Synthesis of highly selective fluorescent peptide probes for metal ions: tuning selective metal monitoring with secondary structure

Metal selective fluorescent peptide probes (dansyl-Cys-X-Gly-His-X-Gly-Glu-NH2, X = Pro or Gly) were developed by synthesizing peptides containing His, Cys, and Glu residues with Pro-Gly sequence to stabilize a turn structure and Gly-Gly sequence to adopt a random coil. The probe containing two Gly-Gly sequences exhibited marked selectivity only for Cu2+ over 13 metal ions including competitive transition and Group I and II metal ions under physiological buffer condition. In contrast, the probe containing double Pro-Gly sequences showed high selectivity for Zn2+. The peptide probe containing one Pro-Gly sequence exhibited selectivity for Zn2+ and Cu2+. CD spectra indicated that the secondary structure of the probes played an important role in the selective metal monitoring and a pre-organized secondary structure is not required for the selective detection of Cu2+ ion, but is required for the detection of Zn2+. We investigated and characterized the binding affinity, binding stoichiometry, reversibility, and pH sensitivity of the peptide probes.     

Discovery of potent furan piperazine sodium channel blockers for treatment of neuropathic pain

The synthesis and pharmacological characterization of a novel furan-based class of voltage-gated sodium channel blockers is reported. Compounds were evaluated for their ability to block the tetrodotoxin-resistant sodium channel Na(v)1.8 (PN3) as well as the Na(v)1.2 and Na(v)1.5 subtypes. Benchmark compounds from this series possessed enhanced potency, oral bioavailability, and robust efficacy in a rodent model of neuropathic pain, together with improved CNS and cardiovascular safety profiles compared to the clinically used sodium channel blockers mexiletine and lamotrigine.     

Effects of plumieride, an iridoid on spermatogenesis in male albino rats.

Oral feeding of male rats with plumieride (15 mg/rat/day) for the period of 60 days did not cause any significant change in the body weight of treated rats. However, the weights of testes, epididymides, seminal vesicle and ventral prostate were significantly reduced when compared to control values. The production of step-19 spermatids was reduced by 87.26% in plumieride treated rats. The population of preleptotene and pachytene spermatocytes were decreased by 64.26% and 55.13% respectively. Spermatogonia and sertoli cell population was also affected. Plumieride treatment resulted in an arrest of spermatogenesis without any systemic side effect. Sperm motility as well as sperm density was reduced significantly. The number of mature Leydig cells was decreased and complete suppression of fertility was observed. A significant fall in the protein and sialic acid contents of the testes, epididymides, seminal vesicle and ventral prostate as well as glycogen content of testes was also noticed. Fructose in seminal vesicle was lowered whereas testicular cholesterol was elevated. There was no significant change in RBC and WBC count, haemoglobin, haematocrit and sugar in the whole blood and total protein, cholesterol, phospholipid and triglycerides in the serum. Conclusion: Plumieride administration arrests spermatogenesis in male rats without noticeable side effects. For the clinical use more experiments should be carried out in a phased programme.     

In vivo immunogold labeling confirms large-scale chromatin folding motifs

The difficulty in localizing specific cellular proteins by immuno-electron microscopy techniques limits applications of electron microscopy to cell biology. We found that in vivo immunogold labeling improves epitope accessibility, ultrastructural preservation and three-dimensional visualization, and allows correlated light and electron microscopy. We detected large-scale chromatin folding motifs within intact interphase nuclei of CHO cells and visualized the ultrastructure of DNA replication 'factories' labeled with GFP-proliferating cell nuclear antigen (PCNA).     

Effect of Elevated CO2 and Drought on Soil Microbial Communities Associated with Andropogon gerardii

Our understanding of the effects of elevated atmospheric CO2, singly and In combination with other environmental changes,on plant-soil interactions is incomplete. Elevated CO2 effects on C4 plants, though smaller than on C3 species, are mediated mostly via decreased stomatal conductance and thus water loss. Therefore, we characterized the interactive effect of elevated CO2 and drought on soil microbial communities associated with a dominant C4 prairie grass, Andropogon gerardii Vitman. Elevated CO2 and drought both affected resources available to the soil microbial community. For example, elevated CO2 increased the soil C:N ratio and water content during drought, whereas drought alone decreased both. Drought significantly decreased soil microbial biomass. In contrast, elevated COz increased biomass while ameliorating biomass decreases that were induced under drought. Total and active direct bacterial counts and carbon substrate use (overall use and number of used sources) increased significantly under elevated CO2. Denaturing gradient gel electrophoresis analysis revealed that drought and elevated CO2, singly and combined, did not affect the soil bacteria community structure.We conclude that elevated CO2 alone increased bacterial abundance and microbial activity and carbon use, probably in response to increased root exudation. Elevated CO2 also limited drought-related impacts on microbial activity and biomass,which likely resulted from decreased plant water use under elevated CO2. These are among the first results showing that elevated CO2 and drought work in opposition to modulate plant-associated soil-bacteria responses,which should then Influence soil resources and plant and ecosystem function.     

Preliminary computational modeling of nitric oxide synthase 3 interactions with caveolin-1： influence of exon 7 Glu298Asp polymorphism

The significance of endothelial nitric oxide synthase 3 （NOS3） activity has been recognized for many years, however it was only recently that the complicated regulation of this constitutively expressed enzyme in endothelial cells was identified. A critical component of the NOS3 regulatory cyde in endothelial cells is its intracellnlar localization to caveolae. The caveolar coordination of NOS3, more specifically its interaction with caveolin-1 （Cav-1）, plays a major role in normal endothelial NOS3 activity and vascular bioavailability of nitric oxide. We have recently shown that the presence of NOS3 exon 7 Glu298Asp polymorphism caused diminished shear-dependent NOS activation, was less extensively associated with caveolae, and had a decreased degree of interaction with Cav-1. Here, we carried out preliminary investigations to identify possible mechanisms of the genotype-dependent endothelial cell responses we observed in our previous investigations. Through this approach we tested the hypothesis that computer simulations could provide insights regarding the contribution of this single nucleotide polymorphism to regulation of the NOS3 isoform. We observed that in the Glu/Asp and Asp/Asp mutant genotypes, the amount of NOS3 associated with Cav-1 was significantly lower. Additionally, we have shown, using a theoretical computational model, that mutation of an amino acid at position 298 might affect the protein-protein interactions and localization of the NOS3 protein. These alterations might also affect the protein function and explain the enhanced disease risk associated with the presence of Glu298Asp polymorphism in the NOS3 protein.     

Analysis of a Gibbs sampler method for model-based clustering of gene expression data

MOTIVATION: Over the last decade, a large variety of clustering algorithms have been developed to detect coregulatory relationships among genes from microarray gene expression data. Model-based clustering approaches have emerged as statistically well-grounded methods, but the properties of these algorithms when applied to large-scale data sets are not always well understood. An in-depth analysis can reveal important insights about the performance of the algorithm, the expected quality of the output clusters, and the possibilities for extracting more relevant information out of a particular data set. RESULTS: We have extended an existing algorithm for model-based clustering of genes to simultaneously cluster genes and conditions, and used three large compendia of gene expression data for Saccharomyces cerevisiae to analyze its properties. The algorithm uses a Bayesian approach and a Gibbs sampling procedure to iteratively update the cluster assignment of each gene and condition. For large-scale data sets, the posterior distribution is strongly peaked on a limited number of equiprobable clusterings. A GO annotation analysis shows that these local maxima are all biologically equally significant, and that simultaneously clustering genes and conditions performs better than only clustering genes and assuming independent conditions. A collection of distinct equivalent clusterings can be summarized as a weighted graph on the set of genes, from which we extract fuzzy, overlapping clusters using a graph spectral method. The cores of these fuzzy clusters contain tight sets of strongly coexpressed genes, while the overlaps exhibit relations between genes showing only partial coexpression. AVAILABILITY: GaneSh, a Java package for coclustering, is available under the terms of the GNU General Public License from our website at http://bioinformatics.psb.ugent.be/software     

Ex vivo glycan engineering of CD44 programs human multipotent mesenchymal stromal cell trafficking to bone

The capacity to direct migration ('homing') of blood-borne cells to a predetermined anatomic compartment is vital to stem cell-based tissue engineering and other adoptive cellular therapies. Although multipotent mesenchymal stromal cells (MSCs, also termed 'mesenchymal stem cells') hold the potential for curing generalized skeletal diseases, their clinical effectiveness is constrained by the poor osteotropism of infused MSCs (refs. 1-3). Cellular recruitment to bone occurs within specialized marrow vessels that constitutively express vascular E-selectin, a lectin that recognizes sialofucosylated determinants on its various ligands. We show here that human MSCs do not express E-selectin ligands, but express a CD44 glycoform bearing alpha-2,3-sialyl modifications. Using an alpha-1,3-fucosyltransferase preparation and enzymatic conditions specifically designed for treating live cells, we converted the native CD44 glycoform on MSCs into hematopoietic cell E-selectin/L-selectin ligand (HCELL), which conferred potent E-selectin binding without effects on cell viability or multipotency. Real-time intravital microscopy in immunocompromised (NOD/SCID) mice showed that intravenously infused HCELL(+) MSCs infiltrated marrow within hours of infusion, with ensuing rare foci of endosteally localized cells and human osteoid generation. These findings establish that the HCELL glycoform of CD44 confers tropism to bone and unveil a readily translatable roadmap for programming cellular trafficking by chemical engineering of glycans on a distinct membrane glycoprotein.     

Plasmonic Perovskite Solar Cells Utilizing Au@SiO<Subscript>2</Subscript> Core-Shell Nanoparticles

The role of Au@SiO₂ core-shell nanoparticles on optical properties of perovskite solar cells has been explored using both the theoretical computations and the experiments. A quasi-static model is used to study the surface plasmon resonances (SPRs) of Au@SiO₂ core-shell nanospheres. Au@SiO₂ core-shell nanoparticles, with varying shell thickness and core radius, were assumed to be embedded in methylammonium lead triiodide (CH₃NH₃PbI₃) perovskite active layer. Enhanced absorption in the active layer is obtained due to the near-field plasmonic effect of the embedded core-shell nanoparticles. Theoretical modelling shows that a shell thickness of 1 nm and core diameter of 20 nm provide absorption enhancement in the orange-red region of the electromagnetic spectrum. Experiments performed using ～20-nm-sized Au@SiO₂ core-shell nanoparticles (with a shell thickness of ～1 nm) clearly demonstrate the enhanced absorption and the resulting enhancement in photocurrent due to the plasmonic effects. An efficiency enhancement of over 18 % is obtained for the best plasmonic perovskite solar cell containing Au@SiO₂ nanoparticles in Au@SiO₂-TiO₂ weight ratio of ～1 %. Incident photon-to-current conversion efficiency (IPCE) data also showed enhancement in photocurrent for the plasmonic device. The quasi-static modelling approach provides a good correlation between theory and experiment.     

Tunable Properties of Surface Plasmon Resonance of Metal Nanospheroid: Graphene Plasmon Interaction

Plasmonics - Graphene plasmonic resonances play a significant role for enhancing the photon absorption inside thin film solar devices. We investigate the field rising at the intersection of...