Investigation of structural stability and functionality of homodimeric gramicidin towards peptide-based drug: a molecular simulation approach

Increasing death rates due to antibiotic resistance deteriorate the existing treatment measures. Antimicrobial peptides have turned into the emerging cure for multidrug resistance. However, the stability and functionality determine an antimicrobial peptide as a drug. Analyses of the homodimeric β-helical peptide, gramicidin have suggested the significant role of gramicidin-A, gramicidin-B, and gramicidin-C as antimicrobial compounds, but the structural basis for understanding the stability and functionality is insufficient to resolve multidrug resistance. To identify the best template among gramicidin types as a therapeutic product, we combined a detailed comparative static analysis and dynamic analysis along with conformational free energy and secondary structure prediction. We observed that the high intramolecular interactions and the geometrical features favored gramicidin-A among other types of gramicidin. Our analyses further revealed that the secondary structure of gramicidin-A showed β sheets with coils along the conformations without any disruption, thereby enhanced its membrane interactions in terms of binding free energy. In conclusion, gramicidin-A has definitely showed enhanced structural stability and functionality; this could be considered the best template for a potential therapeutic product.     

Oxidative stress and the development of diabetic complications - antioxidants and lipid peroxidation in erythrocytes and cell membrane.

Erythrocytes isolated from 131 cases of Non-Insulin Dependent Diabetes Mellitus (NIDDM) were studied for lipid peroxidation, antioxidant defences, and the maximum peroxidisable substrate in the cell membrane. Antioxidant defences are lowered in NIDDM, followed by significant rise in lipid peroxidation products. However, in the erythrocyte membrane, the total polyunsaturated peroxidisable lipids are lower than in normal erythrocytes which may be a causative factor affecting the survival of the cells.     

Involvement of the MAP kinase pathways in induction of GADD45 following UV radiation

Indian hedgehog (Ihh) is highly expressed in prehypertrophic chondrocytes in vivo and has been proposed to regulate the proliferation and maturation of chondrocytes and bone collar formation in the growth plate. In high-density cultures of rabbit growth-plate chondrocytes, Ihh mRNA was also expressed at the highest level in the prehypertrophic stage. To explore endogenous factors that regulate Ihh expression in chondrocytes, we examined the effects of various growth factors on Ihh mRNA expression in this system. Retinoic acid (RA) and bone morphogenetic protein-2 enhanced Ihh mRNA expression, whereas PTH/PTH-related peptide (PTHrP) markedly suppressed Ihh expression. RA at more than 10(-8) M induced the expression of Ihh and Patched 1 (Ptc1) within 3 h, before it increased the type X collagen mRNA level at 6-24 h. Cycloheximide blocked the up-regulation of Ihh by RA, indicating the requirement of de novo protein synthesis for this stimulation. These findings suggest that RA is involved in the up-regulation of Ihh during endochondral bone formation. In contrast to RA, PTH (1-84) at 10(-7) M abolished the mRNA expression of Ihh and Ptc1 within 2-4 h, before it suppressed the expression of type X collagen at 12-24 h. The inhibition of Ihh expression by PTH (1-84) did not require de novo protein synthesis. PTH (1-34), PTHrP (1-34), and (Bu)(2)cAMP also suppressed Ihh expression. On the other hand, Ihh has been reported to induce PTHrP synthesis in the perichondrium. Consequently, the direct inhibitory action of PTH/PTHrP on Ihh appears to be a negative feedback mechanism that prevents excess PTHrP accumulation in cartilage.     

Ligation of HLA class I molecules on endothelial cells induces phosphorylation of Src,paxillin, and focal adhesion kinase in an actin-dependent manner

The development of chronic rejection is the major limitation to long-term allograft survival. HLA class I Ags have been implicated to play a role in this process because ligation of class I molecules by anti-HLA Abs stimulates smooth muscle cell and endothelial cell proliferation. In this study, we show that ligation of HLA class I molecules on the surface of human aortic endothelial cells stimulates phosphorylation of Src, focal adhesion kinase, and paxillin. Signaling through class I stimulated Src phosphorylation and mediated fibroblast growth factor receptor (FGFR) translocation to the nucleus. In contrast, Src kinase activity was not involved in class I-mediated transfer of FGFR from cytoplasmic stores to the cell surface. Inhibition of Src protein kinase activity blocked HLA class I-stimulated tyrosine phosphorylation of paxillin and focal adhesion kinase. Furthermore, HLA class I-mediated phosphorylation of the focal adhesion proteins and FGFR expression was inhibited by cytochalasin D and latrunculin A, suggesting a role for the actin cytoskeleton in the signaling process. These findings indicate that anti-HLA Abs have the capacity to transduce activation signals in endothelial cells that may promote the development of chronic rejection.     

Glucocorticoids Suppress Renal Cell Carcinoma Progression by Enhancing Na,K-ATPase Beta-1 Subunit Expression

Glucocorticoids are commonly used as palliative or chemotherapeutic clinical agents for treatment of a variety of cancers. Although steroid treatment is beneficial, the mechanisms by which steroids improve outcome in cancer patients are not well understood. Na,K-ATPase beta-subunit isoform 1 (NaK-β₁) is a cell-cell adhesion molecule, and its expression is down-regulated in cancer cells undergoing epithelial-to mesenchymal-transition (EMT), a key event associated with cancer progression to metastatic disease. In this study, we performed high-throughput screening to identify small molecules that could up-regulate NaK-β₁ expression in cancer cells. Compounds related to the glucocorticoids were identified as drug candidates enhancing NaK-β₁ expression. Of these compounds, triamcinolone, dexamethasone, and fluorometholone were validated to increase NaK-β₁ expression at the cell surface, enhance cell-cell adhesion, attenuate motility and invasiveness and induce mesenchymal to epithelial like transition of renal cell carcinoma (RCC) cells in vitro. Treatment of NaK-β₁ knockdown cells with these drug candidates confirmed that these compounds mediate their effects through up-regulating NaK-β₁. Furthermore, we demonstrated that these compounds attenuate tumor growth in subcutaneous RCC xenografts and reduce local invasiveness in orthotopically-implanted tumors. Our results strongly indicate that the addition of glucocorticoids in the treatment of RCC may improve outcome for RCC patients by augmenting NaK-β₁ cell-cell adhesion function.     

Arbuscular Mycorrhizal Fungi Community Structure,Abundance and Species Richness Changes in Soil by Different Levels of Heavy Metal and Metalloid Concentration

Arbuscular Mycorrhizal Fungi (AMF) play major roles in ecosystem functioning such as carbon sequestration, nutrient cycling, and plant growth promotion. It is important to know how this ecologically important soil microbial player is affected by soil abiotic factors particularly heavy metal and metalloid (HMM). The objective of this study was to understand the impact of soil HMM concentration on AMF abundance and community structure in the contaminated sites of South Korea. Soil samples were collected from the vicinity of an abandoned smelter and the samples were subjected to three complementary methods such as spore morphology, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) for diversity analysis. Spore density was found to be significantly higher in highly contaminated soil compared to less contaminated soil. Spore morphological study revealed that Glomeraceae family was more abundant followed by Acaulosporaceae and Gigasporaceae in the vicinity of the smelter. T-RFLP and DGGE analysis confirmed the dominance of Funneliformis mosseae and Rhizophagus intraradices in all the study sites. Claroideoglomus claroideum, Funneliformis caledonium, Rhizophagus clarus and Funneliformis constrictum were found to be sensitive to high concentration of soil HMM. Richness and diversity of Glomeraceae family increased with significant increase in soil arsenic, cadmium and zinc concentrations. Our results revealed that the soil HMM has a vital impact on AMF community structure, especially with Glomeraceae family abundance, richness and diversity.     

Establishment of homozygous transgenic rice lines after elimination of unlinked albino traits from transgenic events through segregation

In an analysis of 339 independent T ₀ transgenic rice lines generated by Agrobacterium-mediated transformation, albino plants appeared in the T ₁ generation in two single-copy transgenic lines, O54 and O36 and in one double-copy transgenic line, C18. While the T ₀ plants of these three lines were green, albino and green plants emerged in a 1:3 ratio in the T ₁ generation. The albino phenotype segregated as a monogenic recessive trait. Southern blot analysis of the green and albino plants in the T ₁ generation confirmed that the albino trait and the T-DNA insertion events were unlinked. Segregation of the albino trait from the transgenic trait in the lines O54 and O36 was confirmed in T ₂ and T ₃ generations, respectively. Homozygous transgenic plants free from the albino trait were also identified. In the double-copy transgenic line C18, we genetically separated the two transgenic loci, out-segregated the albino locus from both transgene loci, and identified homozygous plants for each of the transgenic events by Southern blot analysis in the T ₁ generation itself. Thus, we demonstrate that when an albino trait appears in the T ₁ generation and is unlinked to a transgene locus, the albino locus can be segregated from the transgene locus and homozygous transgenic lines free from albinos can be established.     

Ethylene triggers needle abscission in root-detached balsam fir

Post-harvest needle abscission is a major challenge for Christmas tree and greenery industries. It was hypothesized that ethylene triggers abscission in balsam fir. Three experiments were conducted to test this hypothesis. In experiment 1, 70 balsam fir branches were collected, placed in water, and ethylene evolution was observed over time. In experiment 2, a 2 × 5 factorial experiment was designed to determine the effect of exogenous ethylene and an ethylene receptor blocker, 1-methylcyclopropene (1-MCP), on needle abscission. In experiment 3, a 2 × 6 factorial experiment was designed to determine the effect of exogenous ethylene and an ethylene inhibitor, aminoethoxyvinylglycine (AVG), on needle abscission. It was found that ethylene evolution was the highest 1–2 days prior to needle abscission, which was consistent in untreated branches and branches exposed to exogenous ethylene. Exposure to exogenous ethylene significantly decreased needle retention by 63%. When ethylene receptors were blocked by 1-MCP, needle retention increased by 147% despite the presence of ethylene and increased by 73% in the absence of ethylene when compared to the respective controls. When endogenous ethylene synthesis was inhibited by AVG, there was no improvement in needle retention in the presence of ethylene, but there was a 113% increase in needle retention in the absence of exogenous ethylene. Ethylene is strongly implicated as the signal triggering abscission in root-detached balsam fir.