Development of Microbiome Biobanks - Challenges and Opportunities.

The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential.

Identification and Analysis of Key Residues Involved in Folding and Binding of Protein-carbohydrate Complexes.

BACKGROUND: Protein-carbohydrate interactions play vital roles in several biological processes in living organisms. The comparative analysis of binding site residues along with stabilizing residues in protein-carbohydrate complexes provides ample insights to understand the structure, function and recognition mechanism. OBJECTIVE: The main objective of this study is to identify and analyze the residues, which are involved in both folding and binding of the protein-carbohydrate complexes. METHODS: We have identified the stabilizing residues using the knowledge of hydrophobicity, longrange interactions and conservation, as well as binding site residues using a distance cutoff of 3.5Å between any heavy atoms in protein and ligand. Residues, which are common in stabilizing and binding, are termed as key residues. These key resides are analyzed with various sequence and structure based parameters such as frequency of occurrence, surrounding hydrophobicity, longrange order and conservation score. RESULTS: In this work, we have identified 2.45% binding site residues in a non-redundant dataset of 1130 complexes using distance-based criteria and 7.07% stabilizing residues using the concepts of hydrophobicity, long-range interactions and conservation of residues. Further, 5.9% of binding and 2.04% of stabilizing residues are common to each other, which are termed as key residues. The key residues have been analysed based on protein classes, carbohydrate types, gene ontology functional classifications, amino acid preference and structure-based parameters. We found that all-ß, α+ß and α/ß have more key residues than other protein classes and most of the KRs are present in ß-strands, which shows their importance in stability and binding of complexes. On the ligand side, Lsaccharide has the highest number of key residues and it has a high percentage of KRs in SRs and BRs than other carbohydrate types. Further, polar and charged residues have a high tendency to serve as key residues. Classifications based on gene ontology terms revealed that Lys is preferred in all the three groups: molecular functions, biological processes and cellular components. Key residues have 6 to 9 contacts within the protein and make only one contact with the carbohydrate ligand. These contacts are dominant to form polar-nonpolar contacts followed by the contacts between charged atoms. Further, the influence of sequence and structural parameters such as surrounding hydrophobicity, solvent accessibility, secondary structure, long-range order and conservation score has been discussed. CONCLUSION: The results obtained in the present work provide deep insights for understanding the interplay between stability and binding in protein-carbohydrate complexes.

Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems.

Marine ecosystems are home to bacteria which are exposed to a wide variety of environmental conditions, such as extremes in temperature, salinity, nutrient availability and pressure. Survival under these conditions must have necessitated the adaptation and the development of unique cellular biochemistry and metabolism by these microbes. Thus, enzymes isolated from these microbes have the potential to possess quite unique physiological and biochemical properties. This review outlines a number of function-based metagenomic approaches which are available to screen metagenomic libraries constructed from marine ecosystems to facilitate the exploitation of some of these potentially novel biocatalysts. Functional screens to isolate novel cellulases, lipases and esterases, proteases, laccases, oxidoreductases and biosurfactants are described, together with approaches which can be employed to help overcome some of the typical problems encountered with functional metagenomic-based screens.

Synthesis and anticoagulant activity of a new series of 1,4-dihydropyridine derivatives.

A series of 1,4-dihydropyridine derivatives (1a-g) were prepared from three compounds condensation reaction of ethylacetoacetate, aromatic aldehyde and ammonium hydroxide. A new series of compounds (2a-g) were prepared from compounds (1a-g) via reaction with thiosemicarbazide using the condensation method. The synthesized compounds were confirmed by IR, 1H NMR, 13C NMR, mass spectral and elemental analyses. The synthesized compounds (1a-g) and (2a-g) were also screened for anticoagulant properties.

Serodiagnosis of severe leptospirosis: evaluation of ELISA based on the recombinant OmpL1 or LipL41 antigens of Leptospira interrogans serovar autumnalis.

ELISA based on the recombinant OmpL1 and LipL41 antigens of Leptospira interrogans serovar autumnalis strain N2 have been developed, for the serodiagnosis of the severe pulmonary form of leptospirosis on the endemic Andaman Islands. The recombinant OmpL1 and LipL41 were produced using Escherichia coli expression systems and then purified before each was evaluated in an IgM-ELISA. The sera tested came from 224 patients who had the severe form of leptospirosis and pulmonary pneumonitis as major symptoms, 148 patients who, although clinically suspected to have severe leptospirosis, had been found seronegative for leptospirosis, 528 patients with diseases other than lepstospirosis, and 704 apparently healthy individuals, all from the Andaman Islands. Among the patients with the severe pulmonary form of leptospirosis, the ELISA based on the recombinant OmpL1 achieved a sensitivity of 91.1%, a specificity of 86.5%, a positive predictive value of 91.1%, and a negative predictive value of 86.5%. The corresponding values for the assay based on the recombinant LipL41 were 89.3%, 89.2%, 92.6%, and 84.6%, respectively. The good performance of both ELISA indicates that either may be routinely used for the diagnosis of severe pulmonary leptospirosis which, at least on the Andaman Islands, occurs soon after the patient has become leptospiraemic. The evaluated ELISA may also be useful for early case detection and for monitoring the effects of treatment.