Sequencing and In Silico Multi-aspect Analysis of S1 Glycoprotein in 793/B Serotype of Infectious Bronchitis Virus Isolated From Iran in 2003 and 2011

Infectious bronchitis (IB) is an acute, highly contagious, and economically important viral disease of chickens. The S1 subunit from Spike (S) protein plays the major role in protective immunity and is involved in the host-virus interactions, as well as infectious bronchitis virus (IBV) serotyping. Aim of the present study was multi-aspect analysis of the molecular and immunological features of 5' part belonging to the S1 glycoprotein sequence of Iranian 793/B IBV strain isolates. This might ideally help in characterization, prevention, and vaccine development. The tissue samples were prepared, followed by virus isolation, reverse transcription polymerase chain reaction and restriction fragment length polymorphism analysis. In addition, sequencing and registration of the sequences in the National Center for Biotechnology Information were performed. Moreover, 12 sequences were retrieved from Fars province, Iran. The next steps included evaluation of conservation/variability along the sequences, phylogenetic analysis, estimation of the average evolutionary divergence over all the sequence pairs, predicting the phosphorylation/N-glycosylation/palmitoylation sites, and the final analysis of antigenicity. The findings of alignment, entropy plot, and pairwise similarity analysis revealed 17 hypervariable regions. The isolates belonging to Tehran were clustered in phylogenetic tree, and the most similar isolates to them were ADW11182 and ADW11183. Location of some of the N-glycosylation/phosphorylation/palmitoylation points indicated that these sites were conserved among the isolates. Furthermore, the frequency of epitopes and their scores reflect the high immunogenicity of S1 protein in 793/B serotype. Analysis of the primary and secondary structures demonstrated that their parameters had variable values and were different regarding the number and location of α-helix, β-strand, and coils. According to our findings, the Iranian isolates of 793/B serotype change their molecular characteristics during time and in different geographical regions. These alterations might account for failure in prevention programs and differences in virulence and pathogenicity

Molecular barcoding of the Aras reservoir alga Microcystis aeruginosa (Kützing) Kützing 1846 by ITS-2 gene

Today, due to population increase and anthropogenic activities together with sewage and agricultural waste water entrance, aquatic ecosystems have been exposed to high pollutions. Phytoplankton is a group of water floating algae that have crucial roles in providing nutrients and oxygen for other organisms, nitrogen and CO_2 fixation. These organisms are considered as primary producers in aquatic ecosystems. They are found in various water habitats all over the world, affected by environmental variables such as pH, light and temperature and used for determination of water pollution degree and quality. Phytoplankton composition and density may be used as a complementary indicator of water trophy state. Phytoplankton communities indicate short and long term variations of aquatic systems. One of the most obvious problems in freshwater ecosystems is algal bloom or over growth of some blue- green algae which can decrease oxygen, and in some cases bring about toxin excretion and fish and human kills. In addition, many of bloom forming cyanobacteria produce secondary metabolites which can create sever poisoning in mammals including human. The genus Microcystis is a key bloom forming cyanobacteria in aquatic ecosystems. Populations of this genus form intense blooms in water bodies that has attracted more attentions in recent years. Various species of this alga have been distributed in stagnant and eutroph freshwater around the world. Microcystis has been defined by genetic criteria such as 16S rRNA molecular sequencing, but its classification in levels lower than genus is unclear and the presence of its classical morphospecies is doubtful. However, this genus creates sever blooms in eutrophic waters all over the world and many species produce toxins. Therefore, identification of its natural diversity in the levels lower than genus has high importance. However, several characteristics of Microcystis morphotypes which are classified a traditional species, actually are present and observed in different regions of the world. At present, they can be considered as morphospecies that belong to one genotype and have similar ecology. These traditional species with definite phenotypic and ecophysiological characteristics cannot be eliminated completely. Their identification is essential for ecological and ecotoxicological studies. Interistic transcribed separator (ITS) gene is a section of genome which is located between 16s rRNA and 23s genes. This gene has more heterogeneity than 16s rRNA; so it is used to identify many genera of cyanobacteria. The Aras reservoir located in the north-west of Iran plays important roles as fisheries, drinking and agricultural water supply and recreational activities in the region. The present thesis was undertaken to: analyze the Microcystis sp. populations by molecular methods such as ITS in Aras Reservoir. Samples for molecular analysis were collected from 10 sampling sites on 18 August 2013. Samples for molecular study of Microcystis were collected from two different depths (surface and 1 m depth) and transferred to laboratory without any treatments. Microscopic images of Microcystis were sent to professor Komárek and was confirmed