Beer from the early dynasties (3500–3400 cal B.C.) of Upper Egypt,detected by archaeochemical methods

Physical and chemical analyses of beer residues recovered from a vat site at Hierakonpolis (Upper Egypt) were carried out. Radiocarbon dates of the residues suggest a dating of 3500–3400 cal B.C. and are believed to represent the oldest known beer in the world. Macroscopic and microscopic examinations of the residues revealed the presence of intact remains of grains and spikelets of wheat and barley, as well as fragments of dates and grape pips. Chemical analyses included percentages of sample ingredients, pH and total soluble ions, quantitative determinations of sugars, carboxylic acids and free amino acids. A total of 25 compounds were identified, which are components of fermentation processes that are believed to have formed in connection with the preparation of what is called Nekhen-Hoffman beer.     

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.     

Recent insights into cotton functional genomics: progress and future perspectives

Functional genomics has transformed from futuristic concept to well‐established scientific discipline during the last decade. Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for the improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task, which has not progressed at a rapid pace. This article presents a comprehensive overview of the recent tools and resources available with the major advances in cotton functional genomics to develop elite cotton genotypes. This effort ultimately helps to filter a subset of genes that can be used to assemble a final list of candidate genes that could be employed in future novel cotton breeding programme. We argue that next stage of cotton functional genomics requires the draft genomes refinement, re‐sequencing broad diversity panels with the development of high‐throughput functional genomics tools and integrating multidisciplinary approaches in upcoming cotton improvement programmes.     

Diversity and spatial genetic structure of natural Moroccan <Emphasis Type="Italic">Quercus susber</Emphasis> L. assessed by ISSR markers for conservation

Morocco is one of the most important regions of the world in terms of Quercus suber L. number and variation. This species is in decline due to several factors, which can lead to permanent loss of this resource. It would be essential to evaluate the genetic diversity in order to conserve maximum genetic variability of this species. The genetic diversity and differentiation of 16 sites from five regions representing the entire range of Moroccan Cork Oak were assessed. Twenty-three ISSR primers used generated 985 polymorphic fragments with an average of 42.8 bands per primer and showed 100% of polymorphism. The 173 individuals revealed a moderate level of genetic diversity at species level (I?=?0.27, He?=?0.161). The AMOVA showed that the highest level of diversity occurred within populations (64%), this was also confirmed by the coefficient of differentiation (Gst?=?0.47). The estimated gene flow (Nm?=?0.56) and the Mantel test revealed a significant correlation between geographic and genetic diversity (r?=?0.266; p?=?0.001). This genetic structure was further shown by the topology of the UPGMA, sPCA and STRUCTURE analysis. In addition, a core collection of 34 genotypes was established representing the essential diversity detected. This research advocates populations and individuals to preserve in order to improve and conserve this resource in the future.     

New analogues of laminin active fragment YIGSR: synthesis and biological activity in vitro and in vivo.

Eleven analogues of the laminin pentapeptide amide fragment Tyr-Ile-Gly-Ser-Arg-NH2 (YIGSR-NH2) corresponding to a B1 chain fragment of the glycoprotein laminin have been synthesized by the solid phase method, and their biological activity has been studied in vitro by a cell adhesion assay: all of them inhibited the adhesion of LLC tumor cells to laminin. The analogues were found to be more resistant to enzymatic degradation in human serum than YIGSR-NH2 itself. Analogue DatIGSHar-NH2 was selected for an experimental pulmonary metastasis assay in vivo: it had higher antimetastatic activity than YIGSR-NH2.     

Role of DNA barcoding in marine biodiversity assessment and conservation: An update

More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.     

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     

Detection and enumeration of Listeria monocytogenes in a sewage treatment plant in Iraq

Listeria monocytogenes was isolated from a sewage treatment plant in Baghdad, Iraq, at all stages of treatment. The treatment processes did not yield a sewage sludge cake or a final discharge free of listerias. The agricultural practice of using such sewage products as fertilizers could become a route of spreading the organism in Iraq, particularly by infecting animals that consume vegetation in fields spread with such sewage. Dewatering of sewage reduced the number of L. monocytogenes but long periods of exposure to sun would be needed to obtain a 'safe' sewage sludge cake.