Isolation and characterization of biofilm-forming bacteria and associated extracellular polymeric substances from oral cavity

The current work deals with the studies on characterization of two biofilm-forming bacteria isolated from the oral cavity. The major constituent of biofilm other than bacterial cells is the extracellular polymeric substance (EPS) matrix, which is secreted by the bacterial cells themselves. Physical properties of biofilms such as attachment, mechanical strength, antibiotic resistance can be attributed to EPS matrix. Molecular phylogeny confirmed these two isolates as Pseudomonas aeruginosa and Bacillus subtilis. It was observed that cell attachment in both the strains was maximal when xylose was used as the sole carbon source. The EPS characterization result indicated the presence of a macromolecular complex constituting of carbohydrate, protein, lipids and nucleic acids. Test for biofilm formation in the presence of metal salts of iron and zinc showed moderate to high inhibition of biofilm formation. However, calcium, iron and copper have been found to enhance biofilm growth significantly. There was more than 50 % increase in biofilm growth by P. aeruginosa with an increase in calcium concentration up to 80 ppm (Two tailed t-test P?<?0.05), whereas ≥ 15 % increase in biofilm growth by B. subtilis was observed in the presence of 80 ppm of calcium. However, variations were significant (Two way ANOVA, P?<?0.01) between different metals in different concentrations. In this study, attempts have been made to examine the effect of different carbon sources and physiological conditions on biofilm growth.     

ASRDb: A comprehensive resource for archaeal stress response genes

An organism''s survival strategy under the constantly changing environment depends on its ability to sense and respond to changes in its environment. Archaea, being capable to grow under various extreme environmental conditions, provide valuable model for exploring how single-celled organisms respond to environmental stresses. However, no such approach has ever been made to make an integrated classification of various archaeal stress responses.Archaeal Stress Response Database (ASRDb) is a web accessible (http://121.241.218.70/ASRDb) database that represents the first online available resource providing a comprehensive overview of stress response genes of 66 archaeal genomes. This database currently contains almost 6000 stress specific genes of 66 archaeal genomes. All the stress specific genes are grouped into 17 different stress categories. A user-friendly interface has been designed to examine data using query tools. This database provides an efficient search engine for random and advanced database search operations. We have incorporated BLAST search options to the resulting sequences retrieved from database search operations. A site map page representing the schematic diagram will enable user to understand the logic behind the construction of the database. We have also provided a very rich and informative help page to make user familiar with the database. We sincerely believe that ASRDb will be of particular interest to the life science community and facilitates the biologists to unravel the role of stress specific genes in the adaptation of microorganisms under various extreme environmental conditions.     

Oligomeric structure of a cathelicidin antimicrobial peptide in dodecylphosphocholine micelle determined by NMR spectroscopy

The broad spectrum of antibacterial activities of host defense cationic antimicrobial peptides (AMPs) arises from their ability to perturb membrane integrity of the microbes. The mechanisms are often thought to require assembly of AMPs on the membrane surface to form pores. However, three dimensional structures in the oligomeric form of AMPs in the context of lipid membranes are largely limited. Here, we demonstrate that a 22-residue antimicrobial peptide, termed VK22, derived from fowlicidin-1, a cathelicidin family of AMP from chicken oligomerizes into a predominantly tetrameric state in zwitterionic dodecylphosphocholine (DPC) micelles. An ensemble of NMR structures of VK22 determined in 200mM perdeuterated DPC, from 755 NOE constrains including 19 inter-helical NOEs, had revealed an assembly of four helices arranged in anti-parallel fashion. Hydrogen bonds, C(α)H-O=C types, and van der Waals interactions among the helical sub-units appear to be involved in the stabilization of the quaternary structures. The central region of the barrel shaped tetrameric bundle is non-polar with clusters of aromatic residues, whereas all the cationic residues are positioned at the termini. Paramagnetic spin labeled NMR experiments indicated that the tetrameric structure is embedded into micelles such that the non-polar region located inside the lipid acyl chains. Structure and micelle localization of a monomeric version, obtained from substitution of two Tyr residues with Ala, of the peptide is also compared. The mutated peptide VK22AA has been found be localized at the surface of the micelles. The tetrameric structure of VK22 delineates a small water pore that can be larger in the higher order oligomers. As these results provide structural insights, at atomic resolution, into the oligomeric states of a helical AMP in lipid environment, the structural details may be further utilized for the design of novel self-assembled membrane protein mimics.     

Role of hydration on the functionality of a proteolytic enzyme α-chymotrypsin under crowded environment

Enzymes and other bio-macromolecules are not only sensitive to physical parameters such as pH, temperature and solute composition but also to water activity. A universally instructive way to vary water activity is the addition of osmotically active but otherwise inert solvents which also mimic the condition of an intercellular milieu. In the present contribution, the role of hydration on the functionality of a proteolytic enzyme α-chymotrypsin (CHT) is investigated by modulating the water activity with the addition of polyethylene glycols (PEG with an average molecular weight of 400). The addition of PEG increases the affinity of the enzyme to its substrate, however, followed by a decrease in the turnover number (k_cat). Energetic calculations show that entrance path for the substrate is favoured, whereas the exit channel is restricted with increasing concentration of the crowding agent. This decrease is attributed to the thinning of the hydration shell of the enzyme due to the loss of critical water residues from the hydration surface of the enzyme as evidenced from volumetric and compressibility measurements. The overall secondary and tertiary structures of CHT determined from far-UV and near-UV circular dichroism (CD) measurements show no considerable change in the studied osmotic stress range. From kinetic and equilibrium data, we calculate 115 ± 30 numbers of water molecules to be altered during the enzymatic catalysis of CHT. Spectroscopic observation of water relaxation and rotational dynamics of ANS-CHT complex at various concentrations of the osmoting agent also support the dehydration of the hydration layer. Such dehydration/hydration processes during turnover imply a significant contribution of solvation to the energetics of the conformational changes.     

Establishing bioequivalence of racemic venlafaxine formulations using stereoselective assay method: Is it necessary?

A bioequivalence study for venlafaxine generic formulation was conducted as an open label, balanced, randomized, two‐way crossover, single‐dose study. In this study, a comparison of various pharmacokinetic parameters of venlafaxine hydrochloride 150 mg modified release capsules of Ranbaxy and EFEXOR®‐XR 150 mg capsules of Wyeth, in healthy, adult, male, human subjects under fasting condition was performed to conclude bioequivalence. Venlafaxine and its major active metabolite O‐desmethylvenlafaxine (ODV) are racemates. The “(S)‐(+)” and “(R)‐(−)” enantiomers of venlafaxine and ODV are established as being active. Hence, subject samples were analyzed using nonstereoselective and stereoselective assay methods. Both (S)‐(+) and (R)‐(−) enantiomers of venlafaxine and ODV showed similar absorption and disposition. The 90% confidence intervals for venlafaxine, (R)‐(−)‐venlafaxine as well as (S)‐(+)‐venlafaxine were within acceptance range concluding bioequivalence. The results obtained by stereoselective assay were comparable to the nonstereoselective analysis, as sum of concentrations of (S)‐(+)‐ and (R)‐(−)‐enantiomers of venlafaxine and ODV. The mean (S)‐(+)/(R)‐(−) ratios of the enantiomers of venlafaxine and ODV at various time points were consistent in the study subjects. Therefore, the estimation of venlafaxine and ODV using nonstereoselective assay method is effective in distinguishing formulation differences (if any) in bioequivalence studies in a cost‐effective manner. Chirality, 2011. © 2011 Wiley‐Liss, Inc.     

Wnt signaling regulates the proliferation potential and lineage commitment of human umbilical cord derived mesenchymal stem cells

Relatively less is known about the interactions that tightly regulate the mesenchymal stem cells (MSCs) to maintain their pluripotency. Recent studies reports that Wnt proteins might play an important role in governing the MSC cell fate. In this study, we tested the hypothesis that Wnt proteins differentially regulate in vitro differentiation of human umbilical cord derived MSCs. Stromal cells from human umbilical cord (hUCMSCs) were isolated and treated with Wnt inhibitor/activator. FACS analysis of hUCMSCs for CD29, CD90, CD73, CD44, CD45 marker expression and gene expression of Wnt target genes and lineage specific genes were performed after Lithium Chloride (LiCl) and Quercetin treatment for 6 days. The cultured primary hUCMSCs demonstrated elevated MSC surface marker expression with clonogenic properties and differentiation potentials towards osteogenic, adipogenic and chondrogenic lineages. Downregulation in the expression of Wnt with Quercetin treatment was noted. LiCl treatment increased cellular proliferation but did not influence differentiation suggesting that the cells retain pluripotency whereas Quercetin treatment downregulated stemness markers, Wnt target gene expression and promoted osteogenesis as demonstrated by FACS analysis, calcium estimation and gene expression studies. Shift of differentiation potential after the inhibition of Wnt signaling by Quercetin was evident from the gene expression data and elevated calcium production, driving MSCs towards probable osteogenic lineage. The findings in particular are likely to open an interesting avenue of biomedical research, summarizing the impact of Wnt signaling on lineage commitment of MSCs.

     

Evidence that proline focuses movement of the floppy loop of arylalkylamine N-acetyltransferase (EC 2.3.1.87)

Arylalkylamine N-acetyltransferase (AANAT) catalyzes the N-acetylation of serotonin, the penultimate step in the synthesis of melatonin. Pineal AANAT activity increases at night in all vertebrates, resulting in increased melatonin production. This increases circulating levels of melatonin, thereby providing a hormonal signal of darkness. Kinetic and structural analysis of AANAT has determined that one element is floppy. This element, termed Loop 1, is one of three loops that comprise the arylalkylamine binding pocket. During the course of chordate evolution, Loop 1 acquired the tripeptide CPL, and the enzyme became highly active. Here we focused on the functional importance of the CPL tripeptide and found that activity was markedly reduced when it was absent. Moreover, increasing the local flexibility of this tripeptide region by P64G and P64A mutations had the counterintuitive effect of reducing activity and reducing the overall movement of Loop 1, as estimated from Langevin dynamics simulations. Binding studies indicate that these mutations increased the off-rate constant of a model substrate without altering the dissociation constant. The structural kink and local rigidity imposed by Pro-64 may enhance activity by favoring configurations of Loop 1 that facilitate catalysis and do not become immobilized by intramolecular interactions.     

Development and application of anticancer fluorescent CdS nanoparticles enriched Lactobacillus bacteria as therapeutic microbots for human breast carcinoma

Applied Microbiology and Biotechnology - Applications of probiotic bacteria and nanoparticles (NPs) as therapeutic agents have great importance. This study demonstrates a combinatorial approach of...