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Introduction:Manganese is an essential trace element that acts as an activating component of many crucial enzymes such as alginase and pyruvate carboxylase. It is involved in carbohydrate, lipid, and protein metabolism, as well as in vital biochemical reactions (Hassan et al., 2020). Additionally, manganese serves as a cofactor in the synthesis of chondroitin sulfate and plays a significant role in bone formation in broiler chickens (Mwangi et al., 2019). Moreover, manganese is vital for the antioxidant and immune systems of animals (Patra and Lalhriatpuii, 2020; Wang et al., 2018). In the production of broiler chickens, manganese sources commonly used include inorganic Mn (Mn sulfate, Mn carbonate and Mn oxide) and organic Mn (Mn chelated with amino acid and protein). Inorganic sources of manganese are cheaper, although they have low digestibility (Tufarelli and Laudadio, 2017; Yenice et al., 2015). Organic sources have excellent chemical stability and high absorption efficiency. They have not been widely used in poultry diet due to different quality levels of manufactured products, unpredictable effects and high cost (Tufarelli and Laudadio, 2017; Brooks et al., 2012). Therefore, it is important to assess new sources of manganese that have higher digestibility and lower cost. Manganese hydroxychloride is a group of minerals which solubility in water is minimal, but it becomes more soluble in acidic conditions in intestine (Wang et al., 2011). The purpose of this experiment was to investigate the different levels and sources of manganese in the diet of broiler chickens by investigating their effects on growth performance, immunity, the digestibility of different sources in different solvents, and the digestibility using the technique of Everted Gut Sacs.Materials and Methods: Manganese sulfate, organic manganese, and manganese Hydroxychloride were obtained from Ariana company. In order to measurement of the amount of dry matter and ash, one gram in four repetitions was sampled from each of the sources. They were dried at 105°C for 12 hours and dry matter was calculated through subtraction. Then samples were transferred to the oven at 550°C for 16 hours and their ash content was determined. Finally, they were digested in hydrochloric acid and passed through Whatman filter paper No. 42. After making up to volume with mili-Q water, they were read by an atomic absorption device at a wavelength of 520 to 560 nm (AOAC, 1995; Williams, 1972). In order to evaluate the solubility, three samples (0.1 g) were prepared and dissolved in 100 ml of 2% citric acid, 0.4% hydrochloric acid and deionized water (Watson et al., 1970). For assessment ability to absorb minerals by the technique of Everted Gut Sacs, 180 one-day-old broilers of the Ross 308 commercial strain were fed from one to twenty-one days old with corn and soybean based (2018). On the 22nd day to the 28th day, they were fed with a diet free of manganese and on 29th day, they were starved for one day and night. Chickens were grouped into three treatments with Hydroxychloride, organic and manganese sulfate sources with 6 replications and 10 pieces per replication. Three parts were selected from each replication for the test steps (Feng et al., 2006). Samples prepared from jejunum and ileum in two buffers, Mis-Krebs and Tris-Krebs. In order to determine the relative bioavailability of different manganese sources, an experiment was conducted with 12 treatments included four different levels of manganese (35, 70, 105 and 140 mg/kg) with three different sources including Hydroxychloride, organic and sulfate.Results and Discussion: The highest amount of dry matter of manganese was related to manganese sulfate (99.23%). The lowest was manganese hydroxychloride (92.58%). The highest ash percentage was related to manganese hydroxychloride with 86.14% and the lowest was related to organic manganese with 21.56%. The amount of manganese calculated after testing organic sources, hydroxychloride and sulfate was 5.64, 34.64 and 34.47% respectively. The organic form of manganese had the highest solubility in 2% citric acid and the lowest in deionized water with 96.12 and 34.14%, respectively. Manganese hydroxychloride also had the highest solubility in 2% citric acid solution. Manganese sulfate had the highest solubility in hydrochloric acid and the lowest solubility in deionized water. In general, manganese sulfate had the highest solubility in deionized water compared to the other two sources. Also, the highest solubility of organic manganese in 2% citric acid was 96.12% in the whole experiment. It has been reported in studies that binding minerals with proteins will be a weak chelate and when they are placed in solvents, their chelate breaks easily and dissolve (Cao et al., 2000). The results related to performance traits and primary and secondary response of antibody titer against sheep red blood cells (SRBC) showed that experimental treatments had no significant effect on them. Conclusion: The results showed that the highest solubility of the organic form of manganese was in citric acid (96.12%) and the lowest was in deionized water (34.13%). Manganese hydroxychloride had the highest solubility in 2% citric acid, while manganese sulfate had the highest solubility in 0.4% hydrochloric acid. Overall, manganese exhibited the highest solubility in hydrochloric acid and the lowest in deionized water. The results of the technique of inverted intestinal segments showed that the most absorption of manganese occurs in the ileum, and these results were in line with the results of other researchers who had performed this experiment in vitro and in vivo Among the experimental treatments, the highest absorption in the technique of inverted intestinal segments was related to the organic source of manganese, and the lowest was related to the form of sulfate, 3.25% and 1.99%, respectively. At the end, the use of organic manganese in broiler diet is recommended due to its high absorption level.

Introduction :Ascites syndrome, as a metabolic disorder, is one of the most non-infectious causes of death in the old age of breeding in the poultry industry, which causes annual losses of over one hundred million dollars and is an important economic concern. The growth rate of broiler and their high need for oxygen causes an increase in pumping, followed by heart failure, and heart failure is often associated with other diseases. Due to the relationship between the heart and the kidney, chronic heart failure leads to a decrease in filtered blood volume and a decrease in kidney function, which over time causes permanent damage to the kidneys. lncRNAs play important roles in a variety of different mechanisms related to cellular homeostasis and in a wide range of pathophysiological processes and pathogenesis of many diseases, including cardiovascular disorders, respiratory and kidney diseases, preliminary studies in human samples show shows that lncRNAs are strongly involved in the development and disease of the kidney. For this reason, the lncRNAs obtained from the RNA-seq data of the kidney tissue were investigated in the occurrence of ascites.Materials and Methods :700 one-day-old chicks from one of the paternal lines of a commercial strain were kept under standard conditions until 21 days old. On the 21st day of the breeding period, cold stress (24 degrees Celsius) began and continued until the age of 48 days. After applying cold stress, the birds with ascites symptoms were grouped in the Ascites group and the rest in the Healthy group. On the 39th day of the breeding period, 70 slaughtered birds and kidney tissue samples from each bird were immediately transferred to the liquid nitrogen tank after separation. 16 ascites birds and 16 healthy birds were used for RNA extraction. Total RNA extraction was done individually using trizol (YTzol) solution, and then an equal amount of RNA from four tissue samples was combined and then cDNA was prepared from 4 ascites tissue samples and 4 healthy tissue samples. All small RNAs, such as rRNAs, tRNAs, etc., were removed by dt oligo beads, and finally, all mRNAs were used to prepare the library. Novagen company was used for sequencing using Illumine hiseq 2500 technology and paired-end reads. Several software such as hisat2, cufflinks, stringtie, cuffmerge and cuffdiff were used for mapping, aligning and analysis of gene expression differences. In order to extract coding and non-coding genes, FEELnc software was used with default settings. Potential target genes of lncRNAs were investigated by searching for protein coding genes located within 100 kb upstream and downstream of each lncRNA. In the following, a positive and negative correlation of 90% was obtained between two groups of coding and non-coding genes based on the degree of expression change. In order to investigate the metabolic, structural and functional pathways of significant genes, the Enrichr database, which is connected with other databases such as KEGG, was used.Results and Discussion:In the current research, a total of eight samples produced 187640642 million paired reads with a size of 150 nucleotides and after quality control, 185258819 uncontaminated reads were obtained. The number of 1421 lncRNA transcripts related to 921 gene loci and 154 related target genes were identified in the comparison between ascites and healthy birds. Then, this number of genes were identified (154 genes) in order to check their functional characteristics using the Enrichr database, five functional pathways Glycine, serine and threonine metabolism, Rap1 signaling pathway, Sphingolipid metabolism, Phosphatidylinositolsignaling system, Mucin type O-glycan biosynthesis and related genes were significant. Out of 13 significant lncRNAs in these biological pathways, 12 are located on the antisense direction and one is located on the sense direction. In addition, 9 lncRNAs are exonic, 3 intronic and 1 in downstream position. These pathways are activated as damage modifiers in hypoxic conditions caused by ascites and provide the required energy and maintain kidney homeostasis in response to oxygen tension caused by ascites. On the other hand, they act as cell survival, increase proliferation and anti-apoptosis, which on the one hand reduce kidney damage and on the other hand make it function better, and in this way, reduce complications caused by ascites kidney damage.Conclusion: Therefore, by targeting the important pathways of biology obtained and the genes affecting them for the prevention and treatment of ascites disease, it will provide a new insight for breeding.

Introduction: 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.Materials and Methods: 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.Results and Discussion: 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.Conclusion: 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.

Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.Materials and Methods: The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.Results and Discussion: The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.Conclusion: The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved.

Introduction: 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. Materials and Methods: 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. Results and Discussion: 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. Func­tional 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. Conclusion: 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.

[1]Introduction: Poultry and meat products are the largest sources of non-typhoid salmonella infections in most countries. Studies have shown that raw foods of animal origin, especially poultry and its products, are the main source of contamination of kitchens and restaurants. In terms of growth conditions, these microorganisms are resilient bacteria and easily adapt to their environmental conditions. Salmonella has been known to cause intestinal disease for many years and has been reported as the most important cause of food poisoning. According to Iranian and international standards, there should be no S. enteritidis or S. typhimurium in 25 grams of food. DNA-based methods for the identification and differentiation of Salmonella serovars have been designed and applied using specific primers at the genus and serovar levels. Therefore, they can be used as useful and rapid screening tests, as well as to supplement or replace conventional biochemical and serological tests. Real-time PCR, with the most accurate and reliable results using a fluorescence probe, which of course has a high cost. In this method, sequence specific fluorescence probes are used, and as a result, in the target molecule, screening and determination the presence or even the concentration of specific sequences is possible. Therefore, even in the presence of other types of nucleic acid molecules, the results are obtained quickly and have a high level of specificity. Under these conditions, if specific probes with different florescence dyes are used, even multiple targets can be detected in a single PCR reaction. The aim of this study was to identify S. enteritidis or S. typhimurium by PCR and Salmonella spp. by real time PCR method in poultry products. Material and Method: In total, 45 samples of poultry products, including chicken breast, liver and gizzard (15 samples each) were purchased from different regions of Mashhad and from various companies and transferred to the laboratory in accordance with hygienic standards. For each sample, 25 g of tissue was isolated and homogenized under sterile conditions and DNA extraction was then performed using a DNA extraction kit. The extracted DNA was evaluated by agarose gel electrophoresis. The purity and quantity of DNA extracted from each sample was examined by spectrophotometry method. In the next step, in order to identify the genus Salmonella, the samples were examined by real time PCR. In this method we used an internal control to ensure that negative results are not false negative due to inhibitors. The results of real time PCR showed that out of 45 samples, nine samples were infected with Salmonella. Then, these nine samples were evaluated for Salmonella typhimurium and Salmonella enteritidis infection by conventional PCR method. Result and Discussion: The results showed that out of nine samples that were positive in real time PCR test, seven samples were contaminated with Salmonella typhimurium, of which five samples were related to chicken breast and two to liver. Regarding Salmonella enteritidis infection, out of nine samples, only one sample was contaminated, which was related to chicken breast. Conventional methods have been traditionally used to enumerate target bacteria in food. However, these methods have some limitations and require considerable time and labor. Previous studies have already shown that real time PCR is more effective than conventional bacteriological methods for the detection of Salmonella spp. In a study by Whyte et al. (2002) The presence of Salmonella was assessed by traditional culture methods and by a Salmonella-specific polymerase chain reaction (PCR) test. Salmonella was recovered from 16% of samples using traditional culture methods. In contrast, the PCR assay proved to be more sensitive and detected Salmonella DNA in 19% of the examined samples (Whyte et al. 2002). Results of PCR with specific primers showed that reactions in real time PCR with general primers of Salmonella spp. were done correctly. Despite of accuracy and speed of real time PCR to detect DNA of microorganisms, further studies are developed to have more advantages. Loop-mediated isothermal amplification (LAMP) showed a higher sensitivity of Salmonella detection in compare to qPCR (Vichaibun & Kanchanaphum, 2020). Although LAMP could detect trace amount of Salmonella DNA but primer design for this reaction is very difficult. However, it is important to highlight that non-viable cells can be detected by real time PCR or other DNA-based methods, which does not occur in traditional methods of culture and isolation that require viable cells for quantification (Zeng et al., 2016).

Introduction: Cow's milk is one of the most important animal products for any country and known as an important source for fat and protein originated from animals (Fenelon and Guinee, 1999, Martini et al., 2016). Milk fat has a high impact on taste of milk and other dairy products (Spelman et al., 1996). The liver in ruminant animals including dairy cows plays an important role in the metabolism of carbohydrates, fats, vitamins, hormones, and etc. The absorbed nutrients pass through the liver from the gastrointestinal tract and enter the blood circulation system, and eventually enter the mammary glands of dairy cows. Therefore, the liver plays an essential role in cow lactation (Graber et al., 2010 and Schlegel et al. 2012). All of the components that determine milk quality can be considered as quantitative traits that are controlled by many genes and are influenced by environmental factors. If genetic markers can explain a significant part of the variation, they can be considered as ideal candidates for genomic selection (Shi etal. 2019). Previously, microsatellite markers were frequently used to identify quantitative trait locus (QTL). With the progress of science, the advent of the single-nucleotide polymorphisms (SNP) are used in genome-wide association studies (GWAS) to identify QTL. In dairy cows, some of the major genes with significant effects on milk fat have been identified in previous GWAS studies. Therefore, with the existence of a large number of GWAS in dairy cows, these studies can be combined using meta-analysis to achieve higher power results. These studies contribute to our current understanding of the genetic regulation of milk fat yield traits. This approach provides a better understanding of the genetic architecture of complex traits. The network clustering algorithm and cluster identification are important tools in the structural analysis of networks. Various types of clustering algorithms are used for protein-protein interactions (PPIs) networks analysis. In this study, we used an algorithm known as MCODE to identify dense regions in the PPIs diagram (Bader and Hogue, 2003). The overall purpose of PPIs network clustering is grouping of genes or proteins that according to various scales are related to each other. The network of PPIs contains different proteins important in different pathways. These genes or proteins are clustered based on the similarity of metric and are known as matrix distances. It is also important to predict molecular assemblies of protein interaction data because it provides another level of functional annotation (Gollapalli et al., 2015). The purpose of this study was to conduct a meta-analysis of GWAS in cluster analysis to identify genes that are effective in milk fat yield in dairy cows. Material and methods: In this study, the data used were GWAS summary data. All data were collected from 19 published studies from 2010 to 2019. This research included main papers and dissertation (valid dissertations with published papers). All available genes were combined, synthesized, and evaluated using a meta-analysis method. The Cytoscape v3.7.2 software was used to analyze and visualize the genes examined by the STRING v1.5.0 plugin and to extract clusters from the MCODE v1.5.1 algorithm. Therefore, the results of the GWAS summary data were combined in molecular networks with PPIs, which have a significant role in increasing the association studies power to identify genes affecting milk fat trait. Also, the DAVID server was used to identify the gene ontology (GO) term enrichment in order to detect enriched biological terms associated with genomic regions and to identify gene networks using functional annotation clustering tools based on enriched pathways analysis. Results and discussion: In this study, we analyzed 223 genes using the STRING plugin in Cytoscape software. These genes were associated with at least another gene and had a direct and partial correlation with each other. In the gene network, the correlation created for milk fat yield trait included 213 genes or nodes and 219 edges (gene connection). The P-value calculated in the STRING network was statistically significant for enriched pathways in PPIs ( ). The collection of important and popular genes were evaluated using the MCODE plugin. Seven clusters were identified and grouped in this network. For instance, proteins in cluster 1 included: ARHGAP39, CPSF1, CYHR1, PPP1R16A, GRINA, MROH1, and SMPD5 genes. As shown in Table 2, cluster 1 (score=7) was connected with 7 node density to 21 nodes. This cluster showed proteins that play important roles in the internal space of the endoplasmic reticulum (cellular components), metal ion binding (molecular function), and integral to the membrane (cellular components). CPSF1, CYHR1, and GRINA were the major genes involved in the internal space of endoplasmic reticulum, metal ion binding, and membrane integral, respectively. It was found that clusters 1 and 2 have the highest score between all reported clusters. Conclusion: These results show that using data from different sources can increase the reliability and accuracy of GWAS studies. We were able to identify the most important genes in the network pathways using the GWAS summary data in cluster analysis. This method determines the quality of proteins involved in fat yield while facilitating our understanding of the molecular structures of proteins. The most important genes with high scores were identified in cluster one (ARHGAP39, CPSF1, CYHR1, PPP1R16A, GRINA, MROH1, and SMPD5) and two (HERC1, UBR4, ASB17, TRIM9, KLHL2, and BTRC). These clusters based on existing biological knowledge can help data mining and system models understand network interactions and pathways. These protein clusters provide a deep insight into how genes interact with each other in network analysis for fat yield. Moreover, it was observed that meta-analysis of GWAS summary data can play an important role in the wide understanding of network visualization and cluster analysis of identified genes in enriched pathways. Therefore, cluster analysis can improve the identified genes power for economically important traits such as milk fat yield in a population of dairy cows and can be used in future genomic evaluations and breeding programs.

Objective Due to high cytotoxicity effect, ribonucleases (RNases) are known as pharmacological agents with therapeutic potential. The high potential of these enzymes in the destruction of RNA strand and their other substrates and subsequently, cell destruction or cessation of cell division causes a very high cytotoxic effect of this enzyme in various cancer cells. Hence, this review investigates the therapeutic applications of ribonucleases, cell pathways and their mode of action as cytotoxic agents in order to pay attention to them in researches related to the health and therapy fields. Materials and methods In this study the keywords such as cancer, ribonuclease, ribonuclease inhibitor and RNA were used to search in databases including Scopus, SID, IranDoc, PubMed, Google Scholar, Web of Science and IranMedex. In order to select the documents used, all articles published in non-English and Persian languages, duplicate articles, articles that could not be accessed to the full text, as well as articles that were presented as abstracts were removed. Finally, the selected cases were thoroughly studied and summarized in order to prepare the current review. Results The study and review of research conducted showed that ribonucleases have the ability to kill tumor cells and that these enzymes have antiviral properties. Bovine pancreatic ribonuclease (RNase A), bovine seminal ribonuclease (BS-RNase), Onconase, and angiogenin are known as RNases with high antitumor activity which exert cytotoxic activity on cancer cells selectively by involving different cellular pathways and/ or enhance the cytotoxicity by mutation. Also, the study of articles related to the function of ribonucleases showed that the investigation of genetic pathways of synthesis and mechanisms of cytotoxicity in these enzymes will provide the development of new pharmaceutical products in the future. Utilization of engineering processes and chemical changes in ligand / receptor structure may increase the toxicity of ribonuclease molecules in order to select cytotoxic pathways on malignant cells. Therefore, it is necessary to discover the therapeutic potential and to study in detail the therapeutic values of ribonucleases. Conclusions Ribonucleases are potentially bioavailable drug candidates, and in regard to their toxicity, which is based on the selective hydrolysis of intracellular RNA molecules and specific cell membrane recognition processes, these enzymes can be used as anti-tumor drugs or therapeutic agents.

Objective Immunotoxins are one of the most promising ways in therapeutic fields, specially cancer therapy which have a unique toxin-antibody structure, and kill the cancer cell by passing through the cell membrane and entering the target cell. The aim of this study was to engineer and design bovine pancreatic enzyme (RNase A) for to escape from ribonuclease inhibitor (RI) as a toxin segment in designing of immunotoxins used in therapeutic fields. Materials and Methods After bioinformatics investigation using PyMol software, engineering and substitution of target amino acid in wild gene coding RNase A sequence (K91A) were performed. The wild type and recombinant proteins in E.coli (BL21(D3) strain) were expressed and refolded, and then approved using SDS-PAGE. The purification of produced proteins was conducted using an immobilized-metal affinity chromatography for His-tagged proteins. Results The results showed that the protein concentrations were 3 and 2.2 g/L for wild RNase A and recombinant enzyme. The hydrolysis activity measurement of the produced enzymes, in presence of different concentrations of RI, indicated that recombinant variant had lower sensitivity and higher catalytic activity in comparison with the wild enzyme. The results obtained from enzyme activity of recombinant enzyme compared to the wild enzyme, in presence or absence of RI, demonstrated that the interaction effect between RNase A and RI can be disrupted by manipulation of amino acids involved in this interaction. Conclusion In respect to the current results, it was concluded that RNase A enzyme can be used as a promising drug in engineering and production of immunotoxins.

Objective 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. Materials and Methods 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. Results 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. Conclusions 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.

This study was conducted to assess the effect of whey powder and physical form of feed on humoral immunity and transcript abundances of interleukin-4(IL-4) and interferon-gamma (In-γ) genes on 240 Ross-308 day-old-chickens. The experiment was conducted in a completely randomized design in 6 treatments in factorial arrangement (2×3), whey powder at three levels (0, 4,8%) and physical form in two levels (mash, pellet) in broiler chicken diet with 4 repeats and 10 chickens per replicate. The diets formulated based on nutritional requirements of Ross strain-308 (2009) and were fed to the birds in three periods. To determine the immunity titer of ND, IBV, IBD and influenza blood samples were collected at day 10, 31 and 42. At the end of periods, one chicken was selected from experimental units and slaughtered; lymphatic organs were weighted and gene expression of IL-4 and In-γ measured after mRNA extraction and cDNA synthesis. It was found that the addition of whey powder did not have a significant effect on the weights of the spleen and bursa of Fabricius, but the pelleting in the growing stage had a significant effect on the weight of spleen (p

Background and Aim: Short tandem repeat (STR) markers, are conserved region in human genome and highly polymorphic between individuals. Nowadays, genotyping of STR marker is widely known and used for the genetic identification of individuals in forensic DNA analyses. Based on allelic frequencies of STR loci varies between populations, investigation of genetically and forensically parameters in each population and characterization of these markers is necessary. The objective of this study was to optimizing laboratory method for application of 10autosomal STR loci (TPOX، vWA، D7S820، D8S1179، D13S317، D16S539، D18S51، D5S818، THO1، D21S311) in Kurd and Arab ethnics of Iran and investigation of population and forensic genetics parameter of these markers in these populations. Materials and Methods: In this semi-experimental study, blood samples from 93 Arab and 94 Kurd individuals were collected. After DNA extraction, PCR amplification was carried out for 10 autosomal STR loci, individually. Then, acrylamide gel electrophoresis was used to determine the genotype of each individual in each site. Results: Deviation from Hardy Weinberg equilibrium even after Bonfferroni correction was seen in the locus of D13S317in both Populations. After D13S317 loci, the highest observed heterozygosity was seen in D21S311loci for Kurd population (94%) and in THO1, vWA and D5S818 locifor Arab population (84%). The lowest observed heterozygosity (0.71 and 0.72) was seen in TPOX loci for both populations form Arab and Kurd ethnics, respectively. Investigation of forensic genetic parameters (PI, PE, PD, and PIC) showed that in except of the D13S317 loci other remaining evaluated locus had proper properties for using in genetics fingertips in both of Kourd and Arab ethnics. Conclusion: The results of current study indicate that the necessity investigation of forensic genetics for rapid characterization of the different ethnicities which located in different geographic parts of Iran in order to choose the appropriate data set to calculate of forensic genetics parameters not only within each ethnic but also between them.

Identification of the genetic features of Persian mugger crocodile, the Gando, is crucial in management planning for conservation and preservation of this endangered species. Therefore, this study is aimed to investigate the genetic characteristics of Gando in Iran, based on population studies of the conserved and variable regions of the mitochondrial DNA. For this purpose, 12 samples of skin tissue and blood were collected from three regions of Chabahar city, south east of Iran. After DNA extraction, conserved and variable regions of the mitochondrial genome Cyt b and D-loop were amplified using PCR. The PCR products were sequenced and results were analyzed using bioinformatics software based on nucleotide data as well as protein codons. Results revealed that all samples had similar nucleotide sequences and no genetic variation was found among the samples. The closest species to Gando were Crocodylus palustris and then C. porosus. Comparison of sequences with other Crocodile species revealed the presence of 12 polymorphic loci among 1156 loci studied and also 5 haplogroups were introduced. As we didn’t find any nucleotide diversity among studied samples, therefore, to increase the genetic diversity of the Gando, it is essential to include specific conservational plans for this endangered species.