Nanoparticles in Biological Hydrogen Production: An Overview

Biological hydrogen (H₂) production enhancement through the use of nanoparticles (NPs) supplement in the media is being recognized as a promising approach. The NPs, including those of metal and metal oxides have shown a significant improvement in the BHP. A number of organisms as pure or mixed cultures can produce H₂ in presence of NPs from pure sugars and biowaste as a feed. However, their H₂ production efficiencies have been found to vary significantly with the type of NPs and their concentration. In this review article, the potential role of NPs in the enhancement of H₂ production has been assessed in dark- and photo-fermentative organisms using sugars and biowaste materials as feed. Further, the integrative approaches for commercial applications of NPs in BHP have been discussed.     

Oxygen uptake rate as a tool for on-line estimation of cell biomass and bed temperature in a novel solid-state fermentation bioreactor

Bioprocess and Biosystems Engineering - Direct measurement of cell biomass is difficult in a solid-state fermentation (SSF) process involving filamentous fungi since the mycelium and the solid...     

Searching Biomarkers in the Sequenced Genomes of <Emphasis Type="Italic">Staphylococcus</Emphasis> for their Rapid Identification

Bacterial identification using rrs (16S rRNA) gene is widely reported. Bacteria possessing multiple copies of rrs lead to overestimation of its diversity. Staphylococcus genomes carries 5–6 copies of rrs showing high similarity in their nucleotide sequences, which lead to ambiguous results. The genomes of 31 strains of Staphylococcus representing 7 species were searched for the presence of common genes. In silico digestion of 34 common genes using 10 restriction endonucleases (REs) lead to select gene-RE combinations, which could be used as biomarkers. RE digestion of recA allowed unambiguous identification of 13 genomes representing all the 7 species. In addition, a few more genes (argH, argR, cysS, gyrB, purH, and pyrE) and RE combinations permitted further identification of 12 strains. By employing additional RE and genes unique to a particular strain, it was possible to identify the rest 6 Staphylococcus aureus strains. This approach has the potential to be utilized for rapid detection of Staphylococcus strains.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-016-0565-9) contains supplementary material, which is available to authorized users.     

EFFICACY OF ‘SAFE’ LEVELS OF ANTIMICROBIAL FOOD ADDITIVES TO CONTROL MICROBIAL CONTAMINANTS IN A SYNTHETIC DIET FOR AGRIA AFFINIS LARVAE

The ability of eight antimicrobial food additives to suppress the growth of seven micro-organisms in a chemically defined diet for an insect, Agria affinis auct. nec Fallén, was tested by inoculating a standard number of the microorganisms into the diet and determining the amount of microbial growth and the effects on the rate of growth and survival of the insect. The antibiotics, mycifradin sulfate, streptomycin sulphate, and tetracyn, suppressed the growth of bacteria, and aerosporin suppressed the growth of yeast at concentrations that were innocuous for the insect. Mold inhibitors were less effective, and failed to suppress the growth of a species of Aspergillus. Potassium sorbate suppressed the growth of yeast, bacteria, and species of Penicillium, but only at concentrations that adversely affected the rate of growth and survival of the insect.Antimicrobial compounds that are added to synthetic diets of insects to control contamination by microorganisms must be chosen carefully with due regard for the species of micro-organisms that are responsible for the most serious contamination, for the tolerance of the insect to the effective concentrations of the antimicrobials, and for the nutritional level of the synthetic diet.

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Résumé Ce travail montre que les contaminations expérimentales d'un milieu synthétique pour l'élevage axénique des larves d'Agria affinis a des effets défavorables ou nocifs, soit en retardant le développement, soit en provoquant une mortalité des divers stades. L'adjonction d'antibiotiques au milieu d'élevage, peut avec des doses appropriées, éviter les contaminations, sans affecter la croissance ou la survie de l'insecte.Les micro-organismes utilisés pour la contamination du milieu d'élevage sont: 2 bactéries (Serratia marcescens Bizio et Providencia alcalifaciens (De Salles Gomes), 1 levure (Rhodotorula sp.) 4 moississures (Penicillium sp. A, B et C et Aspergillus sp.).Les composés anti-microbiens utilisés sont: 5 antibiotiques (Aerosporin, Sulfate de Mycifradin, Penicilline G potassium, sulfate de Streptomycine, et Tetracyn) 3 mycostatiques (sorbate de potassium, benzoate de sodium et propionate de sodium). La mycifradine, la streptomycine et la tetracyne empêchent bien la développement des deux bactéries testées, l'aerosporine supprime celle de la levure (tout cela à des concentrations non-nocives pour l'insecte). Les mycostatiques furent moins efficaces en particulier contre une espèce d'Aspergillus. Le sorbate de potassium inhibe la croissance de la levure, des bactéries et de Penicillium, mais seulement à des doses qui sont défavorables à la croissance et à la survie de l'insecte. Les micro-organismes semblent exercer leurs effets nocifs en modifiant la consistance ou la valeur nutritive du milieu alimentaire des larves, plutôt qu'en provoquant des infections directes.Le choix des composés anti-microbiens qui peuvent être adjoints à un milieu alimentaire d'élevage pour des larves d'insectes doit donc être réalisé avec soin, en tenant compte d'une part, de leur efficacité réelle sur les germes dont on doit éviter la prolifération, d'autre part, de leur inocuité sur l'insecte aux doses utilisées.

     

Substitution of serine for alpha 1(I)-glycine 844 in a severe variant of osteogenesis imperfecta minimally destabilizes the triple helix of type I procollagen. The effects of glycine substitutions on thermal stability are either position of amino acid specific

Recent reports have demonstrated that a series of probands with severe osteogenesis imperfecta had single base mutations in one of the two structural genes for type I procollagen that substituted amino acids with bulkier side chains for glycine residues and decreased the melting temperature of the triple helix. Here we demonstrate that the type I procollagen synthesized by cultured fibroblasts from a proband with a severe form of osteogenesis imperfecta consisted of normal molecules and molecules over-modified by post-translational reactions. The thermal stability of the intact type I collagen was normal as assayed by protease digestion under conditions in which a decrease in thermal stability was previously observed with eight other substitutions for glycine in the alpha 1(I) chain. In contrast, the thermal stability of the one-quarter length B fragment generated by digestion with vertebrate collagenase was decreased by 2-3 degrees C under the same conditions. Nucleotide sequencing of cDNAs and genomic DNA established that the proband had a substitution of A for G in one allele of the pro alpha 1(I) gene that converted the codon for alpha 1-glycine 844 to a codon for serine. The results also established that the alpha 1-serine 844 was the only mutation that could account for the decrease in thermal stability of the collagenase B fragment. There are at least two possible explanations for the failure of the alpha 1-serine 844 substitution to decrease the thermal stability of the collagen molecule whereas eight similar mutations decreased the melting temperature. One possibility is that the effects of glycine substitutions are position specific because not all glycine residues make equivalent contributions to cooperative blocks of the triple helix that unfold in the predenaturation range of temperatures. A second possible explanation is that substitutions of glycine by serine have much less effect on the stability of protein than the substitutions by arginine, cysteine, and aspartate previously studied.     

Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5Mg of Aegilops geniculata

Next‐generation sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole‐genome shotgun sequencing is cost‐prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing. This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines, followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow‐sorted chromosome 5M^g from a wheat/Aegilops geniculata disomic substitution line [DS5M^g (5D)] and sequenced it using an Illumina HiSeq 2000 system at approximately 50 × coverage. Paired‐end sequences were assembled and used for structural and functional annotation. A total of 4236 genes were annotated on 5M^g, in close agreement with the predicted number of genes on wheat chromosome 5D (4286). Single‐gene FISH indicated no major chromosomal rearrangements between chromosomes 5M^g and 5D. Comparing chromosome 5M^g with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza sativa), sorghum (Sorghum bicolor) and barley (Hordeum vulgare). Chromosome 5M^g‐specific SNPs and cytogenetic probe‐based resources were developed and validated. Deletion bin‐mapped and ordered 5M^g SNP markers will be useful to track 5M‐specific introgressions and translocations. This study provides a detailed sequence‐based analysis of the composition of a chromosome from a distant wild relative of bread wheat, and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement.     

Lysine 624 of the amyloid precursor protein (APP) is a critical determinant of amyloid β peptide length: support for a sequential model of γ-secretase intramembrane proteolysis and regulation by the amyloid β precursor protein (APP) juxtamembrane region

γ-Secretase is a multiprotein intramembrane cleaving aspartyl protease (I-CLiP) that catalyzes the final cleavage of the amyloid β precursor protein (APP) to release the amyloid β peptide (Aβ). Aβ is the primary component of senile plaques in Alzheimer's disease (AD), and its mechanism of production has been studied intensely. γ-Secretase executes multiple cleavages within the transmembrane domain of APP, with cleavages producing Aβ and the APP intracellular domain (AICD), referred to as γ and ε, respectively. The heterogeneous nature of the γ cleavage that produces various Aβ peptides is highly relevant to AD, as increased production of Aβ 1-42 is genetically and biochemically linked to the development of AD. We have identified an amino acid in the juxtamembrane region of APP, lysine 624, on the basis of APP695 numbering (position 28 relative to Aβ) that plays a critical role in determining the final length of Aβ peptides released by γ-secretase. Mutation of this lysine to alanine (K28A) shifts the primary site of γ-secretase cleavage from 1-40 to 1-33 without significant changes to ε cleavage. These results further support a model where ε cleavage occurs first, followed by sequential proteolysis of the remaining transmembrane fragment, but extend these observations by demonstrating that charged residues at the luminal boundary of the APP transmembrane domain limit processivity of γ-secretase.     

Multiplicity of Quorum Quenching Enzymes: A Potential Mechanism to Limit Quorum Sensing Bacterial Population

Bacteria express certain of their characteristics especially, pathogenicity factors at high cell densities. The process is termed as quorum sensing (QS). QS operates via signal molecules such as acylhomoserine lactones (AHLs). Other bacteria inhibit QS through the inactivation of AHL signals by producing enzymes like AHL-lactonases and -acylases. Comparative genomic analysis has revealed the multiplicity of genes for AHL lactonases (up to 12 copies per genome) among Bacillus spp. and that of AHL-acylases (up to 5 copies per genome) among Pseudomonas spp. This genetic evolution can be envisaged to enable host to withstand the attacks from bacterial population, which regulates its functioning through QS.     

Theoretical study on binding of Hoechst 33258 with oligonucleotides

Computer modelling with an energy minimization procedure is used here to obtain stereochemical and energetic details for complexes of the dye Hoechst 33258 with different oligonucleotide sequences. An optimised model of the dye with d(A)5 X d(T)5 is in conformity with previous proposed models. It has bifurcated hydrogen bonds between N2H and N4H of benzimidazole rings with N3 of adenine and O2 of thymine. Relative binding energies with different oligonucleotides show preference for AT containing sequences, with an intermediate affinity between that for netropsin and distamycin-2. Reduced binding is observed at high ionic concentration. The benzimidazole rings are twisted with respect to the phenol ring in the optimal model. This gives desired curvature to the molecule which is stabilised by intermolecular forces.