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The availability of genomic data, such as quantitative trait loci (QTL), has played a pivotal role in understanding the genetic components of various traits. This study aims to investigate critical and hub genes related to economic traits such as growth rate, body fat deposition, and feed consumption by investigating known QTLs by using protein-protein interaction networks (PPI) in chicken species. QTL coordinates for these traits were acquired through the Animal QTL database. Then, genes related to each QTL were obtained from the chicken reference genome (Gallus gallus bGalGal1.mat.broiler. GRCg7b) provided in the NCBI database. Critical genes related to known QTLs based on PPI were identified using Network Analyzer, CytoHubba, and MCODE applications in Cytoscape_v3.8.0 software. The results of this study showed 452, 83, and 75 genes involved in growth rate, body fat deposition, and feed consumption traits, respectively. Several new hub genes related to each trait were found and confirmed by PPI in Cytoscape. Some novel genes for studied traits were EEF1D, UBE2D1, TRIP13, PSMB3, and FZR1 for growth rate, ARPC2, NCAN, and SUGP1 for body fat deposition and LAP3, and SGPP2 for feed consumption. Some hub genes reported in previous studies were also identified in this research for growth rate (NCAPG, MED1, KPNA3, and EP300), body fat deposition (TULP), and feed consumption (MED9, LCORL, COPS3, LAP3, and TAPT1). The common important genes identified between the three traits that were reported in previous studies related to the traits were MNR2, CRYBA2, and MIR375 genes. It can be concluded that novel genes have molecular functions related to economically important traits. Therefore, newly discovered hub genes can be suggested to be used for selecting birds in future broiler breeding programs and basic research on functional genomics.

The current study aimed to determine the optimum level of ground flaxseed needed to improve performance and enrich broiler meat with omega-3 fatty acids (n-3 FA). A total of 360 twenty-five-day-old male broilers (Ross 308) were reared on floor pens and fed diets supplemented with ground flaxseed during the finisher phase (d 25-45). The chickens were assigned to four treatments of six replicates as follows: 1) corn-soybean meal (CSM) based diet as control; 2) CSM supplemented by 3% ground flaxseed (flax3); 3) CSM supplemented by 6% ground flaxseed (flax6); 4) CSM supplemented by 9% ground flaxseed (flax9). Results showed that flax6 increased (P < 0.05) daily gain (ADG) and feed intake (ADFI), while it did not affect feed conversion ratio (FCR). In addition, flax9 decreased (P < 0.05) ADG and ADFI, and impaired (P < 0.05) FCR compared to the control group at the end of the experiment (d 45). Feeding flax6 increased (P < 0.05) polyunsaturated fatty acids (PUFA) and n-3 FA in breast and thigh muscles and lowered (P < 0.05) abdominal fat pad weight compared to the control group. Results revealed that feeding birds with ground flax6 improves growth performance, reducing fat depots and enriching meat with n-3 PUFA without negatively affecting gut morphology.

In ovo injection of camel lactoferrin (cLF36) as an antimicrobial peptide was applied in Ross 308 fertile eggs and tested in 320 post-hatched chickens challenged with Clostridium perfringens (Cp). In 8 treatments and five replicates of 8 birds each, performance, jejunum morphometry and ileal microbial counts of chickens were assayed. Feed intake and feed conversion ratio of the chickens affected by treatments. Together with the positive control group under the Cp (10 8 cfu/g) challenge and the negative control group under the antibiotic (AB) challenge, the highest villi length was observed. The highest crypt depth was related to the treatment with the Cp challenge and the lowest value was related to the in ovo injection of cLF36 group and combined Cp and AB challenges. The number of Clostridium spp. in the ileal contents increased in the chickens challenged with Cp (P < 0.05). The greatest change was observed in the treatment with injection of cLF36 during the embryonic period and challenge with Cp and the lowest value was related to negative control treatment. In addition, the difference between treatments with cLF36 in ovo injection during the embryonic period and challenge with or without Cp challenge was significantly increased. In the groups under the Cp challenge, the population of E. coli was numerically increased. Based on the obtained results, cLF36, derived from camel milk, could change some of the indices in performance. It caused morphological changes in the villi of ilium and caused a decrease the microbial counts of Clostridium spp., similar to the AB group in the chickens challenged with Cp. Our research attempts to create a new window for in ovo administration of cLF36, according to its beneficial effects in the present study, can be introduced as a candidate for growth-promoting antibiotics.

IntroductionIdentifying genomic regions under selection is the most challenging issue for improving important traits in animals. Few studies have focused on identifying genomic regions under selection in sheep. The aim of this study was to identify selective sweeps and to explore the relationship between these and quantitative trait loci (QTL) in both domestic and wild sheep species using single nucleotide polymorphism markers (SNPs).MethodsGenomic data were obtained from the NextGen project, which included genotyping 20 domestic and 14 wild sheep using the Illumina Ovine SNP50K BeadChip. The XP-EHH, iHS, and RSB methods were employed to detect signatures of positive selection.ResultsThe results of the iHS method indicated 405 and 275 selective sweeps in domestic and wild sheep, respectively. Additionally, RSB and XP-EHH analyses revealed approximately 398 and 479 selective sweeps in domestic and wild sheep, respectively. Some of the genes associated with important QTL traits in domestic sheep include ADGRB3, CADM1, CAPN2, GALNT10, MTR, RELN, and USP25, while in wild sheep, the relevant genes include ACAN, ACO1, GADL1, MGST3, and PRDM16. Selective sweeps identified in domestic sheep were associated with body weight, muscle weight, milk protein percentage, and milk yield. In contrast, selective sweeps found in wild sheep were linked to average daily gain, bone weight, carcass fat percentage, and dressing percentage.DiscussionThese results indicate that selection by humans and the environment have largely progressed in harmony, highlighting the importance of both economic and environmental traits for survival. Additionally, the identification of potential candidate genes associated with economic traits and genomic regions that have experienced selection can be utilized in sheep breeding programs. However, due to the incomplete information regarding the functional annotation of genes in sheep and the limited sample size, further research with a larger sample group is essential to gain a deeper understanding of the candidate genes linked to economic traits in both domestic and wild sheep. Advancing knowledge in this area can significantly enhance the effectiveness of breeding strategies. The quantitative trait loci identified in this study have the potential to be incorporated into breeding plans for both domestic and wild sheep.

IntroductionSex differences in prenatal growth may contribute to sex-dependent programming effects on postnatal phenotype. MethodsWe integrated for the first time phenotypic, histomorphological, clinico-chemical, endocrine and gene expression analyses in a single species, the bovine conceptus at mid-gestation. ResultsWe demonstrate that by mid-gestation, before the onset of accelerated growth, the female conceptus displays asymmetric lower growth compared to males. Female fetuses were smaller with lower ponderal index and organ weights than males. However, their brain:body weight, brain:liver weight and heart:body weight ratios were higher than in males, indicating brain and heart ‘sparing’. The female placenta weighed less and had lower volumes of trophoblast and fetal connective tissue than the male placenta. Female umbilical cord vessel diameters were smaller, and female-specific relationships of body weight and brain:liver weight ratios with cord vessel diameters indicated that the umbilico-placental vascular system creates a growth-limiting environment where blood flow is redistributed to protect brain and heart growth. Clinico-chemical indicators of liver perfusion support this female-specific growth-limiting phenotype, while lower insulin-like growth factor 2 (IGF2) gene expression in brain and heart, and lower circulating IGF2, implicate female-specific modulation of key endocrine mediators by nutrient supply. ConclusionThis mode of female development may increase resilience to environmental perturbations in utero and contribute to sex-bias in programming outcomes including susceptibility to non-communicable diseases.

Habitat eradication and loss of animal species have created a new international hazard for wildlife conservation. National parks are considered as suitable places that can serve dual functions of biodiversity conservation and ecotourism. As recommended by the Food and Agriculture Organization (FAO), microsatellites have been used for animal biodiversity assessment. For this reason, Iranian urials population genetic diversity was studied by analyzing of 10 microsatellite markers in 75 skeletal muscle samples that were collected from Tandooreh National Park, Northeastern of Iran. Species of samples validated by sequencing of the control region from mtDNA. Allelic frequencies for each locus in the population and different measurements of within-breed genetic variations were computed by the POPGENE32 software. The number of alleles per locus counted from 5 to 8, with an average of 6.1. The polymorphism information content was calculated between 0.66-0.74 with the average of 0.7. Observed heterozygosity ranged from 0.223 (MaF214) to 0.776 (OarFCB128) with an average about 0.584 while the average expected heterozygosity for all studied loci was 0.785 ranging from 0.765 (BM8125) to 0.807 (MaF36). High levels of expected heterozygosity can be attributed to some factors such as low level of inbreeding, low selection pressure, and high allele number. However, findings of the present study of the high variability of the Iranian urials showed the presence of a possible ‘hot spot’ genetic diversity for wild urial population in the Northeast of Iran. In conclusion, values of genetic diversity revealed that the Iranian urial population harbor unique and appreciable reservoirs of diversity.

[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).

The effects of curcumin and its nano-micelle form on body weight, insulin resistance, adiponectin, and blood biochemical parameters of streptozotocin-induced diabetic rats were studied. Diabetes was induced in fifty male Wistar rats which were divided into five groups treated with 1) no dietary supplements, 2 and 3) 40 and 80 mg curcumin/kg of feed, and 4 and 5) 40 and 80 mg nano-micelle curcumin/kg of feed. A group of ten untreated male Wistar rats was also considered a healthy control group. The serum concentrations of AST, ALT, glucose, insulin, triglycerides, cholesterol, HDL-C, LDL-C, and adiponectin, as well as insulin resistance, were assessed. Body weight and weight of liver, heart, and pancreas were also evaluated. Induction of diabetes increased the serum concentrations of AST, ALT, glucose, triglycerides, cholesterol, LDL-C, and insulin resistance and decreased the serum levels of insulin, adiponectin, and HDL-C, as well as body weight and weight of the heart and pancreas (p < 0.05). Nano-micelle form of curcumin alleviated the negative effects of glucose, lipid profile, and liver enzymes in diabetic rats (p < 0.05). In conclusion, the nano-micelle form of curcumin showed better efficiency compared to curcumin for improving the adverse effects of diabetes. It can be suggested that the nano-micelle form of curcumin at specific doses might be useful for diabetes treatment.

Abstract Background Lactoferrin is a versatile protein with important modulatory functions in inflammation and immune response. This glycoprotein can bind and sequester iron and LPS, thereby intervening in certain signaling pathways and biological processes. In the present meta‐analysis, we aimed to pool experimental data regarding the immunomodulatory effects of lactoferrin and its derived peptides on the NF‐κB signaling pathway. Materials We searched PubMed, Google Scholar, and Web of Science databases and obtained all related articles published before April 2022. Finally, 25 eligible studies were selected, and their reports were analyzed. Methods We used Review Manager Version 5.2 to compute the standardized mean difference (SMD) and its 95% confidence interval. In addition, the source of heterogeneity was explored using meta‐regression and sensitivity analysis. The symmetry of the funnel plot and Egger's test were also used to evaluate publication bias utilizing Comprehensive Meta‐Analysis Version 2. Results Comparing the group of cells and animals exposed to lipopolysaccharide alone with the group that received pretreatment with lactoferrin and its derivatives, we observed significant reductions in TNF‐α, IL‐1 beta, and IL‐6 levels by 8.73 pg/mL, 2.21 pg/mL, and 3.24 pg/mL, respectively, in the second group. Additionally, IKK‐β, p‐IκB, and NF‐κB (p65) levels were significantly lower by 7.37‐fold, 15.02‐fold, and 3.88‐fold, respectively, in various cells and tissues. Conclusion Based on the results of this meta‐analysis, lactoferrin and its derived peptides can be considered potent prophylactic and therapeutic candidates against inflammation‐associated diseases by targeting the NF‐kB pathway.

The objective of this study was to investigate the effect of whey protein concentrate (WPC) and selenium (Se) supplementation on sperm quality, antioxidant enzymes activity and lipid peroxidation in seminal plasma, liver and testis of roosters. Forty-five Ross-308 broiler breeder roosters aged 60 weeks were used for an eight-week period in a 3 × 3 factorial arrangement of dietary treatments. Three levels of WPC (0.0, 1.5 and 3.0% of diet) and selenium supplementation (0.0, 0.2 and 0.4 mg/kg of diet) with five replications were tested. Total and progressive sperm motility, sperm concentration, plasma membrane integrity, and sperm viability were significantly lower in birds treated with Se supplementation-free diet (P < 0.05). Also, abnormal sperms were significantly higher in Se supplementation-free diets when compared to the diets supplemented with 0.4 mg/kg Se (P < 0.05). The use of 1.5% of WPC resulted in significantly increased total and progressive sperm motility compared to the WPC-free diet (P < 0.05). Selenium at the level of 0.4 mg/kg along with 3.0% WPC were associated with significantly increased Glutathione peroxidase and superoxide dismutase activity in seminal plasma as compared to other levels (P < 0.05). The highest level of total antioxidant capacity (TAC) in seminal plasma was observed at the level of 0.2 mg Se (P < 0.05). Further, 3.0% WPC resulted in significantly increased TAC concentration in seminal plasma compared to the WPC-free diet (P < 0.05). Moreover, the Malondialdehyde (MDA) level of seminal plasma in selenium supplementation-free diets was significantly higher than those of other levels (P < 0.05). Glutathione peroxidase activity, TAC, and MDA levels in the testis and liver were not affected by the WPC and Se levels. It can be concluded that dietary inclusion of WPC and Se improved the semen quality, increased antioxidant enzymes activity and decreased lipid peroxidation in seminal plasma of broiler breeder roosters.

Objective(s): Early, specific, and sensitive detection methods of COVID-19 are essential for force stopping its worldwide infection. Although CT images of the lung and/or viral RNA extraction followed by real-time reverse-transcriptase-polymerase chain reaction (rRT-PCR) are widely used; they have some limitations. Here, we developed a highly sensitive magnetic bead-based viral RNA extraction assay followed by rRT-PCR. Materials and Methods: Case group included oropharyngeal/nasopharyngeal and blood samples from 30 patients diagnosed positive by PCR test for COVID-19 and control group included 30 same samples from COVID-19 negative PCR test individuals. RNA was extracted, using viral RNA extraction kit as well as using our hand-made capture bead-based technique. A one-step cDNA synthesis and Real Time PCR was conducted. A two-step comparison of the different viral RNA extraction methods for oropharyngeal/nasopharyngeal and blood samples was performed. Student t-test was applied with a P

Copyright of Poultry Science Journal is the property of Gorgan University of Agricultural Sciences & Natural Resources and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Poultry Science Journal is the property of Gorgan University of Agricultural Sciences & Natural Resources and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Introduction: Identifying genomic regions under selection is the most challenging issue for improving important traits in animals. Few studies have focused on identifying genomic regions under selection in sheep. The aim of this study was to identify selective sweeps and to explore the relationship between these and quantitative trait loci (QTL) in both domestic and wild sheep species using single nucleotide polymorphism markers (SNPs). Methods: Genomic data were obtained from the NextGen project, which included genotyping 20 domestic and 14 wild sheep using the Illumina Ovine SNP50K BeadChip. The XP-EHH, iHS, and RSB methods were employed to detect signatures of positive selection. Results: The results of the iHS method indicated 405 and 275 selective sweeps in domestic and wild sheep, respectively. Additionally, RSB and XP-EHH analyses revealed approximately 398 and 479 selective sweeps in domestic and wild sheep, respectively. Some of the genes associated with important QTL traits in domestic sheep include ADGRB3, CADM1, CAPN2, GALNT10, MTR, RELN , and USP25 , while in wild sheep, the relevant genes include ACAN, ACO1, GADL1, MGST3 , and PRDM16. Selective sweeps identified in domestic sheep were associated with body weight, muscle weight, milk protein percentage, and milk yield. In contrast, selective sweeps found in wild sheep were linked to average daily gain, bone weight, carcass fat percentage, and dressing percentage. Discussion: These results indicate that selection by humans and the environment have largely progressed in harmony, highlighting the importance of both economic and environmental traits for survival. Additionally, the identification of potential candidate genes associated with economic traits and genomic regions that have experienced selection can be utilized in sheep breeding programs. However, due to the incomplete information regarding the functional annotation of genes in sheep and the limited sample size, further research with a larger sample group is essential to gain a deeper understanding of the candidate genes linked to economic traits in both domestic and wild sheep. Advancing knowledge in this area can significantly enhance the effectiveness of breeding strategies. The quantitative trait loci identified in this study have the potential to be incorporated into breeding plans for both domestic and wild sheep. [ABSTRACT FROM AUTHOR]

Abstract KRAS mutation is responsible for 40–50% of colorectal cancers (CRCs). RNA-seq data and bioinformatics methods were used to analyze the transcriptional profiles of KRAS mutant (mtKRAS) in comparison with the wild-type (wtKRAS) cell lines, followed by in-silico and quantitative real-time PCR (qPCR) validations. Gene set enrichment analysis showed overrepresentation of KRAS signaling as an oncogenic signature in mtKRAS. Gene ontology and pathway analyses on 600 differentially-expressed genes (DEGs) indicated their major involvement in the cancer-associated signal transduction pathways. Significant hub genes were identified through analyzing PPI network, with the highest node degree for PTPRC. The evaluation of the interaction between co-expressed DEGs and lncRNAs revealed 12 differentially-expressed lncRNAs which potentially regulate the genes majorly enriched in Rap1 and RAS signaling pathways. The results of the qPCR showed the overexpression of PPARG and PTGS2, and downregulation of PTPRC in mtKRAS cells compared to the wtKRAS one, which confirming the outputs of RNA-seq analysis. Further, significant upregualtion of miR-23b was observed in wtKRAS cells. The comparison between the expression level of hub genes and TFs with expression data of CRC tissue samples deposited in TCGA databank confirmed them as distinct biomarkers for the discrimination of normal and tumor patient samples. Survival analysis revealed the significant prognostic value for some of the hub genes, TFs, and lncRNAs. The results of the present study can extend the vision on the molecular mechanisms involved in KRAS-driven CRC pathogenesis.

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.

The effect of different levels of Scrophularia striata extract in normal and challenged conditions with E. coli on performance, carcass characteristics, cellular immune response, blood antioxidant status, intestinal histo-morphometry, and microbial population (E.coli and Lactobacillus) of Cobb 500 broilers were evaluated. The experiment was performed in a complete block design with a 2 × 4 factorial arrangement with five replications of 10 birds each for 35 days in two separated halls [include challenge (C) and non-challenge (N)] with similar experimental conditions. Experimental treatments in two breeding halls were: 1) basal diet or control (CONT), 2) basal diet + 0.1 g/kg of herbal extract (EXTR 1), 3) basal diet +0.2 g/kg of herbal extract (EXTR 2), 4) Basal diet +0.1 g/kg an antibiotic (Oxytetracycline) (ANTB). On the 16th and 24th days of the experiment, one dose of 1×107 CFU K99 E. Coli was gavaged to chickens in a challenged conditioned hall. The results showed that average body weight and daily weight gain in the whole period (days 35 and 1-35) in EXTR 2 was better than the control treatment (P < 0.05). The percentage of breast weight in the ANTB was significantly different from the control treatment (P < 0.05). Glutathione peroxidase (GPX) in EXTR 2 was better than the control treatment (P < 0.05). Malondialdehyde (MDA) in EXTR 1 was significantly lower than the control group (P < 0.05). The values of E. coli in the treatment ANTB were less than control treatment (P < 0.05). Lactobacillus value in treatment EXTR 2 was higher than control treatment (P < 0.05). The value of total immunoglobulin in 28 days in ANTB, EXTR 1, and EXTR 2 were significantly higher than that of control treatment (P < 0.05). The length of villi was affected by treatments (P < 0.05). In conclusion, dietary inclusion of 0.2 g/kg of Scrophularia striata extract may improve the health status of the birds during E. coli challenge.

In ovo injection of camel lactoferrin (cLF36) as an antimicrobial peptide was applied in Ross 308 fertile eggs and tested in 320 post-hatched chickens challenged with Clostridium perfringens (Cp). In 8 treatments and five replicates of 8 birds each, performance, jejunum morphometry and ileal microbial counts of chickens were assayed. Feed intake and feed conversion ratio of the chickens affected by treatments. Together with the positive control group under the Cp (108 cfu/g) challenge and the negative control group under the antibiotic (AB) challenge, the highest villi length was observed. The highest crypt depth was related to the treatment with the Cp challenge and the lowest value was related to the in ovo injection of cLF36 group and combined Cp and AB challenges. The number of Clostridium spp. in the ileal contents increased in the chickens challenged with Cp (P < 0.05). The greatest change was observed in the treatment with injection of cLF36 during the embryonic period and challenge with Cp and the lowest value was related to negative control treatment. In addition, the difference between treatments with cLF36 in ovo injection during the embryonic period and challenge with or without Cp challenge was significantly increased. In the groups under the Cp challenge, the population of E. coli was numerically increased. Based on the obtained results, cLF36, derived from camel milk, could change some of the indices in performance. It caused morphological changes in the villi of ilium and caused a decrease the microbial counts of Clostridium spp., similar to the AB group in the chickens challenged with Cp. Our research attempts to create a new window for in ovo administration of cLF36, according to its beneficial effects in the present study, can be introduced as a candidate for growth-promoting antibiotics. [ABSTRACT FROM AUTHOR]

Due to the increasing global demand for Gamma-aminobutyric acid (GABA) in the food and pharmaceutical industries, the expression of the recombinant Glutamate decarboxylase (GAD) and its industrial production is currently requested. Culture conditions were optimized to increase the expression level of the recombinant enzyme in different pH, temperature, incubation time, aeration levels, inoculation concentrations, concentrations of IPTG, and several carbon sources using the RSM based on a central composite design. According to the results of the quadratic regression equation, recombinant Escherichia coli BL21 (DE3) had the highest GAD expression at pH=7.2, aeration at about 120 rpm, inoculation concentrations of about 3% v/v, 2.25 mM IPTG, 37 °C, and 6 h of incubation time in the presence of 0.2% glucose. Using pure glucose as a carbon source on an industrial scale is not cost-effective for producing recombinant proteins. Therefore, using low-cost carbon sources such as corn syrup and molasses with concentrations of 1.5 and 5.65% (w/v) is an efficient method for the industrial production of recombinant GAD. The concentration of purified recombinant GAD in carbon sources of 0.2% glucose, 1.5 corn syrup and 5.65% molasses was 2.155, 2.07 and 1.96 mg/mL, respectively. In this way, the global need for GABA can be met by the industrial production of GAD. [ABSTRACT FROM AUTHOR]

Abstract There is a continuing need to prevent the increasing use of common antibiotic and find the replacement to combat the drug/antibiotic resistant bacteria such as antimicrobial peptides (AMPs) such as thanatin peptide. In this study, recombinant thanatin peptide was expressed in the HEK293 cell line. Then the antimicrobial properties of this peptide on some poultry and farm animal’s pathogen strains were assessed. The thermal-stability of thanatin was predicted in various temperatures through in silico analysis. Afterwards, according to Minimum Inhibitory Concentration (MIC) results, Escherichia coli and Pseudomonas aeruginosa were chosen to test the hypothesis of LptA/LptD–thanatin interaction, computationally. Relative amino acid sequences and crystallography structures were retrieved and missed tertiary structures were predicted. The interaction of thanatin with LptA and LptD of Escherichia coli and Pseudomonas aeruginosa were analyzed subsequently. The antibacterial activity of thanatin peptide was evaluated between 6.25 and 100 μg/mL using minimum inhibitory concentration. Also, the amounts of minimum bactericidal concentrations (MBC) were between 12.5 and 200 μg/mL. The bioinformatics analysis followed by the in vitro assessment, demonstrated that thanatin would be thermally stable in the body temperature of poultry and farm animals. Thanatin could penetrate to the outer membrane domain of LptD in Escherichia coli and it could block the transition path of this protein while the entrance of LptD in Pseudomonas aeruginosa was blocked for thanatin by extra residues in comparison with Escherichia coli LptD. In addition, the quality of interaction, with regard to the number and distance of interactions which leads to higher binding energy for thanatin and LptD of Escherichia coli was much better than Pseudomonas aeruginosa. But the site and quality of interaction for thanatin and LptA was almost the same for Escherichia coli and Pseudomonas aeruginosa. Accordingly, thanatin can prevent the assembly of LptA periplasmic bridge in both pathogens. The antibacterial and thermal stability of the thanatin peptide suggested that thanatin peptide might serve as a natural alternative instead of common antibiotics in the veterinary medicine. The outcome of this in silico study supports the MIC results. Therefore, a probable reason for different level of activity of thanatin against Escherichia coli and Pseudomonas aeruginosa might be the quality of LptA/LptD–thanatin interaction.

Sheep satellite cells more than satellite cells of the rat and mouse are similar to human satellite cells. These cells are widely used in the modeling and treatment of diseases like heart insufficiency, neurological diseases, muscular dystrophy, cerebral cell transplantation for the treatment of migraines, screening, and the production of new drugs. This study was aimed to isolate and culture primary satellite cells (PSCs) obtained from sheep fetus, and perform clonal expansion of transfected PSCs. Skeletal muscle tissues of hind limbs were collected from sheep fetuses obtained from a local abattoir. After enzymatic digestion, flasks were replaced after 3 hours to isolate non-myogenic cells, such as fibroblasts. After six days, the cells were differentiated to myoblasts. Using a differentiation medium containing the horse serum, myotube cells were observed in the flask, indicating that the cultured cells were satellite cells. The mRNA expression of the PAX7 gene was used to confirm the presence of satellite cells. In addition, the results showed that satellite cells grow in a culture medium containing 5% FBS without differentiation, while 10% FBS initiates their differentiation.

To investigate the effects of dietary supplementation with industrial vinegar (IV) and waste date vinegar (WDV) on growth performance, intestinal morphology, and immune response of broilers, five hundred Ross 308 chickens were randomly divided into 50 cages in a 42-day breeding period. The experiment consisted of ten treatments with five replications in each treatment including; control 1 (standard feed without WDV or IV), control 2 (control 1 + 2% water into the feed), 1, 2, and 3% of WDV and 2% industrial vinegar (IV) into the feed and 0.5, 1, and 1.5% of WDV and 1% industrial vinegar (IV) into the water. One chicken from each replicate was slaughtered on days 24 and 42 to investigate gastrointestinal tissue growth as well as intestinal morphology. The results showed that growth performance was not affected by treatments in any period. The height and width of the villus in the treatments containing 1% of WDV into the water and 2% of WDV into the feed increased with time compared to the control treatments. On day 42 of the experiment, the crypt depth was also higher in the treatment containing 1% of WDV into the feed compared to the other treatments. The ileal coliforms were also affected by WDV addition into the feed at 42 days of age compared to other groups (P < 0.05). The highest amount of IgM and IgG were found to levels of 2% and 1% of WDV into the diet, respectively (P < 0.05). However, SRBC, ND titter was not affected by treatments. Also, no difference was found between industrial vinegar in water or feed in most of the studied parameters. The results of this study showed that supplementation of the diet with WDV had a positive effect on intestinal morphology and immune system of broilers compared to industrial vinegar.

This study was performed to investigate the effects of dietary threonine (Thr). level on performance, metabolizable energy, intestinal morphology, and immune system in coccidian–infected broiler chickens. The diets contained: 88%, 100% (Non challenged (NC) and challenged control (PC)), 112%, 124%, and 136% of Thr requirement according to Cobb 500 recommendation and fed during grower (pre challenged) and finisher (post challenged) periods. On d 23 (end of grower period), each bird received 0.5 mL of distilled water or received around 24000 sporulated oocysts. On d 23 and 31, one bird per replicate was slaughtered to measure the performance criteria. Mean dietary apparent metabolizable energy corrected for nitrogen (AMEn) and digestible energy were greater in NC birds than the challenged birds fed on 88% or 100% Thr diets. Feed intake and blood parameters were not significantly influenced by increasing levels of Thr in the diet. Compared with unchallenged birds with coccidia (NC), the growth performance, morphological parameters (not crypt depth), and immune responses decreased (P < 0.05) in the birds (PC) that were challenged with coccidia, and oocyte numbers were enhanced. Growth performance, jejunal morphology, and immune responses improved and oocyte count decreased in coccidian- challenged birds fed on the diets with greater levels of Thr (P < 0.05). Feeding the challenged birds with the diet containing greater levels of Thr improved (P < 0.05) their growth performance, morphology, and immune responses and decreased oocyte number. The birds fed on the diet with 124% Thr demonstrated a similar response as the NC birds. Increased diet Thr level linearly increased average daily gain and decreased feed conversion ratio in the grower and the whole experimentation periods. The AMEn and digestibility of crude protein were enhanced linearly Thr level increased in coccidian-challenged birds. It is concluded that diets containing 124% of Thr recommendation led to the greatest efficacy on the intestinal immuneresponse and normal growth maintenance of the birds contaminated with coccidia.

Hilsa species are broadly described as largely anadromous fish with a large valuable population size. It is well-known as one of the most critical commercial and occurs in marine, estuarine and riverine environments Hilsa shad, Tenualosa ilisha locally known as Sbour, migrates to the freshwater environment of the Shatt Al-Arab River systems for breeding. It was determined the genetic variation in 70 specimens of T. ilisha from four sites at the Shatt Al-Arab River, the mtDNA cytochrome-b gene was selected as a molecular marker for detecting genetic diversity, origin, and divergence of the population through comparing them with 6 samples from different locations at Indo-Pacific. The AMOVA analysis showed that the variation between groups is 60.97% and 39.02% within population indicating statistically significant P value (P

This study aimed to monitor the effect of including rumen-protected L-carnitine (Carneon 20 Rumin-Pro, Kaesler Nutrition GmbH, Cuxhaven, Germany) in the transition diet on the productive and metabolic responses of multiparous high-producing Holstein dairy cows. Thirty-two multiparous cows were allocated in a completely randomized design to receive the same diet plus 60 g fat prill containing 85% palmitic acid (control, n = 16) or 100 g rumen-protected L-carnitine (RLC, n = 16); at 28 days before expected calving until 28 days in milk (DIM). Fat prill was included in the control diet to balance the palmitic acid content of both experimental diets. Milk production over the 28 DIM for the control and RLC groups was 46.5 and 47.7 kg, respectively. Milk fat content tended to increase upon rumen-protected L-carnitine inclusion (p = 0.1). Cows fed rumen-protected L-carnitine had higher fat- and energy-corrected milk compared with the control group. Pre- and post-partum administration of L-carnitine decreased both high- and low-density lipoprotein concentrations in peripheral blood of post-partum cows. The results of this study indicated that the concentration of triglycerides and beta-hydroxybutyrate was not significantly different between the groups, whereas the blood non-esterified fatty acid concentration was markedly decreased in cows supplemented with L-carnitine. Animals in the RLC group had a significant (p < 0.05) lower blood haptoglobin concentration at 7 and 14 DIM than the control. Animals in the RLC group had a lower concentration of blood enzymes than those of the control group. The mRNA abundance of Toll-like receptors 4, cluster of differentiation 14, and myeloid differential protein 2 did not significantly change upon the supplementation of L-carnitine in the transition diet. In summary, the dietary inclusion of RLC improved dairy cow's performance during the early lactation period. Greater production, at least in part, is driven by improved energy utilization efficiency and enhanced metabolic status in animals during the periparturient period.

In the present study, kashk samples were collected from two regions of Iran, the Fars (Abadeh) and Razavi Khorasan (Kalat) provinces. Fifteen bacteria were isolated and physiological and biochemical assays were performed. After identification to the genus level, eight isolates were identified as lactic acid bacteria (LAB) and subjected to molecular identification and probiotic properties assays. The results revealed that the isolates were Enterococcus faecium KKP 3772 (KF1), Enterococcus faecium C1 (KF2), Pediococcus pentosaceus H11 (KF3), Pediococcus pentosaceus VNK-1 (KK4), Lactococcus lactis RSg (KK1), Enterococcus faecalis P190052 (KK2), Enterococcus mundtii CECT972T (KK3), and Lactiplantibacillus plantarum PM411 (KK5). Only the numbers of L. lactis RSg (KK1) and Lpb. Plantarum PM411 (KK5) decreased to below 9 Log CFU/mL after acidic conditions (pH = 3) and showed weak antibacterial activity. Enterococcus mundtii CECT972T (KK3) and E. faecium C1(KF2) were highly susceptible to bile salts, while P. pentosaceus VNK-1 (KK4) and P. pentosaceus H11 (KF3) showed the highest resistance. All of the isolates were resistant to tetracycline and sensitive to chloramphenicol and gentamicin. The antimicrobial activity of P. pentosaceus VNK-1 (KK4) and P. pentosaceus H11 (KF3) was higher than other isolates and consequently, their inhibition zones were larger. The adhesion capabilities of LAB isolates to intestinal epithelial cells were evaluated by examining the auto-aggregation factor and cell surface hydrophobicity. The highest and lowest cell surface hydrophobicity and auto-aggregation were obtained from P. pentosaceus VNK-1 (KK4) and E. mundtii CECT972T (KK3), respectively. In general, P. pentosaceus VNK-1 (KK4) and P. pentosaceus H11 (KF3) have shown better probiotic properties as compared to other isolates.

Bovine leukemia virus (BLV) is the etiologic agent of enzootic bovine leucosis (EBL) for the bovine host. In this study to examine gene expression changes in the manifestation of the EBL malignancy, four pooled RNA samples (three RNAs in each sample) were applied for transcriptome sequencing using RNA-seq technique. Differential expression analysis was done to compare the infected bovine group with the healthy bovine group using DESeq2 package in R software. Furthermore, functional gene ontology (GO) term and KEGG pathway enrichment analysis were stablished using the DAVID online database to identify involved GO terms and pathways in the host response to BLV infection. Our results suggested that 371 up- and 72 downregulated genes were involved in EBL with statistically significant threshold log2foldchange (LFC) = 1 and false discovery rate (FDR)