Phylogenic relationships among the Iranian populations of bisexual Artemia (Nough pool and Urmia Lake samples) were inferred by PCR-RFLP analysis of the mitochondrial 16S rRNA gene with comparison by two reference sample, Artemia Urmiana and Artemia franciscana. Four different haplotypes of A. franciscana were detected in Nough and nine different haplotypes of A. Urmiana in Urmia by using 10 restriction enzymes. Phylogenic analysis of molecular data showed Iranian populations of bisexual Artemia clustered into two clades including: 1- Nough samples and two haplotypes of Urmia 2- Seven different haplotypes of Urmia. Obtained results also show the ability of the used technique for dividing of different bisexual populations of Artemia in Iran. Our study resolve phylogenic relationship among bisexual samples of Iran and it has been determined that there is considerable differences in nucleotide arrangement, at least in ribosomal fragment, between A. Urmiana and A. franciscana that similar to same previous studies.

Newcastle Disease Virus (NDV)is one of the most contagious viral diseases of poultry with rapid spread around the world. It identified by respiratory symptoms, nervous and digestive disorders, and high mortality. NDv causes significant economic losses in poultry industry throughout the world. Avian paramixovirus serotype 1(APMV-1) is a member of family paramyxoviridae, the genus Avulavirus, Newcastle disease virus belongs to APMV-1. The aim of this study to recognize and phylogenic analysis of Newcastle disease Virus isolated from poultry farms in Markazi Province by RT-PCR. In this research, recognition and phylogenic analysis was performed based on F gene of Newcastle disease virus. About 30 samples including brain, trachea, lung and spleen were obtained from suspected farms. Then, They were inoculated to 9 - 11 days age SPF embryonic eggs. After that 2-5 days, The Allantoic fluid harvested, the HA test was performed and genetically analysis using specific primer for F gene was done by RT PCR. In this study, Among the samples 13 of them was confirmed as Newcastle disease virus. Phylogeny tree was constructed for F gene using MEGA 6 software. The results showed that all isolates NDV belonged to genotype VII and subgenotype VII-j. These obtained data can use to improve the efficacy of the vaccine and disease prevention program, as well as its use for vaccine production against the Newcastle-disease causative agents.

Leishmaniasis as an emerging and reemerging disease is increasing worldwide with high prevalence and new incidence in recent years. For epidemiological investigation and accurate identification of Leishmania species, three nuclear and mitochondrial genes (ITS-rDNA, Hsp70, and Cyt b) were employed and analyzed from clinical samples in three important Zoonotic Cutaneous Leishmaniasis (ZCL) foci of Iran.
In this cross-sectional/descriptive study conducted in 2014-15, serous smears of lesions were directly prepared from suspected patients of ZCL in Turkmen in northeast, Abarkouh in center and Shush district in southwest of Iran. They were directly prepared from suspected patients and DNA was extracted. Two nuclear genes of ITS-rDNA, Hsp70 and one mitochondrial gene of Cyt b within Leishmania parasites were amplified. RFLP was performed on PCR-positive samples. PCR products were sequenced, aligned and edited with sequencher 4.1.4 and phylogenic analyses performed using MEGA 5.05 software.
Overall, 203 out of 360 clinical samples from suspected patients were Leishmania positive using routine laboratory methods and 231 samples were positive by molecular techniques. L. major L. tropica, and L. turanica were firmly identified by employing different molecular genes and phylogenic analyses.
By combining different molecular genes, Leishmania parasites were identified accurately. The sensitivity and specificity three genes were evaluated and had more advantages to compare routine laboratory methods. ITS-rDNA gene is more appropriate for firm identification of Leishmania species.

Brucellosis is a well-known domestic animal infectious disease, which is caused by Brucella bacterium. The outer membrane protein 25 kDa (Omp25) gene plays an important role in simulating of TNF-α, IFN-α, macrophage, and cytokines cells. In the current study molecular cloning and expression analysis of Omp25 gene for designing a subunit vaccine against Brucella was investigated. Amplifying the full length of candidate gene was performed using specific primers. Sub-cloning of this gene conducted using pTZ57R/T vector in TOP10F`strain of Escherichia coli(E.coli) as the host. Also, pET32(a) vector used for expression in BL21 (DE3) strain of E.coli. Omp25 gene with 642 bp size was amplified and cloned successfully. The expression results were confirmed by sequencing and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analyses which showed 42 kDa protein band correctly. Also, phylogenic analysis showed this gene has a near genetic relation with other Brucella strains. According to our results we can propose this gene as a candidate useful for stimulation of cell-mediated and humoral immunity system in future study.

The widespread use of herbicides containing 2,2-dichloropropionic acid (2,2-DCP) as a recalcitrant halogen compound poses significant environmental risks and can be harmful for human. Consequently, it is important that the bio-based detoxification method is developed in an environmental manner. This study was aimed to isolate and identify a possible degradation 2,2-DCP bacterial strain as the sole source of carbon. A bacterial dehalogenase producing 2,2-DCP was isolated named as WM. The WM strain was shown to have 98% sequence identity and characteristics similar to Enterobacter sp. based on 16s rRNA analysis, biochemical and morphological tests. Phylogenic analysis showed that the WM strain is Enterobacter sp.. In media with 20 mM 3CP, the bacteria were well growing at 37°C, although an optimal chloride ion release was 0.48 μmol Cl/mL. Our finding is first report of an Enterobacter sp. strain which can use 2, 2-DCP as sole carbon source in a competent manner.

Pasteurella multocida is known as an important heterogenic bacterial agent causes some severe diseases such as fowl cholera in poultry and haemorrhagic septicaemia in cattle and buffalo. A polymerase chain reaction (PCR) assay was developed using primers derived from conserved part of 16S-23S rRNA gene. The PCR amplified a fragment size of 0.7 kb using DNA from nine avian P. multocida isolates. Sequence alignment of the 16S-23S rRNA genes (ITS) revealed a considerable heterogenicity among the isolates. The percentage of similarity varied from 83.3 to 100% among the isolates. An interesting finding from this study was the presence of an inserted sequence (seven nucleotides) in the 16S-23S rRNA region in 55% of the isolates. According to phylogenic analysis based on ITS sequence alignment, the P. multocida isolates classified into 2 distinct clusters. The virulence of isolates in cluster II were higher than those in cluster I. Ribotyping of P. multocida by using 16S-23S rRNA gene PCR sequencing could be used as a marker in epidemiologic studies.

Hepatitis Delta virus (HDV) is a degenerate RNA virus or virusoid and a satellite of Hepatitis B virus (HBV). Three distinct genotypes are described for HDV; genotype I is distributed worldwide but other genotypes appear to be more restricted geographically. In the present study, an RT-nested PCR method was set up to detect delta infection from serum samples. Moreover, the target amplified sequences corresponding to the Hepatitis delta antigen (HDAg) C-termini were used for genotyping. The results showed that 63.6% (23 of 36) of (HDAb) positive serum samples (as determined by ELISA) were also positive for HDV-RNA. Sequencing and phylogenic analysis of three Iranian HDV isolates revealed the most homology (93%) with an Italian isolate indicating a close relationship and probably a common origin for these isolates.

Brucellosis is a well-known infection among domestic animals which caused by Brucella bacterium. Omp31 is an outer membrane protein that play important roles in simulate CD4 T and CD8 T cells. In current study molecular, cloning and also phylogenic analysis of Omp31 gene as a candidate for designing subunit vaccine against brucella was investigated. Amplifying performed using specific primers. Cloning of this gene performed using pMB57R/T vector in TOP10F`strain of E.coli as host. Also, pET32a vector used for expression. Omp31 gene with 723 bp amplified successfully. After that clone using TA cloning approach within cloning vector. Expression of this gene has done in pET32a vector by inducing IPTG. Results confirmed with sequencing and SDS PAGE showed 48 KD protein band correctly. According this results we can propose this gene as a candidate for designing subunit vaccine against brucella in future study.According this results we can propose this gene as a candidate for designing subunit vaccine against brucella in future study.

Maintaining genomic diversity in goat populations in different parts of Iran is essential for breeding programs, increasing production, survival, resistance to diseases, and various environmental changing conditions. The aim of the present study was to determine the sequence of HVR1 from the mitochondrial genome of Iranian native goats including Sistani, Pakistani, Black and Lorry ecotypes (each of 4 heads), examine the probable variation in these populations, and plotting their phylogen relationship in comparison with some animal species. Total DNA extraction was performed using phenol-chloroform method. The extracted DNA was used as template for proliferation of HVR1 region of mitochondrial genome was used and the obtained bands were sequenced by Sanger method. The nucleotide sequences with 30 sequences from the same region of the mitochondrial genome related to other animal species derived from the National Center for Biotechnology Information (NCBI) were used for genetic analysis and phylogenetic tree mapping. The average of haplotype diversity and nucleotide diversity among species were 0.994 and 0.12891, and, in the ecotypes were 1 and 0.09299, respectively. The numerical value of the replacement rate of dn/ds for the studied ecotypes and other species was calculated at 1.17 and 1.12, respectively, which indicates a positive selection in the process of evolution of this gene. The results of phylogenic tree of nucleotide sequence of HVR1 region were estimated from two major branches and 7 subspaces. Among the studied species, goat ecotypes were similar to sheep species. The genetic and phylogenic analysis of the studied species indicates the distinction and evolutionary path of each species and the HVR1 region can lead to the proper grouping of the species and sub-species that are split from them.

One of the most important species of the Bartonella genus is B. henselae that causes a zoonotic infection, cat scratch disease (CSD). The main source of the bacteria is cat and the carrier is Ctenocephalides felis flea. One hundred and forty nail and saliva samples were collected from 70 domestic cats. Positive samples for B. henselae were characterized by polymerase chain reaction (PCR) and sequencing. Sequences of gltA gene were trimmed using BioEdit software and then compared with the sequences of the same gene from B. henselae isolated from cats and humans in GenBank database. Phylogenic tree was constructed using CLC Sequence Viewer software and unweighted pair group method with arithmetic mean (UPGMA) method. Molecular assessments showed that five samples out of 70 nail samples (7.14%) and one sample out of 70 saliva samples (1.42%) were genetically positive for B. henselae. At least an 87.00% similarity was seen between the gene sequences from the current study and the reference sequences from the GenBank database. Phylogenic analysis has shown that strains isolated in this study were grouped in a different haplo group, compared to other strains.Among the Asian countries, the prevalence of the bacteria in Iran was close to that in Japan and Turkey. In conclusion, findings of this study showed the prevalence of B. henselae in Iranian cats which is important due to its public health issues, especially for the immunocompromised pet owners.