Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus.

BACKGROUND: The hepatitis C virus (HCV) has six major genotypes. The purpose of this study was to phylogenetically investigate the differences between the genotypes of HCV, and to determine the types of amino acid codon usage in the structure of the virus in order to discover new methods for treatment regimes. METHODS: The codon usage of the six genotypes of the HCV nucleotide sequence was investigated through the online application available on the website Gene Infinity. Also, phylogenetic analysis and the evolutionary relationship of HCV genotypes were analyzed with MEGA 7 software. RESULTS: The six genotypes of HCV were divided into two groups based on their codon usage properties. In the first group, genotypes 1 and 5 (74.02%), and in the second group, genotypes 2 and 6 (72.43%) were shown to have the most similarity in terms of codon usage. Unlike the results with respect to determining the similarity of codon usage, the phylogenetic analysis showed the closest resemblance and correlation between genotypes 1 and 4. The results also showed that HCV has a GC (guanine-cytosine) abundant genome structure and prefers codons with GC for translation. CONCLUSIONS: Genotypes 1 and 4 demonstrated remarkable similarity in terms of genome sequences and proteins, but surprisingly, in terms of the preferred codons for gene expression, they showed the greatest difference. More studies are therefore needed to confirm the results and select the best approach for treatment of these genotypes based on their codon usage properties.

Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus.

BACKGROUND: Hepatitis B virus (HBV) as an infectious disease that has nine genotypes (A - I) and a 'putative' genotype J. OBJECTIVES: The aim of this study was to identify the rare codon clusters (RCC) in the HBV genome and to evaluate these RCCs in the HBV proteins structure. METHODS: For detection of protein family accession numbers (Pfam) in HBV proteins, the UniProt database and Pfam search tool were used. Protein family accession numbers is a comprehensive and accurate collection of protein domains and families. It contains annotation of each family in the form of textual descriptions, links to other resources and literature references. Genome projects have used Pfam extensively for large-scale functional annotation of genomic data; Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). The Pfam search tools are databases that identify Pfam of proteins. These Pfam IDs were analyzed in Sherlocc program and the location of RCCs in HBV genome and proteins were detected and reported as translated EMBL nucleotide sequence data library (TrEMBL) entries. The TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of European molecular biology laboratory (EMBL) nucleotide sequence entries not yet integrated in SWISS-PROT. Furthermore, the structures of TrEMBL entries proteins were studied in the PDB database and 3D structures of the HBV proteins and locations of RCCs were visualized and studied using Swiss PDB Viewer software®. RESULTS: The Pfam search tool found nine protein families in three frames. Results of Pfams studies in the Sherlocc program showed that this program has not identified RCCs in the external core antigen (PF08290) and truncated HBeAg gene (PF08290) of HBV. By contrast, the RCCs were identified in gene of hepatitis core antigen (PF00906 and the residues 224 - 234 and 251 - 255), large envelope protein S (PF00695 and the residues 53-56 and 70 - 84), X protein (PF00739 and the residues 10 - 24, 29 - 83, 95 - 99. 122 - 129, 139 - 143), DNA polymerase (viral) N-terminal domain (PF00242 and the residues 59 - 62, 214 - 217, 407 - 413) and protein P (Pf00336 and the residues 225 - 228). In HBV genome, seven RCCs were identified in the gene area of hepatitis core antigen, large envelope protein S and DNA polymerase, while protein structures of TrEMBL entries sequences found in Sherlocc program outputs were not complete. CONCLUSIONS: Based on the location of detected RCCs in the structure of HBV proteins, it was found that these RCCs may have a critical role in correct folding of HBV proteins and can be considered as drug targets. The results of this study provide new and deep perspectives about structure of HBV proteins for further researches and designing new drugs for treatment of HBV.

The interaction between morphine and propranolol in chemical and electrical seizure models of mice.

OBJECTIVES: Morphine and propranolol have different effects on seizure. Several studies have shown interaction between adrenergic and opioid systems in different models. In this study, interaction between morphine and propranolol in different seizure models was examined in mice. METHODS: In this study, three seizure models, including intravenous pentylenetetrazole (PTZ), intraperitoneal PTZ and electroshock, were examined in mice. Animals were injected with different doses of morphine or propranolol in the 60th and 45th min, before seizure induction, respectively. RESULTS: Acute administration of propranolol or lower doses of morphine induced an anticonvulsant effect in intravenous PTZ, intraperitoneal PTZ and electroshock-induced seizure models; on the contrary, higher doses of morphine exert proconvulsant effects in all three models. Also additive anticonvulsant effect of propranolol and lower doses of morphine was observed in all examined models. The additive anti-seizure effect of propranolol and lower doses of morphine was blocked by naltrexone in intraperitoneal PTZ model. Moreover, the anticonvulsant effect of propranolol was inhibited by naltrexone in intraperitoneal PTZ seizure model of mice. Propranolol restrained the proconvulsant effects in higher doses of morphine in clonic seizures of intravenous and intraperitoneal PTZ models. DISCUSSION: In conclusion, we believe that this is the first study that has indicated the interaction of propranolol and lower doses of morphine in the anticonvulsant effects in three seizure models of intravenous PTZ, intraperitoneal PTZ and electroshock. The involvement of µ-opioid receptor in this interaction was also demonstrated. Simultaneously, we showed the interaction between propranolol and higher doses of morphine in proconvulsant effects.

The involvement of nitric oxide in the anti-seizure effect of acute atorvastatin treatment in mice.

OBJECTIVES: In addition to reducing the serum level of cholesterol, statins have various pleiotropic effects such as increasing nitric oxide and reducing oxidative stress, neuroinflammation, and neurotoxicity. Increasing evidence indicates that statins are neuroprotective in several conditions, including stroke, cerebral ischemia and traumatic brain injury. However, only a few studies have investigated whether statins modulate seizure activity. METHODS: In the current study, we investigated whether acute treatment with atorvastatin alters the seizures induced by electroshock or pentylenetetrazole in mice. We also evaluated whether nitrergic system is involved in the effects of acute atorvastatin on seizure. RESULTS: The results of the present study demonstrate that acute atorvastatin (10 and 20 mg/kg) treatment decreased the incidence of tonic seizure and death in electroshock-induced seizure model. We also showed that acute atorvastatin (10 mg/kg) treatment increased the clonic seizure threshold in pentylenetetrazole-seizure model. Acute L-NAME (5 mg/kg), a non-selective inhibitor of nitric oxide synthase, or aminoguanidine (100 mg/kg), a selective inhibitor of inducible nitric oxide synthase, administration prevented the anti-convulsant effect of atorvastatin in electroshock-induced seizure model. We also demonstrated that acute L-NAME (5 mg/kg) or aminoguanidine (100 mg/kg) administration decreased the enhanced clonic latency of clonic seizure threshold induced by atorvastatin in mice in pentylenetetrazole model. DISCUSSION: In conclusion, anti-convulsant effect of atorvastatin was demonstrated in two seizure models of electroshock and intraperitoneal pentylenetetrazole. Nitric oxide release, probably through inducible nitric oxide synthase at least in part is responsible for this effect.

Chronic administration of atorvastatin induced anti-convulsant effects in mice: the role of nitric oxide.

Atorvastatin has neuroprotective effects, and there is some evidence that nitric oxide is involved in atorvastatin effects. In this study, we evaluated whether the nitrergic system is involved in the anticonvulsant effects of chronic atorvastatin administration. Intravenous and intraperitoneal pentylenetetrazol were used to induce seizures in mice. Chronic atorvastatin treatment significantly increased the seizure threshold which is induced by both intravenous and intraperitoneal pentylenetetrazol. Intraperitoneal pentylenetetrazol also decreased the incidence of tonic seizure and death in atorvastatin-treated groups. Chronic co-administration of a non-selective nitric oxide synthase inhibitor, l-NAME, or a selective inducible nitric oxide synthase inhibitor, aminoguanidine, with atorvastatin inhibited atorvastatin-induced anticonvulsant effects in intravenous model of pentylenetetrazol. Acute injection of l-NAME or aminoguanidine inhibited the anticonvulsant effects of atorvastatin in both models of intravenous- and intraperitoneal-pentylenetetrazol-induced seizures. In conclusion, we demonstrated that nitric oxide signaling probably through inducible nitric oxide synthase could be involved in the anticonvulsant effects of atorvastatin.