Development of an Optimized Process for Functional Recombinant SARS-CoV-2 Spike S1 Receptor-Binding Domain Protein Produced in the Baculovirus Expression Vector System

To map the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and evaluate immune response variations against this virus, it is essential to set up efficient serological tests locally. The SARS-CoV-2 immunogenic proteins were very expensive and not affordable for lower- middle-income countries (LMICs). For this purpose, the commonly used antigen, receptor-binding domain (RBD) of spike S1 protein (S1RBD), was produced using the baculovirus expression vector system (BEVS). In the current study, the expression of S1RBD was monitored using Western blot under different culture conditions. Different parameters were studied: the multiplicity of infection (MOI), cell density at infection, and harvest time. Hence, optimal conditions for efficient S1RBD production were identified: MOI 3; cell density at infection 2-3 × 106 cells/mL; and time post-infection (tPI or harvest time) of 72 h and 72-96 h, successively, for expression in shake flasks and a 7L bioreactor. A high production yield of S1RBD varying between 4 mg and 70 mg per liter of crude cell culture supernatant was achieved, respectively, in the shake flasks and 7L bioreactor. Moreover, the produced S1RBD showed an excellent antigenicity potential against COVID-19 (Wuhan strain) patient sera evaluated by Western blot. Thus, additional serological assays, such as in-house ELISA and seroprevalence studies based on the purified S1RDB, were developed.

Seasonal variation in the diet and the morphometric parameters of the genus Pseudo-phoxinus sp. (Cyprinidae) in Eastern Algeria

The diet and the morphometric parameters of the Pseudophoxinus sp. (Cyprinidae) in the El Mellah ravine (M’sila, Algeria) were studied by determining body measurements and analyzing the contents of digestive tracts of 320 fish from December 2018 to November 2019. The obtained results show marked diversity within the fish species diets, which can be grouped into three main fractions: (i) a plant fraction; (ii) an animal fraction composed mainly of invertebrate prey; and (iii) fraction consisting of fish eggs (digested by males during the breeding season). The plant fraction was present in all the analyzed digestive tracts, mainly being composed of phytoplankton (algae), namely, Spirogyra sp., Melosira sp. and Navicula sp. with the total relative abundances of 38.7%, 34.4% and 4.1%, respectively. On the other hand, the animal fraction was represented by the Chironomus sp., Austrosimulium sp., and Ecdyonurus sp. dipterans with a total relative abundance of 7.3%, 6.7% and 5.9%, respectively. Pseudophoxinus sp. eggs can also be considered as part of this fraction with the total relative abundance of 2.9%. The age of the fish seems to have an influence on their feeding behaviour. The juveniles of Pseudophoxinus sp. in the study area had a purely phytophagous diet, while adults showed a phytophagous behaviour with an omnivorous tendency. The present study shows that not only the age of the fish but also the seasonal changes (climatic conditions and entry into the breeding season) may have a significant influence on the diet and morphometric parameters of Pseudophoxinus sp. in El Mellah ravine.

Seasonal variation in the diet and the morphometric parameters of the genus Pseudo-phoxinus sp. (Cyprinidae) in Eastern Algeria

The diet and the morphometric parameters of the Pseudophoxinus sp. (Cyprinidae) in the El Mellah ravine (M’sila, Algeria) were studied by determining body measurements and analyzing the contents of digestive tracts of 320 fish from December 2018 to November 2019. The obtained results show marked diversity within the fish species diets, which can be grouped into three main fractions: (i) a plant fraction; (ii) an animal fraction composed mainly of invertebrate prey; and (iii) fraction consisting of fish eggs (digested by males during the breeding season). The plant fraction was present in all the analyzed digestive tracts, mainly being composed of phytoplankton (algae), namely, Spirogyra sp., Melosira sp. and Navicula sp. with the total relative abundances of 38.7%, 34.4% and 4.1%, respectively. On the other hand, the animal fraction was represented by the Chironomus sp., Austrosimulium sp., and Ecdyonurus sp. dipterans with a total relative abundance of 7.3%, 6.7% and 5.9%, respectively. Pseudophoxinus sp. eggs can also be considered as part of this fraction with the total relative abundance of 2.9%. The age of the fish seems to have an influence on their feeding behaviour. The juveniles of Pseudophoxinus sp. in the study area had a purely phytophagous diet, while adults showed a phytophagous behaviour with an omnivorous tendency. The present study shows that not only the age of the fish but also the seasonal changes (climatic conditions and entry into the breeding season) may have a significant influence on the diet and morphometric parameters of Pseudophoxinus sp. in El Mellah ravine.

Comparison of the metabolism of 10 chemicals in human and pig skin explants

Skin metabolism is important to consider when assessing local toxicity and/or penetration of chemicals and their metabolites. If human skin supply is limited, pig skin can be used as an alternative. To identify any species differences, we have investigated the metabolism of 10 chemicals in a pig and human skin explant model. Phase I metabolic pathways in skin from both species included those known to occur via cytochrome P450s, esterases, alcohol dehydrogenases and aldehyde dehydrogenases. Common Phase II pathways were glucuronidation and sulfation but other conjugation pathways were also identified. Chemicals not metabolized by pig skin (caffeine, IQ and 4‐chloroaniline) were also not metabolized by human skin. Six chemicals metabolized by pig skin were metabolized to a similar extent (percentage parent remaining) by human skin. Human skin metabolites were also detected in pig skin incubations, except for one unidentified minor vanillin metabolite. Three cinnamyl alcohol metabolites were unique to pig skin but represented minor metabolites. There were notable species differences in the relative amounts of common metabolites. The difference in the abundance of the sulfate conjugates of resorcinol and 4‐amino‐3‐nitrophenol was in accordance with the known lack of aryl sulfotransferase activity in pigs. In conclusion, while qualitative comparisons of metabolic profiles were consistent between pig and human skin, there were some quantitative differences in the percentage of metabolites formed. This preliminary assessment suggests that pig skin is metabolically competent and could be a useful tool for evaluating potential first‐pass metabolism before testing in human‐derived tissues.

We have investigated the metabolism of 10 chemicals in viable pig and human skin. Phase I and II metabolic pathways were present in skin from both species. Chemicals not metabolized by pig skin were also not metabolized by human skin. Six chemicals metabolized by pig skin were also metabolized to a similar extent by human skin. Pig and human skin produced common metabolites, although some species differences were observed and as their relative amounts differed.

Immunohistochemical Characterization Improves the Reproducibility of the Histological Diagnosis of Ovarian Carcinoma

Background: Ovarian cancer is the leading cause of gynecologic cancer-related death. Histological assessment remains the standard clue for the diagnosis of ovarian carcinoma. Misinterpretation and inconsistent application of histological criteria may lead to significant interobserver variability and poor reproducibility of the diagnosis. In this study, we investigated the discrepancy in histological diagnosis and the significance of a designed panel of immunohistochemical markers for the improvement of the diagnostic reproducibility of ovarian carcinomas. Methods: We performed a retrospective study on 74 ovarian carcinomas. All tumor slides were independently reviewed by two pathologists. The results for seven available immunomarkers as p53, WT-1, p16INK4A, CK7, CK20, and estrogen and progesterone receptors were determined for all cases by immunohistochemistry. Results: The histological diagnosis review performed using standard histology showed a concordance of diagnoses in 86% of cases with Cohen’s kappa of 0.80. Immunohistochemical results increased significantly the diagnosis reproducibility with a concordance of 91% and a Cohen’s kappa of 0.86 (P = 0.001). Conclusion: Although the histological diagnosis remains reliable, the use of a designed panel of immunohistochemical markers improves significantly the interobserver concordance and the classification accuracy of ovarian carcinomas.

Measuring the environmental sustainability performance of global supply chains: A multi-regional input-output analysis for carbon, sulphur oxide and water footprints

Measuring the performance of environmentally sustainable supply chains instead of chain constitute has become a challenge despite the convergence of the underlining principles of sustainable supply chain management. This challenge is exacerbated by the fact that supply chains are inherently dynamic and complex and also because multiple measures can be used to characterize performances. By identifying some of the critical issues in the literature regarding performance measurements, this paper contributes to the existing body of literature by adopting an environmental performance measurement approach for economic sectors. It uses economic sectors and evaluates them on a sectoral level in specific countries as well as part of the Global Value Chain based on the established multi-regional input-output (MRIO) modeling framework. The MRIO model has been used to calculate direct and indirect (that is supply chain or upstream) environmental effects such as CO₂, SO₂, biodiversity, water consumption and pollution to name just a few of the applications. In this paper we use MRIO analysis to calculate emissions and resource consumption intensities and footprints, direct and indirect impacts, and net emission flows between countries. These are exemplified by using carbon emissions, sulphur oxide emissions and water use in two highly polluting industries; Electricity production and Chemical industry in 33 countries, including the EU-27, Brazil, India and China, the USA, Canada and Japan from 1995 to 2009. Some of the highlights include: On average, direct carbon emissions in the electricity sector across all 27 member states of the EU was estimated to be 1368 million tons and indirect carbon emissions to be 470.7 million tons per year representing 25.6% of the EU-27 total carbon emissions related to this sector. It was also observed that from 2004, sulphur oxide emissions intensities in electricity production in India and China have remained relatively constant at about 62.8 gSO_x/, respectively, $ and 84.4 gSO_x/$ although being higher than in other countries. In terms of water use, the high water use intensity in China (1040.27 L/$) and India (961.63 L/$), which are among the highest in the sector in the electricity sector is exacerbated by both countries being ranked as High Water Stress Risk countries. The paper also highlights many advantages of the MRIO approach including: a 15-year time series study (which provides a measurement of environmental performance of key industries and an opportunity to assess technical and technological change during the investigated time period), a supply chain approach that provides a consistent methodological framework and accounts for all upstream supply chain environmental impacts throughout entire global supply chains. The paper also discusses the implications of the study to environmental sustainability performance measurement in terms of the level of analysis from a value chain hierarchy perspective, methodological issues, performance indicators, environmental exchanges and policy relevance.

Strategies for increasing the efficiency of a genetic algorithm for the structural optimization of nanoalloy clusters

An improved genetic algorithm (GA) is described that has been developed to increase the efficiency of finding the global minimum energy isomers for nanoalloy clusters. The GA is optimized for the example Pt12Pd12, with specific investigation of: the effect of biasing the initial population by seeding; the effect of removing specified clusters from the population ("predation"); and the effect of varying the type of mutation operator applied. These changes are found to significantly enhance the efficiency of the GA, which is subsequently demonstrated by the application of the best strategy to a new cluster, namely Pt19Pd19.

Adaptive hybrid learning for neural networks

A robust locally adaptive learning algorithm is developed via two enhancements of the Resilient Propagation (RPROP) method. Remaining drawbacks of the gradient-based approach are addressed by hybridization with gradient-independent Local Search. Finally, a global optimization method based on recursion of the hybrid is constructed, making use of tabu neighborhoods to accelerate the search for minima through diversification. Enhanced RPROP is shown to be faster and more accurate than the standard RPROP in solving classification tasks based on natural data sets taken from the UCI repository of machine learning databases. Furthermore, the use of Local Search is shown to improve Enhanced RPROP by solving the same classification tasks as part of the global optimization method.

The investigation of a class of capacitated arc routing problems: the collection of garbage in developing countries

The collection, transport and disposal of solid waste, which is a highly visible and important municipal service, involves a large expenditure but receives, scant attention. This problem is even more crucial for large cities in developing countries due to the hot weather. A constructive heuristic which takes into account the environmental aspect as well as the cost is proposed to solve the routing aspect of garbage collection. This is based on a look-ahead strategy which is enhanced by two additional mechanisms. Interesting results were obtained when tested on instances with and without the presence of the effect of the environment.

Viral haemorrhagic septicaemia virus induces vig-2, a new interferon-responsive gene in rainbow trout

An mRNA differential display methodology was used to study the rainbow trout response to viral infection. A new transcript (vig-2) induced by viral haemorrhagic septicaemia virus (VHSV) in rainbow trout leucocytes was identified from the head-kidney. vig-2 was also induced in vivo during experimental infection and following DNA immunisation with a plasmid containing a gene encoding the viral glycoprotein. Viral induction of vig-2 was blocked by cycloheximide (CHX), indicating its dependency on a newly synthesised intermediate protein. This intermediate protein is most probably related to interferon because treatment of cells with a conditioned medium displaying an interferon-like activity resulted in a strong vig-2 expression, which was not blocked by CHX treatment. The cDNA sequence of the vig-2 transcript displays several mRNA destabilisation motifs and two signals characteristic of immediate-early gene expression. Curiously, vig-2 has no evident encoding potential except for a small 51 amino acid putative polypeptide with no clear similarity to any sequence available in the databanks. Therefore, the complete vig-2 genomic sequence was determined from a lambda phage clone retrieved from a genomic DNA library of rainbow trout. The genomic organisation of vig-2 shows five exons delimited with typical splice acceptor and donor sites. A promoter with a canonical ISRE, confirming that vig-2 is an interferon-responsive gene, is also present 115 nt upstream of the first exon.

Identification of a cellular protein specifically interacting with the precursor of the hepatitis B e antigen

In hepatitis B virus (HBV) the precore gene encodes a protein from which derives P22, the precursor of the mature secreted hepatitis B virus e antigen (HBeAg). Circumstantial evidences suggest that HBeAg and/or its precursor P22 are important for establishing persistent infection. Although P22 is essentially present in the secretory pathway, a substantial fraction has been found in the cytosol. In order to get new insights into the biological function of P22, we looked for cellular proteins which could strongly associate with this protein. Using immunoprecipitation studies on human cell extracts, we found that a non-secreted cellular protein of about 32 kDa (P32) bound with a high specificity to P22. P32 associated neither with HBeAg nor with the viral core protein P21 which exhibits the same amino acids sequence as P22 but is N-terminally shorter by 10 residues. We also demonstrated that this interaction depended on the presence of the P22 C-terminal domain. Our data argues for a potential biological function of P22.

The DNA polymerase from the archaebacterium Sulfolobus acidocaldarius: a thermophilic and thermoresistant enzyme which can perform automated polymerase chain reaction

A DNA polymerase purified from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius was used to perform automated DNA amplification at 70 degrees C as well as site directed mutagenesis by Polymerase Chain Reaction (P.C.R.). The yield of amplification performed at optimum MgCl2 concentration for the Taq or the S. acidocaldarius DNA polymerase, for the same DNA target, was equivalent. The ability of S. acidocaldarius DNA polymerase to perform P.C.R. under less stringent requirement of MgCl2 concentration gives this enzyme a non-negligible advantage over the Taq DNA polymerase.

Biosynthesis of hepatitis B virus e antigen: directed mutagenesis of the putative aspartyl protease site

The C gene products of all mammalian hepadnaviruses contain a region with sequence similarities to the catalytic center of the aspartyl proteases. This region could have the capacity to cleave precore proteins, leading to the synthesis of e antigen. By site-directed mutagenesis on a plasmid containing the hepatitis B virus C gene, we have replaced either the Asp residue of the putative aspartyl protease catalytic center or an Asp residue located 3 amino acids upstream. Transient expression of the mutated hepatitis B virus C gene in human and mouse cells showed that none of these mutations prevented the secretion of an accurately processed HBe antigen. Thus, we demonstrated that the aspartyl protease responsible for e antigen precursor processing is not C gene encoded but is more likely to be a cellular enzyme. From these results, we suggest a model for the mechanism of e antigen synthesis.

DNA polymerase from Sulfolobus acidocaldarius. Replication at high temperature of long stretches of single-stranded DNA

The activity of a homogeneous DNA polymerase from the thermophilic archaebacterium, Sulfolobus acidocaldarius, on a singly primed, single-stranded recombinant phage M13 DNA has been examined. At the optimal temperature (70 to 75 degrees C) this template is efficiently replicated in ten minutes using a ratio of enzyme molecule to primed-template of 0.8. Analysis of DNA products during the course of polymerization shows that species of quite homogeneous size are observed and that the number of primers extended by the enzyme is constant, whatever the enzyme molecule to primed template ratio is in the range 1/50 to 2, indicating that the 100 x 10(3) Mr DNA polymerase from S. acidocaldarius is randomly recycled on the template molecules. At non-optimal temperature (60 degrees C and 80 degrees C) the distribution of products observed indicated the presence of arrest sequences; some have been shown to be reversible. One of these pausing signals detected at 80 degrees C has been further analysed, and has been found to be DNA sequence-dependent.

A DNA polymerase from a thermoacidophilic archaebacterium: evolutionary and technological interests

The archaebacteria constitute a group of prokaryotes with an intermediate phylogenetic position between eukaryotes and eubacteria. The study of their DNA polymerases may provide valuable information about putative evolutionary relationships between prokaryotic and eukaryotic DNA polymerases. As a first step towards this goal, we have purified to near homogeneity a DNA polymerase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. This enzyme is a monomeric protein of 100 kDa which can catalyze DNA synthesis using either activated calf thymus DNA or oligonucleotide-primed single-stranded DNA as a template. The activity is optimal at 70 degrees C and the enzyme is thermostable up to 80 degrees C; however, it can still polymerize up to 200 nucleotides at 100 degrees C. These remarkable thermophilic properties and thermostability permit examination of the mechanism of DNA synthesis under conditions of decreased stability of the DNA helix. Furthermore, these properties make S. acidocaldarius DNA polymerase a very efficient enzyme to be used in DNA amplification by the recently developed polymerase chain reaction method (PCR) as well as in the Sanger DNA sequencing technique.