Comparative Molecular Dynamics Simulation of Hepatitis C Virus NS3/4A Protease (Genotypes 1b, 3a and 4a) Predicts Conformational Instability of the Catalytic Triad in Drug Resistant Strains

The protease domain of the Hepatitis C Virus (HCV) nonstructural protein 3 (NS3) has been targeted for inhibition by several direct-acting antiviral drugs. This approach has had marked success to treat infections caused by HCV genotype 1 predominant in the USA, Europe, and Japan. However, genotypes 3 and 4, dominant in developing countries, are resistant to a number of these drugs and little progress has been made towards understanding the structural basis of their drug resistivity. We have previously developed a 4D computational methodology, based on 3D structure modeling and molecular dynamics simulation, to analyze the active sites of the NS3 proteases of HCV-1b and 4a in relation to their catalytic activity and drug susceptibility. Here, we improved the methodology, extended the analysis to include genotype 3a (predominant in South Asia including Pakistan), and compared the results of the three genotypes (1b, 3a and 4a). The 4D analyses of the interactions between the catalytic triad residues (His57, Asp81, and Ser139) indicate conformational instability of the catalytic site in HCV-3a and 4a compared to that of HCV-1b NS3 protease. The divergence is gradual and genotype-dependent, with HCV-1b being the most stable, HCV-4a being the most unstable and HCV-3a representing an intermediate state. These results suggest that the structural dynamics behavior, more than the rigid structure, could be related to the altered catalytic activity and drug susceptibility seen in NS3 proteases of HCV-3a and 4a.     

Identification of Staphylococcus aureus and Escherichia coli isolated from Egyptian food by conventional and molecular methods

Staphylococcus aureus and Escherichia coli were enumerated and isolated from ready-to-eat vegetables salad and meat luncheon on their selective media (Baird-parker and Macconkey agar, respectively). Twenty suspicious colonies of each (10 from each product) were randomly chosen and identified using conventional based on morphological and physiological characteristics. S. aureus and E. coli isolates which gave the highest pathogenicity were chosen for identification and confirmation with molecular method based on 16S rRNA gene. The PCR amplification method of 16S rRNA gave the same identification results as conventional method, but it was sensitive and fast. This molecular method takes about 48 h in comparison with 6 days for conventional method. The 16S rRNA of S. aureus and E. coli were deposited in the Genebank database under accessions (AB599719.1 and AB599716.1, respectively).     

Dietary Patterns Differently Associate with Inflammation and Gut Microbiota in Overweight and Obese Subjects

Background

Associations between dietary patterns, metabolic and inflammatory markers and gut microbiota are yet to be elucidated.

Objectives

We aimed to characterize dietary patterns in overweight and obese subjects and evaluate the different dietary patterns in relation to metabolic and inflammatory variables as well as gut microbiota.

Design

Dietary patterns, plasma and adipose tissue markers, and gut microbiota were evaluated in a group of 45 overweight and obese subjects (6 men and 39 women). A group of 14 lean subjects were also evaluated as a reference group.

Results

Three clusters of dietary patterns were identified in overweight/obese subjects. Cluster 1 had the least healthy eating behavior (highest consumption of potatoes, confectionary and sugary drinks, and the lowest consumption of fruits that was associated also with low consumption of yogurt, and water). This dietary pattern was associated with the highest LDL cholesterol, plasma soluble CD14 (p = 0.01) a marker of systemic inflammation but the lowest accumulation of CD163+ macrophages with anti-inflammatory profile in adipose tissue (p = 0.05). Cluster 3 had the healthiest eating behavior (lower consumption of confectionary and sugary drinks, and highest consumption of fruits but also yogurts and soups). Subjects in this Cluster had the lowest inflammatory markers (sCD14) and the highest anti-inflammatory adipose tissue CD163+ macrophages. Dietary intakes, insulin sensitivity and some inflammatory markers (plasma IL6) in Cluster 3 were close to those of lean subjects. Cluster 2 was in-between clusters 1 and 3 in terms of healthfulness. The 7 gut microbiota groups measured by qPCR were similar across the clusters. However, the healthiest dietary cluster had the highest microbial gene richness, as evaluated by quantitative metagenomics.

Conclusion

A healthier dietary pattern was associated with lower inflammatory markers as well as greater gut microbiota richness in overweight and obese subjects.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01314690","term_id":"NCT01314690"}}NCT01314690     

Lipase-catalyzed biosynthesis of cinnamoylated lipids in a selected organic solvent medium

Biosynthesis of cinnamoylated lipids through the lipase-catalyzed transesterification reaction of cinnamic acid with triolein was investigated in organic solvent media. Electrospray ionization-mass spectroscopy (ESI-MS) structural analysis of the reaction mixture revealed the formation of two major end products, monoleyl-1(3)-cinnamate and dioleyl-2-cinnamate. Decreasing the molar ratio of cinnamic acid to triolein from 1:1 to 1:4.5 resulted in an increase in the maximum bioconversion yield of cinnamoylated lipids from 19 to 42%, which remained constant at a lower ratio of 1:6. However, an excess of triolein appeared to have a more beneficial effect on the formation of dioleyl-2-cinnamate than monoleyl-1(3)-cinnamate, leading to different end product compositions at ratios of substrates. With cinnamic acid to triolein ratios of 1:4.5 and 1:6.0, an increase in the bioconversion yield of cinnamoylated lipids to 55% was achieved by adding 2.2 mgmL(-1) silica gel to the reaction mixture. Radical scavenging activity of cinnamoylated lipids, with 50% of radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging, was found to be higher than that of its corresponding phenolic acid.     

PCR amplification of four genes coding for aminoglycoside-modifying enzymes in bacteria of clinical isolates from Jordan University Hospital

Three species of Gram-negative G(–) bacteria were chosen for this study: Escherichia spp. (29 isolates), Pseudomonas spp. (16 isolates) andEnterobacter spp. (17 isolates), utilizing colony PCR to detect genes coding for aminoglycoside-modifying enzymes. The 62 isolates were purified and cultured on nutrient broth media supplemented with 50 g kanamycin/ml. Only 17 out of the 62 isolates were resistant to kanamycin and were subjected to colony PCR protocol using 20 l cell lysate and eight sets of primers with each isolate. Sizing of the amplified fragments was carried out in order to determine the specificity of PCR. The 17 isolates were shown to carry the rrs, aacC2, aacA-aphD and aphA3 genes.     

Isoflavonoids and flavone glycosides from rhizomes of Iris carthaliniae

Two new isoflavonoid biosides, tectorigenin 4′-glucosyl (1→6)glucoside and iristectorigenin B 7-glucosyl (1→6)glucoside, a new isoflavonoid monoside, 4′-methyltectorigenin 7-glucoside and a new flavone glucoside, 6,4′-dimethoxy-5-hydroxyflavone 7-glucoside, together with tectoridin and tectorigenin 4′-glucoside were isolated from rhizomes of Iris carthaliniae. The structures of the isolated compounds were determined by NMR spectral analysis.     

Biophysical,Rheological, and Functional Properties of Complex of Sodium Caseinate and Olive Leaf Aqueous Polyphenolic Extract Obtained Using Ultrasound-Assisted Extraction

Food Biophysics - This study demonstrated the use of ultrasound-assisted extraction to render aqueous extract polyphenolic compounds from olive leaves. Sodium caseinate-olive leaf extract complexes...     

The Development of a Strategic Prioritisation Method for Green Supply Chain Initiatives

To maintain a competitive position, companies are increasingly required to integrate their proactive environmental strategies into their business strategies. The shift from reactive and compliance-based to proactive and strategic environmental management has driven companies to consider the strategic factors while identifying the areas in which they should focus their green initiatives. In previous studies little attention was given to providing the managers with a basis from which they could strategically prioritise these green initiatives across their companies’ supply chains. Considering this lacuna in the literature, we present a decision-making method for prioritising green supply chain initiatives aligned with the preferred green strategies alternatives for the manufacturing companies. To develop this method, the study considered a position between determinism and the voluntarism orientation of environmental management involving both external pressures and internal competitive drivers and key resources as decision factors. This decision-making method was developed using the analytic network process (ANP) technique. The elements of the decision model were derived from the literature. The causal relationships among the multiple decision variables were validated based on the results of structural equation modelling (SEM) using a dataset collected from a survey of the ISO 14001-certified manufacturers in Malaysia. A portion of the relative weights required for computation in ANP was also calculated using the SEM results. A case study is presented to demonstrate the applicability of the method.     

Lipase-catalyzed transesterification of dihydrocaffeic acid with flaxseed oil for the synthesis of phenolic lipids

Lipase-catalyzed transesterification reaction of dihydrocaffeic acid (DHCA) with flaxseed oil in organic solvent media was investigated. Using equal molar concentration of DHCA and flaxseed oil, only phenolic monoacylglycerols were obtained with a transesterification yield (TY) of 18.9%. A 1:4 DHCA to flaxseed oil ratio resulted in the production of both phenolic mono and diacylglycerols, with TY of 39.6 and 27.8%, respectively. On the other hand, when 1:8 ratio of DHCA to flaxseed oil was used, the TY of phenolic diacylglycerols (46.0%) was higher than that of the phenolic monoacylglycerols (33.3%). The TY of phenolic diacylglycerols increased from 25.1 to 55.8%, when the ratio of the hexane/2-butanone reaction medium was changed from 65:35 to 85:25 (v/v); however, the TY of phenolic monoacylglycerols decreased slightly from 34.0 to 31.8%. The relative proportion of the C(18:3)n-3 was higher in the phenolic mono and diacylglycerols, 64.9 and 59.5%, respectively, as compared to the original flaxseed oil, 53.1%. The radical scavenging ability of phenolic lipids was significant; however, it was about half than that of alpha-tocopherol.     

Enzymatic generation of peptides from potato proteins by selected proteases and characterization of their structural properties

The use of low grade starting material for the generation of peptides with bioactivity properties is of interest. The proteins from the potato starch industry byproduct is a promising source, as several health benefits may be associated with their hydrolysates. The efficiency of selected proteases (Novo Pro‐D, Alcalase, Flavourzyme, and Papain), exhibiting different substrate specificities and cleavage action modes, to hydrolyze potato protein isolate (patatin and protease inhibitors) was investigated. Novo Pro‐D resulted in the lowest degree of hydrolysis, whereas Alcalase, Flavourzyme, and Papain exhibited a high catalytic efficiency for the hydrolysis of potato proteins. The degree of hydrolysis behaved in a concentration dependent manner. However, the end‐product profile (peptides and free amino acids) was dependent not only on the protease specificity, its cleavage action mode (endo/exo) and the availability of the intermediate substrates but also on the contribution of the protease inhibitors to the reaction kinetics through their inhibitory effects. Indeed, the dependence of the exo‐activity on the catalytic efficiency of the endo‐action of protease was shown to be significant. Papain generated more unique peptide sequences with homology assessment matching several potato proteins when compared with Flavourzyme. This can be attributed to the high exo‐peptidase activity of Flavourzyme resulting in the generation of shorter peptides which were difficult to match. Flavourzyme produced more peptides originated from patatin fraction, whereas Papain resulted in the release of more peptides corresponding to the protease inhibitor fractions. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:420–429, 2016