Hematological parameters, antioxidant status, and gene expression of γ-INF and IL-1ß in vaccinated lambs fed different type of lipids.

This study was aimed to evaluate the effects of vegetable oils as calcium salt on immune responses and the expression of immune-related genes in vaccinated lambs. Twenty-four lambs (35 kg body weight, 6 months old) were assigned to four treatments with six replicates in a completely randomized design for 40 days. Four concentrates were formulated in which the calcium salts of palm oil, canola oil, corn oil, and flaxseed oil were used. On day 30 of the experiment, lambs were vaccinated by a dose of foot-and-mouth disease virus. The blood samples were collected from jugular vein 10 days after vaccination. The level of malondialdehyde and the activity of liver enzymes were the highest in lambs receiving corn oil and the lowest in lambs receiving flaxseed oil. The highest lymphocytes and the lowest neutrophil percentages were observed in lambs receiving flaxseed oil. There was a significant difference among treatments for the relative genes expression. Flaxseed oil significantly upregulated interferon-γ and corn oil upregulated interleukin-1ß. The highest titer against foot-and-mouth disease virus was related to lambs receiving flaxseed oil, and the lowest titer was related to lambs that received corn oil. Flaxseed oil had more beneficial effects on immune response than other oils.

A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation.

Within the realms of human thoughts on nature, Fourier analysis is considered as one of the greatest ideas currently put forwarded. The Fourier transform shows that any periodic function can be rewritten as the sum of sinusoidal functions. Having a Fourier transform view on real-world problems like the DNA sequence of genes, would make things intuitively simple to understand in comparison with their initial formal domain view. In this study we used discrete Fourier transform (DFT) on DNA sequences of a set of genes in the bovine genome known to govern milk production, in order to develop a new gene clustering algorithm. The implementation of this algorithm is very user-friendly and requires only simple routine mathematical operations. By transforming the configuration of gene sequences into frequency domain, we sought to elucidate important features and reveal hidden gene properties. This is biologically appealing since no information is lost via this transformation and we are therefore not reducing the number of degrees of freedom. The results from different clustering methods were integrated using evidence accumulation algorithms to provide in insilico validation of our results. We propose using candidate gene sequences accompanied by other genes of biologically unknown function. These will then be assigned some degree of relevant annotation by using our proposed algorithm. Current knowledge in biological gene clustering investigation is also lacking, and so DFT-based methods will help shine a light on use of these algorithms for biological insight.

Bioactive Materials Derived from Menstrual Blood Stem Cells Enhance the Quality of In Vitro Bovine Embryos.

Backgrounds: The aim of this study was to determine whether the addition of bioactive materials derived from Menstrual Blood Stem Cells (MenSCs) to the oocyte maturation medium may improve the quality of bovine embryos in vitro. Methods: MenSCs were collected from 6 healthy women (between 26 and 36 years old) and after 3 days of culture, their bioactive materials were frozen. The bovine Cumulus-Oocyte-Complexes (COCs) were aspirated from ovarian slaughterhouse and the oocytes with more than three layers of cumulus cells were cultured in vitro in media supplemented with (treatment) and without (control) 10% MenSCs' bioactive materials. After IVM/IVF, the presumptive zygotes were cultured for 8 days. Results: The blastocyst rate on day 8 in treatment group was higher than control (40.2±1.9 vs. 23±4.2.3, p=0.001). The ratio of Trophectoderm (TE) and Inner Cell Mass (ICM) (ICM/TE) cells was also greater in treatment group compared to control (30.3±2 vs. 14.9±1; p=0.001). The re-expansion of vitrified blastocysts, 24 hours after warming, in treatment group was higher than control (93.3±2.5 vs. 66.2±8.8; p=0.01). The expression of some genes related to pluripotency and implantation (OCT4, CDX2, and IFNT) were increased in treatment group compared to control (p<0/05). Conclusion: In conclusion, the addition of MenSCs' bioactive materials during in vitro maturation of bovine oocytes could improve the quantity and quality of bovine IVP embryos. Also, the expression of some genes associated with pluripotency and implantation in the blastocyst would be increased.

Genotype by climate zone interactions for fertility, somatic cell score, and production in Iranian Holsteins.

The objective of this study was to investigate genetic variation and genotype by environment (G × E) interactions for fertility (including age at first calving and calving interval), somatic cell score (SCS), and milk production traits for Iranian Holsteins. Different environments were defined based on the climatic zones (cold, semi-cold, and moderate) and considering the herd location. Data were collected between 2003 and 2018 by the National Animal Breeding Center of Iran (Karaj). Variance and covariance components and genetic correlations were estimated using 2 different models, which were analyzed using Bayesian methods. For both models, performance of traits in each climate were considered as different traits. Fertility traits were analyzed using a trivariate model. Furthermore, SCS and production traits were analyzed using trivariate random regression models (records in different climate zones considered as different traits). For the fertility traits, the largest estimates of heritability were observed in cold climate. Fertility performance was always better in cold environment. Genetic correlations between climatic zones ranged from 0.85 to 0.94. For daily measurements of SCS and production traits, heritability ranged from 0.031 to 0.037 and 0.069 to 0.209, respectively. Genetic variances were the highest in the semi-cold and moderate climates for the SCS and production traits, respectively. Furthermore, across the studied climates, 305-d genetic correlation ranged from 0.756 to 0.884 for SCS and from 0.925 to 0.957 for the production traits. The structure of genetic correlation within each climate indicated a negative correlation between early and late lactation for SCS, especially in the cold climate and for milk production in the moderate climate. For fat percentage, in all climatic zones, the lowest genetic correlations were observed between early and mid-lactation. In addition, for protein production in the cold climate, a negative correlation was observed between early and late lactation. Results indicated heterogeneous variance components for all the studied traits across various climatic zones. Estimated genetic correlations for SCS revealed that the genetic expression of animals may vary by climatic zone. Results indicated the existence of G × E interaction due to the climatic condition, only for SCS. Therefore, in Iranian Holsteins, the effect of G × E interactions should not be neglected, especially for SCS, as different sires might be optimal for use in different climatic zones.

The role of Rho-associated kinase inhibitor, Y-27632 on primary culture of ovine spermatogonial stem cells.

The access to sufficient numbers of spermatogonial stem cells (SSCs) is a prerequisite for the study of their regulation and further biomanipulation. Rho kinase (ROCK) belongs to a family of serine/threonine kinases and involves in a wide range of fundamental cellular functions. The aim of the present study was to study the effect of ROCK inhibitor, Y-27632 (0.1-40 µM), during the primary culture of ovine SSCs. SSCs were collected from 3-5-month-old's lamb testes. The viability of SSCs, the apoptosis assay of SSCs, the intracellular reactive oxygen species (ROS) analysis, and the SSCs markers and apoptosis-related gene expressions were detected by MTT reduction assay, Annexin V-FITC/ Propidium Iodide (PI) dual staining, flow cytometry and real-time-PCR studies, respectively. Morphological analyses indicated that the 5-10 µM Y-27632 had an optimal effect on the number of presumptive SSCs colonies and the area covered by them after a 10 days culture. The cell viability, apoptosis and necrosis of SSCs after 10 days' culture were not affected in comparison with the control group, and the 20 µM of Y-27632 resulted in significantly decreased cell viability (P<0.05) and an increased necrosis of cells. On day 10 after culture, the expression of P53 was decreased with an increase from 0 to 10 µM in the Y-27632 dose. In the 20 µM Y-27632 group, the expressions of P53 and Bax were higher and the Bcl-2 was lower than other groups and these values were significantly different from 5 and 10 µM Y-27632 groups (P<0.05). The level of intracellular ROS was decreased with an increase in the Y-27632 dose from 5 to 20 µM in comparison with the control group. In conclusion, the present study demonstrated that Y-27632 at a concentration of 5-10 µM provided optimal culture conditions for the primary culture of ovine SSCs.

Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types.

Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.

Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes.

Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima's D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.

Identification of Bactrian camel cell lines using genetic markers.

Iranian Bactrian camel population is less than 100 animals. Iranian biological resource center produced more than 50 Bactrian camel fibroblast cell lines as a somatic cell bank for conservation animal genetic resources. We compared two type markers performance, including 14 random amplified polymorphic DNA (RAPDs) (dominant) and eight microsatellite (co-dominant) for cell line identification, individual identification and investigation genetic structure of these samples. Based on clarity, polymorphism, and repeatability, four RAPD primers were selected for future analysis. Four RAPD primers and eight microsatellite markers have generated a total of 21 fragments and 45 alleles, respectively. RAPD primers revealed fragment size between 150 to 2000 bp and gene diversity since 0.27 (IBRD) to 0.46 (GC10), with an average of 0.37. Microsatellite markers generated number of alleles per locus ranged from 3 to 11, with an average of 5.62 alleles. The observed heterozygosity ranged from 0.359 (IBRC02) to 0.978 (YWLL08), and expected heterozygosity ranged from 0.449 (IBRC02) to 0.879 (YWLL08). Bottleneck analysis and curve showed that Bactrian camel population did not experience a low diversity. RAPD profiles were especially suitable for investigation population genetics. All primers generated novel and polymorphic fragments. Briefly, our results show that a multiplex PCR based on these markers can still be valuable and suitable for authentication of cell lines, investigating gene diversity and conservation genetic resources in Bactrian camel, while new technologies are continuously developed.

Energy sources and levels influenced on performance parameters, thyroid hormones, and HSP70 gene expression of broiler chickens under heat stress.

The present study was conducted to evaluate the effects of energy sources and levels on body and organs weights, thyroid hormones, and heat shock protein (HSP70) gene expression in broilers under heat stress. In a completely randomized design, 600 1-day-old Cobb chickens were assigned to five dietary treatments and four replicates. The chickens were fed diet based on corn as main energy source and energy level based on Cobb standard considered as control (C), corn-based diet with 3 % lesser energy than the control (T1), corn-based diet with 6 % lesser energy than the control (T2), corn and soybean oil-based diet according to Cobb standard (T3), and corn and soybean oil-based diet with 3 % upper energy than the control (T4). Temperature was increased to 34 °C for 8 h daily from days 12 to 41 of age to induce heat stress. The chickens in T1 and T2 had lower thyroid hormones and corticosterone levels than those in C, T3, and T4. The highest liver weight was for C and the lowest one was for T4. The highest gene expression was found in chickens fed T4 diet, and the lowest gene expression was for those in T2 group. The highest feed intake and worse feed conversion ratio was related to chickens in T2. The chickens in T3 and T4 had higher feed intake and weight gain than those in C. The results showed that the higher energy level supplied from soybean oil could enhance gene expression of HSP70 and decline the level of corticosterone and thyroid hormones and consequently improved performance.

Assessing and comparison of different machine learning methods in parent-offspring trios for genotype imputation.

Genotype imputation is an important tool for prediction of unknown genotypes for both unrelated individuals and parent-offspring trios. Several imputation methods are available and can either employ universal machine learning methods, or deploy algorithms dedicated to infer missing genotypes. In this research the performance of eight machine learning methods: Support Vector Machine, K-Nearest Neighbors, Extreme Learning Machine, Radial Basis Function, Random Forest, AdaBoost, LogitBoost, and TotalBoost compared in terms of the imputation accuracy, computation time and the factors affecting imputation accuracy. The methods employed using real and simulated datasets to impute the un-typed SNPs in parent-offspring trios. The tested methods show that imputation of parent-offspring trios can be accurate. The Random Forest and Support Vector Machine were more accurate than the other machine learning methods. The TotalBoost performed slightly worse than the other methods.The running times were different between methods. The ELM was always most fast algorithm. In case of increasing the sample size, the RBF requires long imputation time.The tested methods in this research can be an alternative for imputation of un-typed SNPs in low missing rate of data. However, it is recommended that other machine learning methods to be used for imputation.

Comparison of three boosting methods in parent-offspring trios for genotype imputation using simulation study.

BACKGROUND: Genotype imputation is an important process of predicting unknown genotypes, which uses reference population with dense genotypes to predict missing genotypes for both human and animal genetic variations at a low cost. Machine learning methods specially boosting methods have been used in genetic studies to explore the underlying genetic profile of disease and build models capable of predicting missing values of a marker. METHODS: In this study strategies and factors affecting the imputation accuracy of parent-offspring trios compared from lower-density SNP panels (5 K) to high density (10 K) SNP panel using three different Boosting methods namely TotalBoost (TB), LogitBoost (LB) and AdaBoost (AB). The methods employed using simulated data to impute the un-typed SNPs in parent-offspring trios. Four different datasets of G1 (100 trios with 5 k SNPs), G2 (100 trios with 10 k SNPs), G3 (500 trios with 5 k SNPs), and G4 (500 trio with 10 k SNPs) were simulated. In four datasets all parents were genotyped completely, and offspring genotyped with a lower density panel. RESULTS: Comparison of the three methods for imputation showed that the LB outperformed AB and TB for imputation accuracy. The time of computation were different between methods. The AB was the fastest algorithm. The higher SNP densities resulted the increase of the accuracy of imputation. Larger trios (i.e. 500) was better for performance of LB and TB. CONCLUSIONS: The conclusion is that the three methods do well in terms of imputation accuracy also the dense chip is recommended for imputation of parent-offspring trios.

Effect of Linolenic acid during in vitro maturation of ovine oocytes: embryonic developmental potential and mRNA abundances of genes involved in apoptosis.

PURPOSE: To study the effect of α-linolenic acid (ALA) on meiotic maturation, mRNA abundance of apoptosis-related (Bax and Bcl-2) molecules, and blastocyst formation in ovine oocytes. METHODS: A preliminary experiment was conducted to analyze the concentration of ALA in "small" (≤2 mm) and "large" (≥6 mm) follicles using gas chromatography/mass spectrometry analysis. The concentration of ALA in small and large follicles was determined to be in a range of 75.4 to 125.7 µM, respectively. In vitro maturation (IVM) of oocyte was then performed in presence of 0 (control), 10 (ALA-10), 50 (ALA-50), 100 (ALA-100), and 200 (ALA-200) µM of ALA. Meiotic maturation and mRNA abundance of Bax, and Bcl-2 genes was evaluated after 24 h of IVM. The embryonic cleavage and blastocyst formation following parthenogenetic activation were also determined for each group. RESULTS: The highest concentration of ALA (ALA-200) decreased the oocyte maturation rate compared with the control group. Analysis of apoptosis-related genes in oocytes after IVM revealed lesser transcript abundances for Bax gene, and higher transcript abundances for Bcl-2 gene in ALA-treated oocytes as compared with the control oocytes. In term of cleavage rate (considered as 2-cell progression), we did not observe any differences among the groups. However, ALA-100 group promoted more blastocyst formation as compared with the control group. CONCLUSION: Our results suggested that ALA treatment during IVM had a beneficial effect on developmental competence of ovine oocytes by increasing the blastocyst formation and this might be due to the altered abundance of apoptosis-regulatory genes.

Plasmin digest of κ-casein as a source of antibacterial peptides.

This study investigated the antibacterial properties of plasmin, the plasmin hydrolysis of bovine κ-casein and the fractions (named κC1, κC2, κC3, κC4, and κC5) liberated from it using RP-HPLC. The target bacteria were Escherichia coli, Staphylococcus aureus (pathogenic), Lactobacillus casei and Lactobacillus acidophilus (probiotic). Three peptides (kC1, kC3, and kC4) were found to have antibacterial activity, with κC3 peptide being the most active. The plasmin digest of bovine κ-casein proved to be stronger than any of its fractions in terms of antibacterial potential. Measurement of the minimum inhibitory concentration (MIC) showed that Gram-positive bacteria are generally more sensitive to antibacterial activity than Gram-negative bacteria. The MIC of nisin, as a bacteriocin peptide, was also measured. The three antibacterial peptides were identified using LC-Mass. The molecular mass of kC1, kC3, and kC4 corresponded to the f(17-21), f(22-24), and f(1-3) of bovine κ-casein, respectively. It was also found that the positive charge and hydrophobicity of a peptide are not key factors in antibacterial activity. On the whole, the present study demonstrated that the plasmin digest of κ-casein has a high antibacterial potential and can be considered as a natural antibacterial agent in the food chain.

The effect of multiplex-PCR-assessed major pathogens causing subclinical mastitis on somatic cell profiles.

The major pathogens causing mastitis were evaluated by multiplex-polymerase chain reaction (M-PCR) with self-designed primers in four quarters of the first, third, and fifth parities in industrial, semi-industrial, and traditional dairy cattle farms in Iran. With the incidence of infection in the quarters by Staphylococcus aureus and Streptococcus agalactiae, the mean log somatic cell count (log SCC) increased from 5.06 to 5.77. The smallest changes occurred with Escherichia coli. Contagious pathogens, when compared with environmental pathogens, were more prevalent and common and created more profound quantitative and qualitative changes in SCC profiles. The second part of the study surveyed the diversity of contaminating pathogens and their effect on quantitative and qualitative profiles of somatic cells. M-PCR was used to determine the absence (M-PCR(-)) and presence of one (M-PCR(+1)), two (M-PCR(+2)), and three (M-PCR(+3)) major pathogens in raw milk samples. Quarter log SCC increased from 5.06 (for M-PCR(-1)) to 5.5 (for M-PCR(+1)), 5.7 (for M-PCR(+2)), and 6 (for M-PCR(+3)). Percent changes in polymorphonuclears (PMNs) were not significant between different quarters and parities but were significant between different farms in terms of pathogen diversity (P < 0.05). Therefore, by increasing the number of types of major pathogens involved in subclinical mastitis, SCC of udder quarters and the proportion of PMNs significantly increased, whereas the proportion of lymphocytes significantly decreased. This subject is very important in increasing the shelf life of dairy products, because PMNs are introduced to the enzymatic pools.