The effect of collagenase, water and calcium chloride on the removal of <i>Salmo salar</i> (salmon) and <i>Oncorhynchus mykiss</i> (trout) pin bones

The aim of this study was to determine the influence of the fillet structure on the deboning force required to remove salmon and trout pin bones. Salmon and trout fillets with differing fillet structure were used, in order to study the importance of the fillet structure on the deboning process. In the first test naturally gaping and non-gaping fillets were compared. To confirm the role that the collagen plays within the fillet structure, the fillets underwent series of treatments. Fillets were put into (i) a collagenase solution to remove the collagen in the fillet (ii) a calcium chloride solution to determine if collagen was the main influential factor. Both treated salmon and trout fillets were again compared to untreated fillets from the same batch. The results indicate that collagenase and calcium chloride have a large interaction on deboning force compared to water or no treatments

Development of a gluten free bread enriched with faba bean husk as a fibre supplement

Faba bean husks (FBH) are a high-fibre waste product of faba beans and are primarily used as animal feed with the potential of becoming a fibre supplement. In this study, different levels and particle sizes of FBH flour were used to enhance the fibre content of gluten free bread. Bread properties were evaluated by measuring specific volume, colour (crust and crumb), and crumb texture. The sensory characteristics of breads were assessed by a group of untrained panellists (n = 66) on appearance, aroma, flavour, texture, aftertaste, willingness to buy, and overall acceptability using a nine-point hedonic scale. Volume of bread was affected by the level and particle size of FBH added. Texture analysis showed the importance of level of FBH, and of its particle size in establishing hardness, gumminess, and chewiness (p &lt; 0.05). The added FBH influenced the colour of the crust and crumb. Two formulations of FBH-enriched gluten free bread (particle sizes of 212–300 μm at 5% wheat flour weight substitution, and particle sizes of smaller than 212 μm at 15% wheat four weight substitution) increased the fibre content of the bread, while had no negative impact on sensory evaluation in comparison to control treatment (p &lt; 0.05).</p

Cysteinyl-tRNA formation: the last puzzle of aminoacyl-tRNA synthesis

AbstractWith the exception of the methanogenic archaea Methanococcus jannaschii and Methanobacterium thermoautotrophicum ΔH, all organisms surveyed contain orthologs of Escherichia coli cysteinyl-tRNA synthetase (CysRS). The characterization of CysRS-encoding (cysS) genes and the demonstration of their ability to complement an E. coli cysSts mutant reveal that Methanococcus maripaludis and Methanosarcina barkeri, two other methanogenic archaea, possess canonical CysRS proteins. A molecular phylogeny inferred from 40 CysRS sequences indicates that the CysRS of M. maripaludis and Methanosarcina spp. are specific relatives of the CysRS of Pyrococcus spp. and Chlamydia, respectively. This result suggests that the CysRS gene was acquired by lateral gene transfer in at least one euryarchaeotic lineage

Evaluating the Degradation of Natural Resources in the Mediterranean Environment Using the Water and Land Resources Degradation Index, the Case of Crete Island

Natural resources degradation poses multiple challenges particularly to environmental and economic processes. It is usually difficult to identify the degree of degradation and the critical vulnerability values in the affected systems. Thus, among other tools, indices (composite indicators) may also describe these complex systems or phenomena. In this approach, the Water and Land Resources Degradation Index was applied to the fifth largest Mediterranean island, Crete, for the 1999–2014 period. The Water and Land Resources Degradation Index uses 11 water and soil resources related indicators: Aridity Index, Water Demand, Drought Impacts, Drought Resistance Water Resources Infrastructure, Land Use Intensity, Soil Parent Material, Plant Cover, Rainfall, Slope, and Soil Texture. The aim is to identify the sensitive areas to degradation due to anthropogenic interventions and natural processes, as well as their vulnerability status. The results for Crete Island indicate that prolonged water resources shortages due to low average precipitation values or high water demand (especially in the agricultural sector), may significantly affect Water and Land degradation processes. Hence, Water and Land Resources Degradation Index could serve as an extra tool to assist policymakers to improve their decisions to combat Natural Resources degradation

Evaluating the Degradation of Natural Resources in the Mediterranean Environment Using the Water and Land Resources Degradation Index, the Case of Crete Island

Natural resources degradation poses multiple challenges particularly to environmental and economic processes. It is usually difficult to identify the degree of degradation and the critical vulnerability values in the affected systems. Thus, among other tools, indices (composite indicators) may also describe these complex systems or phenomena. In this approach, the Water and Land Resources Degradation Index was applied to the fifth largest Mediterranean island, Crete, for the 1999&ndash;2014 period. The Water and Land Resources Degradation Index uses 11 water and soil resources related indicators: Aridity Index, Water Demand, Drought Impacts, Drought Resistance Water Resources Infrastructure, Land Use Intensity, Soil Parent Material, Plant Cover, Rainfall, Slope, and Soil Texture. The aim is to identify the sensitive areas to degradation due to anthropogenic interventions and natural processes, as well as their vulnerability status. The results for Crete Island indicate that prolonged water resources shortages due to low average precipitation values or high water demand (especially in the agricultural sector), may significantly affect Water and Land degradation processes. Hence, Water and Land Resources Degradation Index could serve as an extra tool to assist policymakers to improve their decisions to combat Natural Resources degradation

Genomic analysis of recombinant Sabin clinical isolates

Recombination in Poliovirus vaccine strains is a very frequent phenomenon. In this report 23 polio/Sabin strains isolated from healthy vaccinees or from VAPP patients after OPV administration, were investigated in order to identify recombination sites from 2C to 3D regions of the poliovirus genome. RT-PCR, followed by Restriction Fragment Length Polymorphism (RFLP) screening analysis were applied in four distant genomic regions (5' UTR, VP1, 2C and 3C-3D) in order to detect any putative recombinant. The detected recombinants were sequenced from 2C to the end of the genome (3' UTR) and the exact recombination sites were determined with computational analysis. Five of the 23 isolated strains were recombinant in one genomic region, two of them in 2C, isolates EP16:S3/S2, EP23:S3/S1, two in 3D isolates EP6:S2/S1, EP12:S2/S1 and one in 3A isolate EP9:S2/Sl. Point mutations were found in strains EP3, EP6, EP9 and EP12. Recombination specific types and sites re-occurrence along with point mutations are discussed concerning the polioviruses evolution

An Integrated In Silico Approach to Design Specific Inhibitors Targeting Human Poly(A)-Specific Ribonuclease

Poly(A)-specific ribonuclease (PARN) is an exoribonuclease/deadenylase that degrades 3'-end poly(A) tails in almost all eukaryotic organisms. Much of the biochemical and structural information on PARN comes from the human enzyme. However, the existence of PARN all along the eukaryotic evolutionary ladder requires further and thorough investigation. Although the complete structure of the full-length human PARN, as well as several aspects of the catalytic mechanism still remain elusive, many previous studies indicate that PARN can be used as potent and promising anti-cancer target. In the present study, we attempt to complement the existing structural information on PARN with in-depth bioinformatics analyses, in order to get a hologram of the molecular evolution of PARNs active site. In an effort to draw an outline, which allows specific drug design targeting PARN, an unequivocally specific platform was designed for the development of selective modulators focusing on the unique structural and catalytic features of the enzyme. Extensive phylogenetic analysis based on all the publicly available genomes indicated a broad distribution for PARN across eukaryotic species and revealed structurally important amino acids which could be assigned as potentially strong contributors to the regulation of the catalytic mechanism of PARN. Based on the above, we propose a comprehensive in silico model for the PARN's catalytic mechanism and moreover, we developed a 3D pharmacophore model, which was subsequently used for the introduction of DNP-poly(A) amphipathic substrate analog as a potential inhibitor of PARN. Indeed, biochemical analysis revealed that DNP-poly(A) inhibits PARN competitively. Our approach provides an efficient integrated platform for the rational design of pharmacophore models as well as novel modulators of PARN with therapeutic potential. Citation: Vlachakis D, Pavlopoulou A, Tsiliki G, Komiotis D, Stathopoulos C, et al. (2012) An Integrated In Silico Approach to Design Specific Inhibitors Targeting Human Poly(A)-Specific Ribonuclease. PLoS ONE 7(12): e51113. doi:10.1371/journal.pone.005111

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions

Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity