RNA global alignment in the joint sequence–structure space using elastic shape analysis

The functions of RNAs, like proteins, are determined by their structures, which, in turn, are determined by their sequences. Comparison/alignment of RNA molecules provides an effective means to predict their functions and understand their evolutionary relationships. For RNA sequence alignment, most methods developed for protein and DNA sequence alignment can be directly applied. RNA 3-dimensional structure alignment, on the other hand, tends to be more difficult than protein structure alignment due to the lack of regular secondary structures as observed in proteins. Most of the existing RNA 3D structure alignment methods use only the backbone geometry and ignore the sequence information. Using both the sequence and backbone geometry information in RNA alignment may not only produce more accurate classification, but also deepen our understanding of the sequence–structure–function relationship of RNA molecules. In this study, we developed a new RNA alignment method based on elastic shape analysis (ESA). ESA treats RNA structures as three dimensional curves with sequence information encoded on additional dimensions so that the alignment can be performed in the joint sequence–structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. Based on ESA, a rigorous mathematical framework can be built for RNA structure comparison. Means and covariances of full structures can be defined and computed, and probability distributions on spaces of such structures can be constructed for a group of RNAs. Our method was further applied to predict functions of RNA molecules and showed superior performance compared with previous methods when tested on benchmark datasets. The programs are available at http://stat.fsu.edu/ ∼jinfeng/ESA.html.     

The RAM network in pathogenic fungi

The regulation of Ace2 and morphogenesis (RAM) network is a protein kinase signaling pathway conserved among eukaryotes from yeasts to humans. Among fungi, the RAM network has been most extensively studied in the model yeast Saccharomyces cerevisiae and has been shown to regulate a range of cellular processes, including daughter cell-specific gene expression, cell cycle regulation, cell separation, mating, polarized growth, maintenance of cell wall integrity, and stress signaling. Increasing numbers of recent studies on the role of the RAM network in pathogenic fungal species have revealed that this network also plays an important role in the biology and pathogenesis of these organisms. In addition to providing a brief overview of the RAM network in S. cerevisiae, we summarize recent developments in the understanding of RAM network function in the human fungal pathogens Candida albicans, Candida glabrata, Cryptococcus neoformans, Aspergillus fumigatus, and Pneumocystis spp.     

Preserving immunogenicity of lethally irradiated viral and bacterial vaccine epitopes using a radio- protective Mn2+-Peptide complex from Deinococcus

Although pathogen inactivation by γ-radiation is an attractive approach for whole-organism vaccine development, radiation doses required to ensure sterility also destroy immunogenic protein epitopes needed to mount protective immune responses. We demonstrate the use of a reconstituted manganous peptide complex from the radiation-resistant bacterium Deinococcus radiodurans to protect protein epitopes from radiation-induced damage and uncouple it from genome damage and organism killing. The Mn(2+) complex preserved antigenic structures in aqueous preparations of bacteriophage lambda, Venezuelan equine encephalitis virus, and Staphylococcus aureus during supralethal irradiation (25-40 kGy). An irradiated vaccine elicited both antibody and Th17 responses, and induced B and T cell-dependent protection against methicillin-resistant S. aureus (MRSA) in mice. Structural integrity of viruses and bacteria are shown to be preserved at radiation doses far above those which abolish infectivity. This approach could expedite vaccine production for emerging and established pathogens for which no protective vaccines exist.     

Analysis of keystone enzyme in Agar hydrolysis provides insight into the degradation (of a polysaccharide from) red seaweeds

Agars are abundant polysaccharides from marine red algae, and their chemical structure consists of alternating D-galactose and 3,6-anhydro-L-galactose residues, the latter of which are presumed to make the polymer recalcitrant to degradation by most terrestrial bacteria. Here we study a family 117 glycoside hydrolase (BpGH117) encoded within a recently discovered locus from the human gut bacterium Bacteroides plebeius. Consistent with this locus being involved in agarocolloid degradation, we show that BpGH117 is an exo-acting 3,6-anhydro-α-(1,3)-L-galactosidase that removes the 3,6-anhydrogalactose from the non-reducing end of neoagaro-oligosaccharides. A Michaelis complex of BpGH117 with neoagarobiose reveals the distortion of the constrained 3,6-anhydro-L-galactose into a conformation that favors catalysis. Furthermore, this complex, supported by analysis of site-directed mutants, provides evidence for an organization of the active site and positioning of the catalytic residues that are consistent with an inverting mechanism of catalysis and suggests that a histidine residue acts as the general acid. This latter feature differs from the vast majority of glycoside hydrolases, which use a carboxylic acid, highlighting the alternative strategies that enzymes may utilize in catalyzing the cleavage of glycosidic bonds.     

Development of Gelucire 43/01 Beads of Metformin Hydrochloride for Floating Delivery

The objective of this study was to prepare and characterize beads of Gelucire 43/01 for floating delivery of metformin hydrochloride (MH). The beads were evaluated for particle size, surface morphology, percent drug entrapment, percent yield, differential scanning calorimetry (DSC), in vitro floating ability, and in vitro drug release. Aging effect on storage was evaluated using hot stage microscopy (HSM), DSC, scanning electron microscopy, and in vitro floating ability. The formed beads were sufficiently hard and spherical in shape. Photomicrographs show that the surface was porous in nature. The average particle diameter of beads was found to be in the size range of 3.85 to 3.95 mm, and percent entrapment was 83.07% to 86.13%. The beads demonstrated favorable in vitro floating ability. The analysis of DSC thermograms revealed no physical interaction between the lipid and the drug in the prepared beads. Prepared formulations showed better controlled release behavior when compared with its conventional dosage form and comparable release profile with marketed sustained release product. HSM photomicrograph showed presence of some unmelted portion even at 43°C and completely melts on 51°C in aged sample. It was found that there was no significant effect on floating ability of aged beads since it remains floats up to 8 h study period. Thus, it is concluded that beads of Gelucire 43/01 could be serve as an effective carrier for highly water-soluble antihyperglycemic drugs like MH for the controlled delivery.     

Evaluation of synergistic effects of bacterial and cyanobacterial strains as biofertilizers for wheat

An investigation was undertaken to screen, select and evaluate a set of bacterial and cyanobacterial isolates from the wheat rhizosphere for their role as biofertilizers in wheat. From an initial set of 23 cyanobacterial strains and 110 bacterial isolates from wheat rhizospheric soil, 3 bacterial and 3 cyanobacterial strains were selected based on their plant growth promoting potential under laboratory and controlled greenhouse conditions. In vitro compatibility studies revealed positive interactions among the six strains. Pot experiments were conducted with wheat variety HD 2687, with a total of 51 treatments, along with recommended fertilizer controls. Various combinations of the selected set of three bacterial (PW1, PW5 and PW7) and three cyanobacterial isolates (CW1, CW2 and CW3) were used along with 1/3 N and full dose of P and K fertilizers. Significant enhancement in the soil microbiological (Dehydrogenase activity, FDA hydrolase, Alkaline phosphatase and microbial biomass) and plant growth/yield parameters were recorded. Observations revealed a two-fold increase in panicle weight in selected combinations (PW1+PW7+CW3; PW1+ CW1+CW2/CW1+CW3; CW2+CW3), as compared to control treatment involving full dose of chemical fertilizers. Such combinations, which also provided N savings of 40–80 kg N/ha are being further evaluated in field experiments. This study for the first time illustrated the positive and dynamic interactions among bacterial and cyanobacterial strains and their promise in integrated nutrient management of wheat crop.