (130?mm), and therefore this suggests that the current minimum landing size is an adequate management measure.     

Identification and Characterization of the Glucosinolate–Myrosinase System in Caper (<Emphasis Type="Italic">Capparis ovata</Emphasis> Desf.)

Myrosinase (EC 3.2.1.147) catalyzes cleavage of glucosinolates, which consist of a thioglucoside moiety linked to amino acid-derived side chains. Myrosinase activity and expression profiles were investigated together with glucosinolate contents in Capparis ovata (caper) in order to characterize the glucosinolate–myrosinase system. The desulfoglucosinolates—glucocapparin, glucoiberin, progoitrin, epiprogoitrin, sinigrin, gluconapin, glucosinalbin, and glucobrassicin—were extracted and quantified from leaves, seeds, flowers, flower buds, and young shoots. The major desulfoglucosinolate was glucocapparin, which accumulated to values of 39.35 ± 0.09 and 25.56 ± 0.11 μmol g⁻¹ dry weight in seed and leaf extracts, respectively. Myrosinase has high activity in caper seeds, leaves, flowers, and flower bud tissues having the highest total activities in seed extracts (79.23 ± 0.18 U). However, specific activities were the highest in flower bud extracts (200.44 ± 0.09 U mg⁻¹ protein). The myrosinase protein migrated as a single band with a molecular weight of 65 kDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis and on Western blots probed with the myrosinase-specific 3D7 antibodies. Native gel electrophoresis revealed two putative myrosinase isoenzymes in seeds, leaves, and flower tissues. The caper homolog of the Arabidopsis thaliana TGG1 gene was differentially expressed in seeds, leaves, flowers, and flower buds with the highest expression levels in leaves and flower bud tissues.     

E2F-1 binding affinity for pRb is not the only determinant of the E2F-1 activity

E2F-1 is the major cellular target of pRB and is regulated by pRB during cell proliferation. Interaction between pRB and E2F-1 is dependent on the phosphorylation status of pRB. Despite the fact that E2F-1 and pRB have antagonistic activities when they are overexpressed, the role of the E2F-1-pRB interaction in cell growth largely remains unknown. Ideally, it would be better to study the properties of a pRB mutant that fails to bind to E2F, but retains all other activities. To date, no pRB mutation has been characterized in sufficient detail to show that it specifically eliminates E2F binding but leaves other interactions intact. An alternative approach to this issue is to ask whether mutations that change E2F proteins binding affinity to pRB are sufficient to change cell growth in aspect of cell cycle and tumor formation. Therefore, we used the E2F-1 mutants including E2F-1/S332-7A, E2F-1/S375A, E2F-1/S403A, E2F-1/Y411A and E2F-1/L132Q that have different binding affinities for pRB to better understand the roles of the E2F-1 phosphorylation and E2F-1-pRB interaction in the cell cycle, as well as in transformation and gene expression. Data presented in this study suggests that in vivo phosphorylation at amino acids 332-337, 375 and 403 is important for the E2F-1 and pRB interaction in vivo. However, although E2F-1 mutants 332-7, 375 and 403 showed similar binding affinity to pRB, they showed different characteristics in transformation efficiency, G₀ accumulation, and target gene experiments.     

Association of putative concave protein-binding sites with the fluctuation behavior of residues

Here, we propose a binding site prediction method based on the high frequency end of the spectrum in the native state of the protein structural dynamics. The spectrum is obtained using an elastic network model (GNM). High frequency vibrating (HFV) residues are determined from the fastest modes dynamics. HFV residue clusters and the associated surface patch residues are tested for their likelihood to locate at the binding interfaces using two different data sets, the Benchmark Set of mainly enzymes and antigen/antibodies and the Cluster Set of more diverse structures. The binding interface is identified to be within 7.5 A of the HFV residue clusters in the Benchmark Set and Cluster Set, for 77% and 70% of the structures, respectively. The success rate increases to 88% and 84%, respectively, by using the surface patches. The results suggest that concave binding interfaces, typically those of enzyme-binding sites, are enriched by the HFV residues. Thus, we expect that the association of HFV residues with the interfaces is mostly for enzymes. If, however, a binding region has invaginations and cavities, as in some of the antigen/antibodies and in cases in the Cluster data set, we expect it would be detected there too. This implies that binding sites possess several (inter-related) properties such as cavities, high packing density, conservation, and disposition for hotspots at binding surfaces. It further suggests that the high frequency vibrating residue-based approach is a potential tool for identification of regions likely to serve as protein-binding sites. The software is available at http://www.prc.boun.edu.tr/PRC/software.html.