RNA structure and function signals in a novel Nidovirus sequence from the Sea Hare Aplaysia californica

Nidoviruses are enveloped, positive stranded RNA viruses that are among the most complex plus-strand RNA viruses known. My work has discovered the sequence of a new, highly divergent virus, tentatively named Abyssovirus, in a pool of sequenced intracellular RNA from a metazoan. Based on comparison of the genomic organization and replicase subunits, Abyssovirus appears to belong to a new family of nidoviruses. The aim of the present project was to validate the sequence data by studying the function of the predicted unusual translational stop-start signal located in the replicase gene, and to express predicted viral proteases and test their catalytic activity in Sf9 insect cells, E. coli and mammalian expression systems. The translational stop-start signal was found to allow ribosomes to readthrough the natural stop codon in the expression systems tested. Additionally, Abyssovirus Main Protease (MPro) showed evidence of cleavage of fragments from both ends of the expressed protease, as is typical for polyprotein-embedded Nidovirus proteases. These results suggest that the Abyssovirus RNA sequence encodes biologically functional proteins, and therefore that the RNA sequence likely does represent an extant virus with some Nidovirus-like features and an Abyssovirus-specific mechanism to translate the second half of the replicase open reading frame

Pattern Recognition of Phytoconstituents and Bioactivities of Date Pit Extracts from Different Cultivars Grown in the Qassim Area

A huge number of date varieties grow annually throughout the world. The genetic variation between different date varieties is reflected in their variable sensory characters and phytochemical contents. Date pits are considered a waste product of the date industry, despite their rich metabolic content. The present study attempts to generate visual clustering to clarify the diversity among fourteen date cultivars growing in the Qassim region, according to the phytochemical contents and biological potentials of their pits. The results indicated a wide variation in the total phenolic content (11.4–29.7 mg GAE/g), flavonoids content (21.9–37.1 mg RE/g), proanthocyanidine content (12.0–207.0 mg CE/g), and antioxidant potential (10.3–25.5 mg AEAC/g) among the tested cultivars. Screening the antimicrobial activity of extracts from the 14 tested cultivars indicated different activities against Listeria monocytogenes, Staphylococcus aureus, Escherichia coli, Salmonella enterica, and Candida albicans. Multivariate analysis of phytochemical content and biological activity, using different analytical models, allowed the classification of the 14 cultivars into four classes, Class-1: Barhi, Safawi, and Sukkari; Class-2: Khodry and Nabtat Ali; Class-3: Ruthana, Segae, Shaqra, and Sheishee; and Class-4: Hulwa Aljouf, Mabroom, Meneifi, Rushodia, and Wannana. These findings provide a scientific basis for the classification of date pits which facilitates the future selection of promising candidates for more phytochemical and biological exploration

Proposed Mechanism for Emodin as Agent for Methicillin Resistant Staphylococcus Aureus: In Vitro Testing and In Silico Study

In the search for a new anti-MRSA lead compound, emodin was identified as a good lead against methicillin-resistant Staphylococcus aureus (MRSA). Emodin serves as a new scaffold to design novel and effective anti-MRSA agents. Because rational drug discovery is limited by the knowledge of the drug target, α-hemolysin of Staphylococcus aureus was used in this study because it has an essential role in Staphylococcus infections and because emodin shares structural features with compounds that target this enzyme. In order to explore emodin’s interactions with α-hemolysin, all possible ligand binding pockets were identified and investigated. Two ligand pockets were detected based on bound ligands and other reports. The third pocket was identified as a cryptic site after molecular dynamics (MD) simulations. MD simulations were conducted for emodin in each pocket to identify the most plausible ligand site and to aid in the design of potent anti-MRSA agents. Binding of emodin to site 1 was most stable (RMSD changes within 1 Å), while in site 2, the binding pose of emodin fluctuated, and it left after 20 ns. In site 3, it was stable during the first 50 ns, and then it started to move out of the binding site. Site 1 is a possible ligand binding pocket, and this study sheds more light on interaction types, binding mode, and key amino acids involved in ligand binding essential for better lead design. Emodin showed an IC50 value of 6.3 μg/mL, while 1, 6, and 8 triacetyl emodin showed no activity against MRSA. A molecular modeling study was pursued to better understand effective binding requirements for a lead

Bioinformatics and immunoinformatics assisted multiepitope vaccine construct against Burkholderia anthina

Burkholderia anthina is a pathogenic bacterial species belonging to the Burkholderiaceae family and it is mainly considered the etiological agent of chronic obstructive pulmonary diseases associated with cystic fibrosis, due to being intrinsic antibiotic resistant making it difficult to treat pulmonary infections. Hence increased rate of antibiotic-resistant bacterial species vaccine development is the priority to tackle this problem. In research work, we designed a multi-epitope-based vaccine construct against B. anthina using reverse vaccinology immunoinformatics and biophysical approaches. Based on the subtractive proteomic screening of core proteins we identified 3 probable antigenic proteins and good vaccine targets namely, type VI secretion system tube protein hcp Burkholderia, fimbria/pilus periplasmic chaperone and fimbrial biogenesis outer membrane usher protein. The selected 3 proteins were used for B and B cells B-derived T-cell epitopes prediction. In epitopes prediction, different epitopes were predicted with various lengths and percentile scores and subjected to further immunoinformatics analysis. In immunoinformatics screening a total number of 06, IDDGNANAL, KTVKPDPRY, SEVESGSAP, YGGDLTVEV, SVSHDTNGR, and GSKADGYQR epitopes were considered good vaccine target candidates and shortlisted for vaccine construct designing. The vaccine construct was designed by joining selected epitopes with the help of a GPGPG linker and additionally linked with cholera toxin b subunit adjuvant to increase the efficacy of the vaccine construct the sequence of the said adjuvant were retrieved from protein data bank through its (PDB ID: 5ELD). The designed vaccine construct was evaluated for its physiochemical properties analysis in which we reported that the vaccine construct comprises 216 amino acids with a molecular weight of 22.37499 kilo Dalton, 15.55 instability index (II) is computed, and this classifies that the vaccine construct is properly stable. VaxiJen v2.0 web server predicted that the vaccine construct is probable antigenic in nature with 0.6320 predicted value. Furthermore AllerTOP v. 2.0 tool predicted that the designed vaccine construct is non allergic in nature. Molecular docking analysis was done for analysis of the binding affinity of the vaccine construct with TLR-2 (PDB ID: 6NIG), the docking results predicted 799.2 kcal/mol binding energy score that represents the vaccine construct has a good binding ability with TLR-2. Moreover, molecular dynamic simulation analysis results revealed that the vaccine construct and immune cell receptor has proper binding stability over various environmental condition, i.e. change in pressure range, temperature, and motion. After each analysis, we observed that the vaccine construct is safe stable, and probably antigenic and could generate an immune response against the target pathogen but in the future, experimental analysis is still needed to verify in silico base results