مجتبی طهمورث پور

The aim of this study was to propose an efficient algorithm to predict antimicrobial peptides using artificial intelligence algorithms.

In this study, an updated AMP and non-AMP data set including physico-chemical characteristics at the level of amino acids and protein sequence in three animal species and humans was extracted. After data exploration and data pre-processing steps, four methods Supervised learning including Decision Tree, Random Forest, Naive Bayes and SVM on the AMP dataset with 10-fold cross-validation to build models and predict the AMP label using the evaluation criteria of specificity, sensitivity, rate Accuracy, precision, recall, F1 score and area under the rock curve (AUC) were evaluated.

In this study, using an up-to-date dataset, a machine learning model has been successfully trained to predict antimicrobial peptides. A comprehensive set of features has been subjected to feature selection to identify key features of antimicrobial peptides. After selecting the feature, among the different generated models, the model based on the RF model classifier showed the best performance with Accuracy (95 percent), Precision (96 percent), Recall (95 percent), F1 Score (95 percent). the four classification of algorithms, Random Forest algorithm and SVM are the most accurate. The Decision Tree classification algorithm had the least accuracy.

According to the obtained results, the proposed RF model has a better performance than other models for AMP prediction. This model predicted some peptides as peptides with antimicrobial properties. This predictive approach can be useful in extracting AMPs with antimicrobial properties from AMP libraries in useful clinical applications before moving on to experimental studies. On the other hand, several features in the final selection properties indicate that these features are critical determinants of peptide properties and should be considered in the development of models to predict peptide activity. The executable code is available in the attached file.

Among different sheep breeds in the world, the Texel breed is known as a meaty and muscular breed. Skeletal muscle growth is a step-by-step and exponential process from differentiation, development and maturation, which is regulated by gene networks and cell signaling pathways, and several genes and factors are involved in the process of muscle fiber formation and their growth and hypertrophy (Badday Betti et al. 2022). The study of gene expression is done with several methods, and this gene expression information is used in breeding programs as a tool to improve phenotypic choices. Databases are a large source of expression data that can be used by bioinformatics methods to integrate heterogeneous data from different studies and platforms. In this study, by integrating the microarray and RNA-Seq data available in the database belonging to the muscle tissue of Texel breed sheep, the transcriptomic profile of the muscle was compared at two ages of embryonic and adult. Microarray data related to longissimus dorsi muscle tissue with three replicates d-70 embryos from GEO database with accession number GSE23563 and RNA-Seq data related to muscle tissue from six samples with two replicates from adult individuals from ArrayExpress database were selected. Limma, Biobase and GEOquery software packages were used to calculate the expression values of the microarray data related to the embryonic age  in the R environment, and Tuxedo, HTSeq and DESeq2 packages were used in the Linux and R environment to calculate the expression values of the RNA-Seq data (Kamali et al. 2022; Sahraei et al. 2019). Then two types of expression values were integrated and to eliminate non-biological effects, the batch effects were also removed. Next, differential genes were identified with the limma software package. In order to identify the relationship between the identified differential genes, the gene network was drawn between them by software of Cytoscape version 3.7.1 and String 1.5.1 program. next, due to the vastness of the gene network, each network was clustered with MCODE 1.6.1 and CytoCluster 2.1.0 programs (ClusterOne algorithm) and significant clusters (P-value < 0.05) were identified (Saedi et al. 2022). In order to better understand the ontology and function of the identified differential genes, the Gene Ontology of the genes was investigated using software of Cytoscape version 3.7.1 and ClueGO 2.5.9 and CluePedia 1.5.9 programs. After receiving the Gene Ontology results, significant Gene Ontology terms (P-Value < 0.05) related to functional groups were identified. Finally, the selected genes (Adj P-Value < 0.05) were identified and introduced in these two age groups. After quality control, correcting and normalizing the microarray data, the GPL10778 platform annotation file with 1042520 Probe ID was used to calculate their expression values. After relevant analyzes of 9289 Probe ID identified related to the data of this study, 7918 Gene Symbol was identified finally. After quality control, trimming and normalizing the RNA-Seq data in total, the number of Ensembl_Genes based on which the reading values were calculated by HTSeq was 27056. After removing IDs that had zero readings in all 6 samples, 10855 IDs remained. Then, these 10855 Ensembl ID were merged with the annotation file to obtain Gene Symbol, and finally 9417 common genes were identified between the six samples of adult age. The results of differential expression analysis showed that there were significant differences in the expression of 62 genes (37 increased and 25 decreased) in the muscle tissue between adult and embryonic age. By creating a gene network between differential genes, 15 selected genes were identified, including MYH1, ACTN3, CASQ1, TMOD4, FBP2, SLC2A4, MX1, COX4I1, SOD2, MFN2, UQCRB, UCP3, PRKAB2, PHKG2, PPP1R3C. The function of these genes has been proven in cell proliferation, protein synthesis, myofibril formation, and lipid metabolism. Differential gene enrichment analysis revealed some biological processes such as Vasculogenesis, positive regulation of ossification, positive regulation of muscle tissue development, regulation of muscle contraction, contractile fiber part, calcium signaling, calcineurin-NFAT signaling cascade and regulation of receptor signaling pathway via JAK-STAT, the molecular function of regulating cation channel activity and the cellular components of the contractile fiber. This study in addition to confirming the accuracy of the integration method of two types of heterogeneous data, provided a general view of the transcriptomic differences of Texel sheep muscle tissue at two important age points to be a useful source for biological investigations of genes related to muscle growth and development in sheep.

Frequent and excessive use of antibiotics has caused the resistance of pathogenic bacteria to common antibiotics. Considering this issue, researchers are looking for new methods to replace antibiotics, which can be referred to as antimicrobial peptides (AMP). Therefore, the aim of the present study was bioinformatic investigation of the effect of his taq addition on the antibacterial activity of plant beta-defensin peptide and clone this peptide gene in the expression vector pAMJ1653 in Lactococcus lactis bacteria. The third structure of beta defensin peptide with his-taq was predicted through I-TASSER and verified by SAVE 6 and prosA software. Finally, molecular docking was performed through Cluspro software between beta defensin with /without his-taq sequence and Escherichia coli LPTD antigen. In the exprimental section, beta defensin gene was used along with his-taq sequence and secretion signal in pGEM-DFF replication vector and DH5α replication host. After plasmid extraction and enzymatic digestion by Sap1 and Sal1 enzymes, plant beta defensin gene was homogenized into pAMJ1653 expression vector and transferred into Lactococcus lactis strain 1543 bacteria using electroporation method. The positive colonies containing the recombinant vector were checked by PCR colony method and finally enzymatic digestion was performed. In the bioinformatics part, the third structure of beta defensin was predicted with acceptable accuracy. Docking results showed that beta defensin peptide with/without his-taq is in contact with LPTD antigen in the right position. In the laboratory section, it was shown that the gene encoding plant betadefensin was successfully cloned in the pAMJ1653 expression vector

Sheeppox is one of the most common diseases in sheep that can spread quickly in the herd. Currently, there is no specific treatment for this viral disease. The purpose of this study was to investigate the antimicrobial peptide CLF36 and CLFarm on the surface protein of the sheep pox virus P32 protein and the cellular receptors of this protein such as heparin sulfate and UDP-N-acetyl glucosamine. The third structure of P32 was done using software such as I-TASSER. The interactions were performed statically in a computer by bioinformatics tools such as HDOCK software and using Gromacs in the molecular dynamics section. The results of this study showed that the amino acids of CLF36 peptide involved in hydrogen bonding with P32 include D1, K5, V8, Q11, K9, R16, R22, K25, R27 and K34 and for CLFarm include K5, K9, Q11, K13, R27, W30, Q31 and K35. Docking results showed that peptides were attached to three epitope regions EP1,4,8 in P32 protein. In connection with the molecular docking between CLF36 arm and the two receptors UDP-N-acetylglucosamine and heparin sulfate, the hydrogen bonds included Gln 11, Trp 30 and Trp 4, Trp 30, Gln 11, Arg 27, Cys 33, respectively; Although CLF36 had weak binding energy with these two receptors. In the molecular dynamics section, the graph of RMSF and RMSD and Gyrate showed a few fluctuations, which were ignored. Finally, these results showed that both peptides have a good performance against P32 in a period of 50 ns.

Lactoferrin is secreted in the apo-form from epithelial cells in most exocrine fluids, such as saliva, bile, pancreatic and gastric fluids, tears and, particularly, in milk. Lactoferrin is the most dominant protein in milk after casein. This protein plays a crucial role in many biological processes including the regulation of iron metabolism, induction and modulation of the immune system, the primary defense against microorganisms, inhibiting lipid peroxidation and presenting antimicrobial activity against various pathogens such as parasites, fungi, bacteria, and viruses. The major antimicrobial effect of lactoferrin is related to its N-terminal tail where different peptides for instance lactoferricin and lactoferrampin which are important for their antimicrobial abilities are present. cLF chimera (CLF36 peptide ) was derived from camel lactoferrin (cLF) consisting of 42 amino acids and has primary sequence of DLIWKLLVKAQEKFGRGKPSKRVKKMRRQWQACKSSHHHHHH. In addition, the results of previous study showed that cLFchimera had anti-inflammatory and regulatory activity of the immune system. Nuclear factor kappa B (NF-kB) transcription factors regulate several important physiological processes, including inflammation and immune responses, cell growth, apoptosis, and the expression of certain viral genes. NF-kB dimers are located in the cytoplasm in an inactive form through association with any of several IkB inhibitor proteins. The phosphorylation and degradation of IkB have received great attention as key steps for the regulation of Nuclear factor kappa B (NF-kB) complexes. Phosphorylation of the IkB by IKK signals it for ubiquitination at specific lysine residues. The aim of this study was to investigate the inhibitory effects of the recombinant camel Lactoferrampin-Lactoferricin on nuclear factor kappa B (NF-кB) pathway.

CLF36 peptide was prepared through a previous study in Biotechnology Laboratory of Animal Science Department, Faculty of Agriculture, Ferdowsi University of Mashhad (GenBank accession number: MH327768.1). Protein data for inhibitory combinations of the Nuclear factor kappa B (NF-kB) pathway was collected from the Protein Data Bank (PDB) And UniProt.Physico-chemical properties analysis (atomic state, isoelectric point, half-life, hydrophobicity hydrophilicity , barometric and pH) was done using Expasy Prot Param online server. The inhibitory effects of this peptide was assessed by Molecular Docking Simulation (In silico). the simulation of the interaction (Docking) of CLF36 peptide with Nuclear factor kappa B (NF-kB) signaling pathway in upstream, pro-inflammatory cytokines (e.g., TNF-α and IL-6) and in downstream, cytoplasmic IKKB and NF-κBp65 was done using ClusPro 2.0 software online.interaction diagram created by LigPlot+ showing the hydrogen bond network and the hydrophobic interactions of CLF36 peptid with the upstream and downstream Nuclear factor kappa B (NF-kB) pathways.

Bioinformatics analysis on The molecular interaction of this peptide with the active site of NF-κB proteins suggested that in may have role of the modulators and Anti-Inflammatory of immune processes by inhibitory effect on the TNF-α and IL-6 cytokines in upstream and IKK-β and NF-κB-p65 in downstream of the NF-κB signaling pathway. This results are similar to the inhibitory effects of Infliximab, Camelid Fab , NEMO and  GILZ on the Nuclear factor kappa B (NF-kB) signaling pathway. Infliximab (Remicade) is a chimeric mAband its use is not very well tolerated in the majority of patients, infliximab therapy leads to the production of antibodies to infliximab in a small subset of patients. the  Camelid Fab antibody with the highest (femtomolar) potency, displays a very large surface of interaction with IL-6. the regulatory role of NEMO in the IKK complex, since a number of genetic and biochemical studies clearly demonstrate that proinflammatory IKK activation is absolutely dependent upon the presence of functional NEMO. Glucocorticoid-induced leucine zipper (GILZ) is a glucocorticoid responsive protein that links the nuclear factor-kappa B (NFκB) and the glucocorticoid signaling pathways. Func tional and binding studies suggest that the proline-rich region at the carboxy terminus of Glucocorticoid-induced leucine zipper (GILZ) binds the p65 subunit of Nuclear factor kappa B (NF-kB) and suppresses the immunoinflammatory response.

  The results of the interaction (Docking) of CLF36 peptide with Nuclear factor kappa B (NF-kB) signaling pathway indicates that, in upstream, will be inhibitory effect of CLF36 peptide in active site of pro-inflammatory cytokines (e.g., TNF-α and IL-6) and in downstream, cFL36 peptide will bind to protein receptors of cytoplasmic IKKB and NF-κB p65. Therefore, these findings may provide a theoretical basis for therapeutic mechanisms of CLF36 peptide.

Hepatitis C infection is one of the most common chronic infectious diseases in the world and about 3-5 million people are infected with this infection annually. Unfortunately, despite recent advances, there are still widespread problems for the treatment of these people and many needs have not been met. As a result, there is an urgent need for more effective treatment strategies to treat this disease. One of these new therapeutic approaches is the use of recombinant proteins, which have no side effects for the patient and at the same time are cheap and available.

To conduct this study, the three-dimensional structures of virus proteases (NS2, NS3, NS4A, NS5A and NS5B) and recombinant peptide CLF36, were obtained. The chemical structure of new generation drugs was also downloaded from PubChem. To evaluate the stability of the predicted structures and to ensure the accuracy of the third structure of proteins, molecular dynamics simulations were performed using GROMACS software version 2019 and in a duration of 10 nanoseconds. Then, to evaluate the antiviral properties of the peptide, molecular docking was performed for peptides and drugs under static conditions. To evaluate the stability of the complexes, based on the results obtained from molecular docking, complexes with negative values of free binding energy were selected to perform molecular dynamics simulations. Finally, the obtained results were evaluated under dynamic conditions in GROMACS software. The engineered peptides were then designed according to the results and the sequence of the best engineered peptides was sent for synthesis. After cloning and expression of the recombinant peptide in the yeast host, the IC50 level of the peptide on the Huh7.5 liver cell line was determined and the virus-infected cells were treated with the desired peptide. After extracting RNA from the cells, the virus loaded in the sample. Were measured.

Among the results obtained from various dockings performed between virus proteases and recombinant peptides and commercial drugs, it was found that the peptide-binding strength (average -99.92) was much higher than other drugs (average -61.54). This indicates the high antiviral property of the recombinant peptide. The results of molecular dynamics showed that the values of rmsd and hydrogen bonds and binding energy for CLF36 peptide bound to virus proteases compared to other drugs indicate a stronger binding of this peptide. In addition, the engineered peptide showed stronger antiviral activity compared to the natural peptide (binding energy was 8 units stronger). Examination of the function of the peptide in vitro also showed that this peptide has a stronger antiviral effect compared to drugs in that it was able to completely prevent the virus from multiplying in cells.

The final results of this study indicated that recombinant peptide, has strong antiviral properties. However, to confirm these results, additional laboratory studies are needed.

Brucellosis is a common disease between humans and livestock that has caused a great deal of damage to the livestock industry in recent years. One way to prevent this disease is to get a vaccine to immunize disease-prone herds. To produce a successful recombinant vaccine, factors such as: selecting the right adjuvant, selecting the right antigen and the right delivery system are very important. To this end, epitopes have recently been widely used in clinical research, biomedicine, and the production of recombinant vaccines. Surface proteins of this bacterium, including BLS and Omp25 proteins, have antigenic properties and play an important role in causing this disease. Due to the lack of effective vaccines, today the need to produce new and effective vaccines is felt more than ever. The aim of this study was to bioinformatically predict the epitopes of BLS and Omp25 genes of Brucella bacterium in order to introduce a suitable candidate for vaccine production.

For this purpose, SYFFPEITHI, PROPRED and IEDB servers were used to predict epitopes. Since the three-dimensional structure of the protein is required to investigate the interaction of antigens with cell surface receptors, in the next step, the predicted epitopes were modeled using the Pepfold 3 server. In addition, in order to evaluate the stability of the predicted structures and to ensure the accuracy of the third structure of the peptides, molecular dynamics simulations were performed using GROMACS software version 2019 and in a duration of 10 nanoseconds. Then, the three-dimensional structure was obtained by modeling homology method and the docking study of the interaction between epitopes with sheep MHCII and MHCI cells was performed using Autodock vina software.

Then, in order to evaluate the stability of the complexes based on the results obtained from molecular docking, complexes with negative values of free binding energy were selected to perform molecular dynamics simulations. Finally, 8 peptides with better numbers were considered as suggested epitopes. The results obtained from molecular dynamics showed that the rmsd values for interleukin and interleukin bound to the polypeptide did not differ much in the two cases, so these results indicate that the activity of interleukin bound to the polypeptope did not change. The rmsf values also indicate the same stability in both proteins.Finally, the obtained results were evaluated in dynamic conditions in GROMACS software. The results of this study showed that in dynamic conditions, 4 predicted epitopes have high binding power to MHC class 1 and 2 receptors.

 In addition, docking and molecular dynamics results showed that the polypeptide predicted in this study could be used as a candidate polypeptide in the design of a recombinant vaccine against brucellosis. However, to confirm these results, additional and laboratory studies are needed.

H5N8 is one of the subtypes of highly pathogenic avian influenza in Iran that could cause damage to birds in addition humans. Among combat existing and emerging drug-resistant influenza viruses, new antiviral drugs as alternative played pivotal roles. It can mention the CLF36 antiviral peptide, which is the result of the binding of two peptides from the camel lactoferrin protein (chimera) has shown more antimicrobial activity than other species such as blf. The objective of this study was to predicte the structure of CLF36 peptide and two surface antigens of influenza virus as well as the interaction of this peptide with three antigens of nfluenza a virus subtype H5N8 through molecular docking. The physicochemical properties of CLF36 peptide were evaluated by using CLC Main Workbench 5 software. The third structure of this peptide as well as virus antigens were determined through I-TASSER and Swiss-Model softwares. After that, The CLF36 peptide interacts with these antigenes were performed by using the online software ClusPro2.0 and were corrected these structures through the YASARA Energy Minimization software. The quality of the 3D model was evaluated by the SAVES v5.0 software. Finally, the docking results were studied by using PYMOL software. Molecular docking results showed that the position and energy of bonding assessment forhemagglutinin, neuraminidase and Matrix protein 2 were -674.2, -573.4 and -567.0 respectively. Most of peptide’s amino acids involved in hydrogen bonds for all three antigens were lysine and arginine residues. Although analysis of the binding sites showed that CLF36 were not binding to the active site of HA and NA antigens, this peptide is attached to the M2e site in M2 protein. The proline 10 and glutamic acid 8 amino acides belongs to the M2e region, which has hydrogen bonds with the amino acids arginine 27 and 22 of the CLF36 peptide, respectively. It is hoped that these peptide can be treatment for avian influenza in the future.

Salmonella is a Gram-negative, anaerobic, flagellated bacterium of Salmonella type in Enterobacteriaceae family, which is known as a zoonosis infectious agent. In recent years, different types of antibiotics have been used to overcome the Salmonella infection; however, the increasing number of antibiotic-resistant bacteria, the provision of alternative methods seems be necessary. Specific immunoglobulin Y (IgY) originated from egg yolk causes passive immunity in the fetus, and extracting these antibodies from egg yolk is cheaper and more feasible than other antibodies. Numerous studies have shown that the egg yolk IgY has immunogenic function against a wide range of bacterial and viral infections in mammals. The purpose of this study was to produce specific immunoglobulin Y against Salmonella typhimurium and Salmonella enteritidis bacteria in laying hens.

 In the current study, six pullets were inoculated and boosted with one milliliter of killed Salmonella typhimurium and Salmonella enteritidis. Injections were done fortnightly until one week before egg production. After breast muscle injection of chickens, the eggs were collected, and the IgY was extracted from yolk by the Polson method with polyethylene glycol 6000. The produced IgY was approved by SDS-PAGE method. The specific indirect ELISA done by specificity test for purified IgY also approved the specific IgY against both Salmonella typhimurium and Salmonella enteritidis.

The results of SDS - PAGE demonstrated the presence of two protein bands of 27 and 67 kDa representing light and heavy chains of IgY, respectively. The specific indirect ELISA method proved that the specific IgY against Salmonella typhimurium and Salmonella enteritidis was produced in the egg yolk.    

 It might be possible to administer the egg yolk containing specific IgY against both Salmonella typhimurium and Salmonella enteritidis, to induce passive immunity for preventing some pathogenic diseases in calves such as diarrhea.

High blood pressure is a dangerous risk factor for cardio-vascular disease, including coronary artery disease and strokes. In the human body, a system called renin-angiotensin system regulates blood pressure, in which the angiotensin converting enzyme ACE plays an important role in increasing blood pressure. Angiotensin I as a converting enzyme (ACE) catalyzes the conversion of angiotensin I to vasoconstrictor angiotensin II, and also inactivates the antihypertensive vasodilator bradykinin. Inhibition of ACE mainly results in an overall antihypertensive effect. Peptides derived from food proteins can have angiotensin converting enzyme (ACE) inhibiting properties. Casein protein in milk or other dairy products such as cheese is a rich source of bioactive peptides. Bioactive peptides are inactive in the main protein sequence and are released in during milk digestion or milk fermentation by proteolytic bacteria or hydrolysis by proteolytic enzymes. Many of these peptides have several biological activities. Casein-derived peptides, such as opioid peptides, antihypertensive peptides, casein phosphopeptides and glycomacropeptides have various physiological roles, including adjusting and lowering blood pressure by inhibiting angiotensin converting enzyme (ACE). Caseocinin peptide has been derived from the casein Alpha S1 protein It has an ACE-inhibiting enzyme inhibitor and low blood pressure. The purpose of this study was to identify the alpha S1 protein casein and bioactive peptides of the angiotensin converting enzyme (ACE) inhibitor in human milk and compare it with different species of mammals.

At first, genomic and protein data for eight different species of mammals (cattle, sheep, camels, horses, humans, ewes and pigs) was collected from the National Center for Bioinformatics Information (NCBI). Physico-chemical properties analysis (atomic state, isoelectric point, half-life, hydrophobicity hydrophilicity , barometric and pH) and - Multiple sequence alignment of of alpha-s1 casein and the bioactive peptides of Casokinin in 8 species of mammals was done using CLC Main Workbench 5 software. Then, the prediction of bioactive peptide alpha s1 casein and its three-dimensional structure was done with the help of the online software ACCLUSTER Server, I-TASSER and GalaxyWEB. The simulation of the Molecular interaction (docking) of alpha-s1 casein and the bioactive peptides of Casokinin with angiotensin converting enzyme ACE in the cell was done using ClusPro 2.0 software online.

the results of bioinformatics analysis of human milk protein with other mammals showed that camel milk has the most similar physicochemical properties of milk to humans and can be a good alternative to human milk in feeding children. The highest and least percentage of amino acid sequence amino acids in alpha-sec1 casein in different mammals with humans respectively is related to camel and Goat. The results of the determination of the position and energy of the connection show that the most suitable binding location with maximum energy is related to human and camel milk. Among the bioactive peptides identified and predicted in eight species of mammals, due to having more proline amino acid in Caseocinin peptide, the camel milk is more resistant than other species. Therefore, the antihypertensive effect in camel milk is greater than other mammals. According to the results, it can be predicted that three-dimensional structure of protein and peptides will have a great effect on antihypertensive properties and it causes a good interaction with the active site of the angiotensin converting enzyme (ACE) and thus inhibits the ACE enzyme and lowers blood pressure. Investigating the performance of alpha S1 protein casein and Caseocinin peptide identified for eight different species of mammals And comparing its results with human milk in inhibiting ACE enzyme With Molecular interaction (Docking) Protein's Bioinformatics Software showed that milk of camels after human milk has the highest performance in Reducing the risk factors for cardiovascular disease such as inhibition of angiotensin converting enzyme (ACE) and blood pressure in preventing the development and progression of cardiovascular disease.

the alpha S1 protein casein and Caseocinin peptide have many biological properties and are very important in the health of the body.It can be said that camel milk is the most similar to human-like physico-chemical properties and It can be a good alternative to human milk in feeding children. The bioactive Caseocinin peptide has pharmaceutical compounds that can be used to treat high blood pressure and heart disease. Therefore, this peptide can be used as superbenefit and natural additives, an appropriate replacement to antihypertensive drugs.

Around the world, scientists are looking for new animal protein sources and trying to prioritize the animals with the best conversion rates. One of these animals is Camel. Identification of genetic differences in sequences of Mitochondrial Genome by Bioinformatics Tools is a rapid and confident method for identification and categorizing species. This method is one of the most effective ways of evaluating genetic biodiversity and Phylogenetic relationships in different livestock like Camel. This research was done for sequencing of Ribosomal non-coding RNA gene and comparison of its genetic construction between camelus dromedaries and camelus bactrianus of Iran.

We were collecting blood samples from twenty camelus dromedaries and camelus bactrianus. We extracted DNA at the beginning then 12S rRNA with 1326 pair bases was amplified and sequenced by two pair specific primers.

The Presence of 3 Haplotypes in Bactria camels and one haplotype in Dromedary were proved in the study population. These Haplotypes have two single nucleotide polymorphism (SNP) site in camelus bactrianus and there was not any Nucleotides difference among camelus dromedaries. Phylogeny Tree design with using similar mitochondrial 12S rRNA gene sequencing in other species which are in World Gene Bank.

Phylogeny Analysis and defining, Genetic diversity was showing camelus dromedaries and camelus bactrianus are placing in two different groups and Iranian camelus bactrianus have more Genetic Diversity which indicates more historical evolution of this specie. More information about Genetic diversity among the different generation of Camels can facilitate developing generations revising Programs and is a necessity for protecting from Genetic Resources.

Bovine diarrhea is a common disease among calves that causes significant economic losses in the dairy and meat industry because of increased mortality, treatment costs and reduced growth rates and increasing age at first calving. Bovine rotavirus is one of the main causes of diarrhea in calves at the age of one to two weeks. Both vp4 and vp7 proteins form the outer capsid of the virus, producing antibodies and stimulating the immune system. Camel lactoferrampine-Lactoferrin is a potent antiviral that binds to heparin proteoglycine sulfate, prevents virus entry into the host cell and can replace antiviral drugs. The aim of this study was to investigate the possibility of replacement of camel lactoferrin peptide with antiviral drugs.

In this study, the possibility of replacing six recombinant camel lactoferrin peptides named clf36-1, clf36-2, 12A-36F + BC, A_Scaning, AF, Arm with antiviral drugs and efficient binding of these peptides to Surface proteins of bovine rotavirus (vp4 and vp7) was investigated by molecular dynamics simulation using GROMACS software and they were compared due to their bond-dissociation energy in docking step and amount of electric charge before Neutralizing the electric charge of systems in molecular dynamics and finally the best substituted peptide was selected according to Radius of gyration diagram which is the main determinative factor in system efficiency in vivo and also indicates the possibility of stable binding of recombinant lactoferrin peptide to the virus’ surface protein.

The results of this study indicate that the lactoferrin peptide binds well with the rotavirus’ surface proteins and can thus prevent the virus from entering the cells. However, among the six peptides examined, the 12A-36F + BC peptide in both vp4 and vp7 systems seems to be inefficient in vivo in spite of the highest bond-dissociation energy and the most positive electric charge before Neutralizing the electric charge of systems in molecular dynamics. As being unfold and Rg fluctuation during the simulation. Hence this study expects that recombinant peptide clf36-1 and vp4 system will bind well according to the Radius of gyration diagram.

The results of this study show that the clf36-1 peptide was stable and efficiently bound to vp4 surface protein among the six peptides investigated while retaining its structure during the simulation and in this way it can prevent the virus from entering the cells. So it can be an appropriate alternative to antiviral drugs. However, in vivo experiments are needed to prove the efficacy of this peptide.

Unfortunately, using the antibiotics to treat mastitis is increasing in which leads to undesirable side effects. One of the antibiotics alternatives with high potential are antimicrobial proteins like lactoperoxidase. The aim of this study was to predict the peptides of lactoperoxidase protein and compare them in six different species (human, camel, sheep, goat, buffalo and cattle) and also investigate its antibacterial properties against Staphylococcus aureus and Escherichia coli strains through Molecular docking. The study of physicochemical properties of the lactoperoxidase protein and the derived bioactive peptides has been done using the CLC Main Workbench 5 software. The Swiss-model server was applied to predict the third (three-dimensional) structure of lactoperoxidase protein for camel and human. The peptides of lactoperoxidase protein were predicted and ultimately, the interactions of this protein and its derived peptides with the outer membrane proteins of the mentioned names were survived using ClusPro2.0 online software. The results of the position and energy of bonding assessment using molecular docking show that the most suitable binding location, in which the derived lactoperoxidase protein is bound to the outer membrane proteins of bactria membrane, with the lowest energy, related to cattle and goat, respectively. Bioinformatics study of the seven derived peptides from this protein showed that the third peptide of cattle, goat, buffalo, and sheep has a better performance in binding and degrading the outer membrane protein of these bacteria. These peptides can be proposed as replacement antibiotics for the treatment of mastitis in the future.

 In genomic selection, genetic values of individuals are predicted using genetic markers that are distributed all across the genome and are in linkage disequilibrium with quantitative trait locus. Different methods have been introduced to predict genomic breeding values. These methods take into account different assumptions. Non-parametric methods, including artificial neural networks, have fewer assumptions than parametric methods, and can apply nonlinear relationships in genomic predictions so, in theory these approaches are more robust against genetic architecture changes and are able to provide better predictions.

 In current study, the prediction ability of Bayesian neural networks with different architectures (1 to 5 neurons in the hidden layer) and parametric methods (GBLUP, Bayes RR, Bayes A, Bayes B, Bayes C Bayes L) in four simulated genetic architectures and four real traits of mouse (six weeks weight, growth slope, body mass index and body length) were compared using the correlation coefficient between predicted and expected values, mean square error of prediction and computation time. All simulated genetic architectures were additive and the gene effects followed a normal distribution. The number of QTLs in the first and third genetic architecture was 50 and it was 500 for second and fourth genetic architecture. The heritability of the first and second genetic architectures was 0.3 and the heritability of the third and the fourth genetic architectures was 0.7. The real data consisted of 1,296 mice which were genotyped with 9,265 SNP markers.

 The highest prediction accuracy of Bayesian neural networks were 0.640 (4 neuron in the hidden layer), 0.664 (4 neuron in the hidden layer), 0.800 (1 neuron in the hidden layer) and 0.810 (1 neuron in the hidden layer), and the highest prediction accuracy of parametric methods were 0.711(Bayes B), 0.685 (Bayes A), 0.903(Bayes B) and 0.836 (Bayes B) respectively for one to four simulated genetic architectures. These results showed the superiority of parametric methods to Bayesian neural networks in terms of prediction accuracy in genetic architectures with additive effects. In additive genetic architectures, the allelic effects of genetic variations are independent. In parametric models, these effects are assumed to be independent, therefore in additive genetic architectures can be expected that parametric methods are able to provide better predictions than nonparametric methods.  The maximum predictive abilities of Bayesian neural networks to predict  six weeks weight, growth slope, body mass index and body length were 0.474 (1 neuron in the hidden layer), 0.349 (4 neuron in the hidden layer), 0.154 (1 neuron in the hidden layer) and 0.214 (4 neuron in the hidden layer). The predictive abilities of parametric methods to predict these traits were similar and equal to 0.477, 0.336, 0.170, and 0.221 in average. The results showed that the predictive abilities of Bayesian neural networks and parametric methods were similar on real data as the difference between the best predictive ability of Bayesian neural networks and parametric methods for Six weeks weight, growth slope and body length were less than 1%. The difference was slightly higher for the body mass index and equal to 1.8%. The mean squared error of prediction of Bayesian Neural Networks was slightly less than parametric methods in the simulated genetic architectures. The results indicate a slight superiority of Bayesian neural networks compared to parametric methods in terms of mean squared error of prediction as an indicator of overall fit. The mean square prediction error is an appropriate criterion for evaluating the prediction performance of different methods because it contains both accuracy and bias. Considering table (3) and table (5), it can be concluded that the prediction of the Bayesian neural network are less accurate but more unbiased than the parametric methods. This could be due to more applied penalty in parametric methods compared to Bayesian neural networks, which can lead to an increase in the average mean squared error of prediction. In real data, the mean squared error of prediction of the Bayesian neural networks and parametric methods were similar. The computation time of Bayesian neural networks was increased with an increase in the number of neurons in the hidden layer. The computation time of the parametric methods was the same with the exception of GBLUP. The GBLUP method took more computation time. The computation time of neural the networks with 1 to 2 neurons in the hidden layer were less than GBLUP. Genomic prediction using Bayesian Neural Networks with a greater number of neurons is really challenging, and improving their performance in terms of computational cost is necessary before applying them in genomic selection.

 Although parametric methods had better predictive accuracy and predictive ability due to the additive genetic architecture of the studied traits, it can be concluded that Bayesian neural networks are powerful tools in genomic enabled prediction that can predict genomic breeding values with acceptable accuracy. The genomic prediction ability of the neural networks depends on target traits, the animal species, and neural network architecture. Before using Bayesian neural networks in genomic prediction, it is better to compare the results with parametric methods. It is also necessary to improve the computation time of the Bayesian neural networks with a greater number of neurons in hidden layer before applying them in real application of genomic selection.

Processes of muscle development and lipid metabolism that plays important roles during fetal growth and development stages, are different in thin- and fat-tailed sheep breeds. Therefore, in order to have a better perception of differentially expressed genes and their pathways in ovine prenatal muscle tissue , the gene expression data from muscle tissue of two thin- and fat-tailed breeds of sheep derived from the gene expression array experiment (Access number: GSE23563) were analyzed. The LIMMA package in R used to identify 691, 410, 404, 290 and 155 differentially expressed genes at 70, 85, 100, 120, and 135 days from gestation, respectively.Also,identification of significant gene clusters was performed for each fetal stage using Cytoscape. Finally,13 genes were recognized as differentially expressed at all 5 stages of sampling; among them, EEF1A2, ITGAM,NINL and RPL39 were confirmed as genes related to fetal weight, involved in the muscle development and lipid metabolism regulation.Also Gene Ontology and KEGG pathway analysis for differentially expressed genes by DAVID led to identification of significant processes and pathways associated with myogenesis, lipid metabolism and nervous and immune system in the developing muscle tissue transcriptome. The results of this study could provide supplementary information revealing genes with significant impact on the formation of muscle and fat tissues during fetal development and also the pathways involved in these biological processes.These genes might provide some evidence on DNA markers associated with some economic traits including birth weight,carcass and meat quality traits in sheep which can be applied in selection and breeding programs.

In spite of the importance of fertility in different species, there has been little success dissecting the levels of OMICS. To better understand the molecular basis of fertility, we study transcriptome profiling of different tissues.   Materials and methods  liver, muscle, endometrium and corpus luteum tissues between cows with either good or poor genetic merit for fertility using RNA-Seq data sets. We first compiled a master list of genes related to corpus luteum that change with level of fertility and then reconstructed the network.  

A few genes were identified in liver, muscle and endometrium between high and low fertile cows but in corpus luteum circumstance was different. 264 genes and 6 key modules were disclosed through clustering for mRNA master list for corpus luteum. All these genes, being involved in at least one of the biological process, namely proteolysis, actin cytoskeleton organization, immune system process, biological adhesion, cell differentiation and lipid metabolic process, have an overexpression pattern (P < 0.01).

Finally, the identification of genes and the construction of their regulatory networks may give new insights into biological procedures. As well as, this study increases our understanding of the contribution of different tissues transcriptome to phenotypic fertility in dairy cattle.

The objective of this study was to evaluate the performance of genomic selection for milk yield, fat percent and protein percent in Najdi cattle breed from station and Agmari herds using different statistical models. Traditional estimated breeding values obtained with a random regression model using pedigree and phenotypic information for each trait from 1990 to 2016 were used as response variables. Predictability was evaluated by using a 10 replicated Training-Testing scheme and considering four models including genomic best linear unbiased prediction scaled with observed allele frequency (GBLUP), and allele frequency of 0.5 (G05BLUP), BayesA and BayesB. The results showed that GBLUP had better performance than G05BLUP for milk yield (0.411 vs 0.385), but performance of G05BLUP was better for fat percent (0.257 vs 0.302) and protein percent (0.363 vs 0.388). The accuracy of breeding values of milk yield decrease to 0.371 and 0.353, and accuracy of fat percent increased to 0.329 and 0.314 with BayesA and BayesB, respectively. Bayesian methods had same accuracy as GBLUPs for protein percent. Across traits and methods BayesA with 0.14 for protein percent, and G05BLUP with 0.71 for milk yield had smallest and highest bias as deviate from 1, respectively. Accuracy of prediction using Agmariherds in addition station herd increased 0.01 to 0.09 depending on method and trait, but also bias were more than before. In conclusion, accuracy of genomic prediction of milk traits in Najdi cattle breed are moderate but suitable considering small size of population which makes genomic selection feasible in this breed.

In the past decade, many performance traits in chickens have greatly improved to meet the growing demand for chicken meat. On the other hand, due to the 70% share of feed costs in the total cost of livestock production, feed efficiency has become one of the most important genetic traits in livestock and poultry. Residual feed intake (RFI) is the difference between the actual absorption of animal feed and the expected of the animal absorption based on body weight and its level of performance. Selection to improve feed efficiency through RFI is suggested due to its phenotypic independence from body weight and body weight gain. There is evidence for the genetic basis of variation in productivity in all species. Previous studies have shown that some genes may play an important role in controlling RFI through effects on the digestive system and metabolic processes. It seems that changes in the amount of residual feed intake is the result of changes in the expression of the genes associated with it, and the study of transcript changes in chickens with high RFI helps to identify the mechanisms that affect it. Experiments were conducted on Commercial breeds (high production efficiency) and Isfahan Native Chickens (low production efficiency). From each breed, 60 chicks were harvested and caged from day 24 to 42 days for 19 days. The chicks of both groups were raised under the same management conditions. In order to measure the residual feed intake of each bird in individual cages and daily intake (FI) of the amount of feed consumed in 19 d (from day 24 to 42) divided by number of days, and daily gain (DG) of the weight difference 24. Using these figures, the amount of residual feed consumed will be calculated. Ten samples of liver tissue were then collected from each breed and immediately transferred to liquid nitrogen and transferred to the laboratory for total RNA extraction. Two pooled samples of every breed (each consisting of three extracted RNA sample) were prepared. Prior to Alignment, the quality of the raw readings sequence was evaluated using the Fastqc software. The reference genome for the chicken (Galgal4) and the annotated file were obtained from the Ensembl database. After controlling the quality and Trimming the reads, the Hisat2 software was used to mapping obtain reads from the genome of the reference. Analysis of differential gene expression was performed using Cufflinks.. To identify different isoform of the gene and to measure the expression of isoform, it is necessary to examine the position of microwave splicing between the exons. Cuff compare compares the transcripts that are assembled with a reference genome and categorizes each transcript into known, new, and potential new isoform. The phenotypic results showed that the difference in the mean RFI values between the native (+13.430±5.393 g/day) and commercial (-11.212±4.435g/day) chickens was highly significant (P<0.001). About 83% of the sequenced fragments were matched to the reference genome and Duplex analysis of gene expression was performed..Differential expression analysis for more than 45070 isoform Related to 19003 genes using Cuffdiff showed that 28949 and 16121 isoform were up- and down-regulated (adjusted P≤0.05) in the native breed, respectively. 206 Isoform was identified as a change in expression between the native and commercial chickens. Moreover 21081 novel isoform were identified which have not been included in the gene annotation so far. Moreover, the functional enrichment analysis showed that the down-regulated isoform in the native chickens were mainly involved in the different response to stress،response to oxygen-containing compound،response to cytokine،response to nutrient،response to lipid،animal organ development ،single-organism biosynthetic process،regulation of multi-organism process response to nutrient level and lipid biosynthetic process. The Differentially Expressed Genes and their isoform explored between the chickens of the two breeds led to the identification of some important candidate genes for further breed improvement programs, including RSAD2, IL15, EGR1, and DUSP16. These genes could be related to the higher RFI of the native. Our findings showed that a large number of related genes with metabolism (fat, amino acids, carbohydrates, and vitamins), growth, as well as oxidative stress and immunity, can make a difference in the RFI. Identification of the difference genes and their isoform between two breeds of chickens led to the identification of important candidate genes for breeding programs, including RSAD2, IL15, EGR1 and DUSP16.

Streptococcus bovis has been considered to be one of the starch utilizers and lactate producers in the rumen. By considering the role of S. bovis as main lactic acid producer, a large amount of biological information about this strain has been published. But there has not been a systematic analysis of metabolic capabilities for S. bovis so far. In the present study, the first genome-scale metabolic model of S. bovis (iStr472) was reconstructed based on the genome annotation of S. bovis B315. The model was analyzed in terms of sensitivity, topology and capabilities for utilization of other substrates. Results revealed that iStr472 comprises 694 reactions, 626 metabolites and 472 genes. The majority of reactions were located on the nucleotides metabolic pathway. The metabolic genes of model estimated as 27.6 % of all coding genes. Comparison of two models (iStr472 and ModelSEED) indicated that iStr472 has a higher accuracy and validity than the ModelSEED. The 16 highly connected metabolites were found in the model. The results of reaction deletion presented that the model has 126 vital reactions essential for the organism's growth. According to the model prediction, production of biomass was inversely influenced by lactate production. The iStr472 is also capable of utilizing fructose as carbon source. Taken together, it would be possible to use the predictions of iStr472 as a tool for better understanding the metabolism and metabolic engineering of S. bovis for reduced lactate production in the rumen.

Generally, the causes of mastitis classified into two types of infectious factores ( eg Staphylococcus aureus ) and environmental factors such as ( Escherichia coli ). The common method to treat this disease is to use antibiotics Which can cause problems related to human health. the Peptides created in the laboratory or In living organisms from incomplete digestion of proteins and have a specific biological function called bioactive peptides. Casein contains antibacterial peptides called israchidine, Which by destroying the cell membrane or mitochondria membrane, It causes the destruction of bacterial cells. The purpose of this study, was to identify the protein and bioactive anti-bacterial peptides of alpha-s1 casein in eight different species of mammals and Comparison of the antibacterial properties of these peptides in these eight species of mammals against two major bacteria producing Staphylococcus aureus and Escherichia coli. first, genomic and protein data for eight different species of mammals ( cattle , sheep , camels, horses , humans , ewes and pigs ) was collected from the National Center for Bioinformatics Information Center ( NCBI ) And then, The prediction of bioactive peptide alpha s1 casein and its three-dimensional structure was done with the help of the online software ACCLUSTERServer, I-TASSER and Galaxy WEB. In order to evaluate protein and peptide stability under dynamic conditions ( intracellular conditions ), 3Drefine and YASARA software were used. Finally, the simulation of the interaction ( docking ) of alpha-s1 casein and the bioactive peptides of israchidine with mastitis producing bacteria inside the cell was done using ClusPro 2.0 software online. Bioinformatics analysis on The molecular interaction of this protein and its bioactive peptides in eight different species of mammals with surface proteins in the membrane of two major mastitis producing bacteria shows that milk " sheep and pig " has the highest performance in destroying Staphylococcus bacteria , " Human and ewes "also have the best performance against Escherichia coli and prevent mastitis ( mastitis ). Therefore, it seems that israchidine peptides can be used as natural factors and antibiotic substitute materials to reduce the destructive effects of mastitis on human health through the possibility of transferring resistant bacterial strains to antibiotics from livestock to humans and also increase the quality of milk consumed ( reducing the number of body cells in milk , increasing milk production and less damage to Mustache ).

The aim of this study was to investigate the antibacterial effect of the recombinant camel Lactoferrampin-Lactoferricin on the growth rate of Staphylococcus aureus bacteria, one of the causes of mastitis in dairy cows. This peptide, which was prepared through a previous study in Biotechnology Laboratory of Animal Science Department, Faculty of Agriculture, Ferdowsi University of Mashhad. Antibacterial effects of this peptide was assessed by Count Colonies on Methicillin-resistant Staphylococcus aureus )PTCC 1764( and Staphylococcus aureus )ATCC 25923(. Heat resistance properties and freeze drying process of the peptide were evaluated by disk diffusion method in triplicate. The results showed that this recombinant peptide had an antibacterial effect on Staphylococcus aureus (p<0/0001), but had no effect on methicillin-resistant Staphylococcus aureus. Heat resistant of the recombinant peptide also showed that 100 °C temperature for 40 minutes had no significant effect on the anti-bacterial properties of this protein (p<0/0001). This protein showed no loss of activity after freeze drying process. The results obtained from this study proved the stable activity of natural peptides as well as antibacterial properties. This recombinant peptide can be used as an alternative to antibiotics or a therapeutic supplement to cure mastitis in dairy
cows.

Introduction Native chicken breeds are important genetic resource and well adapted to the local environmental conditions. However, growth rate and feed efficiency of these breeds are not appropriate. On the other hand modern broilers grow faster and offer a higher nutritional efficiency than the indigenous chicken breeds. This advantage is the result of the severe genetic selection programs, which were designed to increase production. In this study, a systematic identification of mitoProteome genes and new pathways related to growth rate of pectoralis muscle in chicken has been made using gene expression profiles of two distinct breeds: Isfahan native, a slow-growing Iranian breed possessing low growth rate and Ross 708, a commercial fast-growing broiler line.
Materials and Methods All the birds were reared under the same management, environmental and nutritional conditions. The diet was the same throughout the whole experiment and formulated to contain 20% CP and 3000 kcal ME/kg. The birds received feed and water freely (ad libitum). On day 28 post-hatch, six birds were randomly selected from each breed, weighed and sacrificed. From each bird, 1 to 2 g of tissue was excised from the posterior region of the left pectoralis major muscle. Total RNA was isolated from breast muscle samples. Using Truseq Stranded RNA Prep kit (Illumina), each sample was converted to a uniquely indexed cDNA library, and the resulting cDNA libraries were pooled and sequenced on an Illumina Hiseq 2000 sequencer. An average of 70 million paired end reads (150 bp) were produced from all sample, 70% of which were properly mapped to the reference genome (EnsemblGalgal4). We analyzed the sequence data using bioinformatics tools Hisat2 and Cufflinks. Using Hisat2 aligner, more than 72% of clean reads (in average) were mapped back to the Galgal4 reference genome. In addition, about 90% of reads were aligned concordantly.
Results and Discussion On the first day after hatching, the weight of commercial chicks were heavier than native. This process continued until the end of the test, 28 days. The commercial chickens have a heavier weight, higher growth rate, and lower feed conversion rates than native chickens. The RNA-Seq of four muscle samples yielded around 131, 590, 636 million of raw 150 bp paired end reads, of which 94, 483, 431 and 37, 107, 205 reads were for native and commercial breeds, respectively. We identified 606 differentially expressed genes (DEGs) between two breeds with at least 2-fold differences (P-adjusted (Benjamini) ≤ 0. 05, log2FC ≥ 2). Of these, 249 and 357 genes were up-regulated in native and commercial broilers, respectively. In the native chickens, FoxO3 transcription factor activated the atrophy pathway related to E3 ubiquitin ligases and led to increased proteolysis and reduced the skeletal muscle size as compared to the commercial broilers. Hypoxia and regulation of the metabolic process of the reactive oxygen species (ROS) were among the most important significant biological processes in native chickens. The analysis of the genes associated with the mitoProteome revealed significant changes in the expression of many genes involved in transcription regulation and growth. Also the increased expression of FoxO3 gene and the releasing of amino acids caused by the degradation of proteins, increased the expression of amino acid catabolism enzyme's (such as MCCC2 and TDH), as well increased expression of pyruvate dehydrogenase kinases (PDK4 and PDK3). This led to reducing of the aerobic oxidation of pyruvate and increasing gluconeogenesis. Increasing the UCP3 gene expression in native chickens can partly reduce mitochondrial efficiency and inappropriate feed conversion ratio compared to commercial chickens. These changes were also reflective of a complicated adaptation program that facilitates proteolysis and reduces oxidative metabolism of glucose and pyruvate in the muscles. These metabolic pathways have evolved to reduce the requirements of indigenous chickens and increase the ability of these strains to overcome the circumstances and environmental stress and resist nutritional deficits.
Conclusion Our results suggested that different expression patterns of some genes including SGK1, FBXO32, FBX030, IRS2 ، SP3, CUL, PIK3IP1 and FoxO3 in native breed might represent a cause for the poor growth performance for this breed than commercial breed. Hence, evaluation of native chicken based on these candidate genes would accelerate the efficient native chicken breed in near future. These results expand our knowledge of the genes transcribed in the breast muscle of two breeds and provide a basis for future research of the molecular mechanisms underlying the chicken breed differences.

Brucella is gram-negative intracellular bacterial pathogens of both humans and animals. Among the six recognized Brucella species, Brucella melitensis is the main etiologic agent involved in ovine and caprine brucellosis and is also the most pathogenic species of humans. We amplified by specific primers, two of the best outer membrane antigens Omp31 and Omp25 for this disease, and the construction of recombinant chimeric Omp31-Omp25 combination of them, with using the (EAAAK)2 linker. The sequence analysis results showed that strain Rev1 of melitensis for Omp25 antigen has most homology with the strains melitensis M16 and also Omp31 antigen showed the most homology with of B. Ovis melitensis species. Then recombinant chimera Omp31-Omp25 was cloned into Pet32a vector and transform into BL21 (DE3) host cell for expression

This experiment was conducted to investigate and identify the isoforms related to the structure of muscular proteins between Isfahani native and Ross commercial chickens with different growth rates. We extracted total RNA from breast muscle samples of two groups at end of 4 weeks of age. After paired-end sequencing of samples using the Illumina Hiseq 2000 platform, Hisat2 was applied to align clean reads to chicken reference genome. Then, Cufflinks package was used to assemble transcripts and identify significantly differentially expressed genes. The statistical comparison of the isoforms between two groups revealed 259 isoforms with significant difference in expression, of which 161 isoforms were up-regulated and 98 isoforms were downregulated in commercial chickens. Among the commercial chicken isoforms, four genes (ACTC1, ATF3, CYR61 and FABP4) were upregulated with two different isoforms. In addition, in commercial chicks, the frequency of isoforms associated with slow contraction fibers was greater than that of rapid contraction fibers. Functional study showed that the isoforms in commercial chickens were more related to cell proliferation and differentiation, hypertrophy growth and biosynthesis of muscle proteins, whereas in native chickens, mainly they were associated to immune processes, carriers of ions and metals, binding to metals, DNA and RNA, and factors contributing to degradation of muscle proteins. The results of this study showed that such changes may have been able to strengthen the ability to maintain and overcome the severe environmental and nutritional conditions during the developmental period of the chicken by reducing the level of requirements and enhancing immunity and adaptability in native chicken.

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.