Attribute selection and model evaluation for the maternal and paternal imprinted genes in bovine (Bos Taurus) using supervised machine learning algorithms

Imprinted genes display biased expression of paternal and maternal alleles in mammals. They are marked through epigenetic process during gametogenesis. Characterization of imprinted genes has expanded our understanding of the regulation and function of genes. In the current study, 22 experimentally validated imprinted genes in bovine (Bos Taurus) were analysed. Several supervised machine learning algorithms and attribute weighting methods were used to find characteristics of different types of imprinted genes and suggest a classification method for finding maternally and paternally expressed genes in bovine. For assessing the best model and comparing attributes in other organisms, we have also conducted a comparative analysis for human and sheep imprinted genes. According to the results of the present study, GC contents 10 and 100 kb upstream, Gly and Gln amino acids, Ile/ATC codon usage, LINE and SINE in 100kbup and length of first intron were significantly different between the maternal and paternal genes in cattle. Considering all species together, we found that GC content 100 kb up, LINE 100 kb up and the frequency of amino acids like Gly, Gln and Met were the most important attributes for identifying the paternal and maternal imprinted genes. These findings could imply conservation pattern in the attributes among these species.     

Investigation in early growth traits, litter size, and lamb survival in two Iranian fat-tailed sheep breeds

In the present study, 1,635 lambing records of Ghezel (n?=?766) and Mehraban (n?=?869) breeds were used to evaluate the early growth traits, litter size, and lamb survival in sheep reared in Fars Province, southern Iran, during a 5-year-long period. The least squares means (± SE) of lamb birth weight for Ghezel were 5.27 (±0.22), 5.02 (±0.22), and 3.98 (±0.23) kg for single males, single females, and twin lambs, respectively; whereas, the corresponding values for Mehraban were 4.39 (±0.18), 4.18 (±0.18), and 3.50 (±0.19) kg. The least squares means of pre-weaning lamb growth (gram per day) for Ghezel were 239 (±15), 218 (±15), and 181 (±16) for single males, single females, and twin lambs, respectively, and the corresponding values for Mehraban were 204 (±12), 187 (±12), and 156 (±13). Lambs from 2 year old ewes or younger were on average lighter at birth and at weaning and had a lower average daily gain than those from older ewes (P?<?0.05). The percentage of twin births increased from 1.1 and 1.3 % for ewes aged ≤ 2 years to 19 and 12 % for those aged ≥ 6 years old in Ghezel and Mehraban, respectively (P?<?0.05). The mean pre-weaning lamb mortality was 7.1 and 4.1 % for Ghezel and Mehraban, respectively.     

In vitro maturation and fertilization of prepubertal and pubertal black Bengal goat oocytes

Oocytes retrieval, in vitro maturation (IVM) and fertilization (IVF) efficiency are inevitable steps towards in vitro production of embryos. In the present study, these parameters were investigated in the ovaries of prepubertal (n = 31) and pubertal (n = 61) black Bengal goats obtained from a slaughterhouse. Nuclear maturation was evaluated upon aspiration and following IVM in TCM-199 (Earle''s salt with L-glutamine and sodium bicarbonate) for 27 h at 39℃ under 5% CO₂ in humidified air. The oocytes retrieval and efficiency (mean ± SD) per prepubertal and pubertal goats were 5.2 ± 0.6 and 6.8 ± 0.6, and 77.3 ± 0.1% and 80.5 ± 0.6%, respectively. Anaphase I - telophase I stages differed significantly (7.3 ± 0.8 vs. 2.6 ± 0.2, p < 0.05) between the two groups of goats. After IVM, the percentages of metaphase II were significantly higher (66.3 vs. 60.3, p < 0.05) in pubertal goats than in their prepubertal counterparts. The percentages of normal in vitro fertilization (IVF) in Fert-Tyrode''s albumin lactate pyruvate of pubertal goat oocytes did not differ between Percoll and swim-up sperm separation methods (36.7 ± 0.9% vs. 32.7 ± 1.3%, p > 0.05). Furthermore, sperm capacitation by heparin alone or in combination with ionomycin did not lead to a significant increase in the normal fertilization rate (34.8 ± 1.7 vs. 32.2 ± 1.5%, respectively) in the oocytes of pubertal goats. In conclusion, the ovaries of pubertal black Bengal goats obtained from the slaughterhouse could be used for in vitro embryo production. However, further optimization of the IVM and IVF techniques are necessary for satisfactory in vitro embryo production.     

The Healing Potential of Plantago lanceolata Ointment on Collagenase-Induced Tendinitis in Burros (Equus asinus)

This study was carried out to evaluate the healing potential of water-soluble extract of Plantago lanceolata as a topical ointment on experimental tendinitis in burros. Tendinitis was induced by injection of 2,500 U of bacterial collagenase in the superficial digital flexor tendon of both forelimbs of six male burros. Tendinitis was confirmed ultrasonographically. 48 hours after collagenase injection, two grams of 10% P lanceolata ointment was applied on one limb (treatment group) and the same amount of eucerin (the vehicle of the ointment) on the other limb (control group), every other day for 6 weeks. Ultrasonographic examination of the tendon was performed weekly during the study and mean cross-sectional area of the superficial digital flexor tendon was measured, which was found to increase significantly after injection of collagenase in both groups. From the third week, it decreased significantly in the treatment group in comparison with the control group. At the end of the study, the animals were euthanized for histopathological study of the tendons. In control group, degenerative changes in tendon could be seen, whereas significant degree of healing was observed in the treatment group. It can thus be concluded that the P lanceolata ointment was effective in promoting the healing process of the tendon.     

Effects of tramadol on the minimum alveolar concentration of sevoflurane in dogs

ObjectiveTo evaluate the effect of tramadol on sevoflurane minimum alveolar concentration (MAC_SEVO) in dogs. It was hypothesized that tramadol would dose-dependently decrease MAC_SEVO.Study designRandomized crossover experimental study.AnimalsSix healthy, adult female mixed-breed dogs (24.2 ± 2.6 kg).MethodsEach dog was studied on two occasions with a 7-day washout period. Anesthesia was induced using sevoflurane delivered via a mask. Baseline MAC (MAC_B) was determined starting 45 minutes after tracheal intubation. A noxious stimulus (50 V, 50 Hz, 10 ms) was applied subcutaneously over the mid-humeral area. If purposeful movement occurred, the end-tidal sevoflurane was increased by 0.1%; otherwise, it was decreased by 0.1%, and the stimulus was re-applied after a 20-minute equilibration. After MAC_B determination, dogs randomly received a tramadol loading dose of either 1.5 mg kg^?1 followed by a continuous rate infusion (CRI) of 1.3 mg kg^?1 hour^?1 (T1) or 3 mg kg^?1 followed by a 2.6 mg kg^?1 hour^?1 CRI (T2). Post-treatment MAC determination (MAC_T) began 45 minutes after starting the CRI. Data were analyzed using a mixed model anova to determine the effect of treatment on percentage change in baseline MAC_SEVO (p < 0.05).ResultsThe MAC_B values were 1.80 ± 0.3 and 1.75 ± 0.2 for T1 and T2, respectively, and did not differ significantly. MAC_T decreased by 26 ± 8% for T1 and 36 ± 12% for T2. However, there was no statistically significant difference in the decrease between the two treatments.Conclusion and clinical relevanceTramadol significantly reduced MAC_SEVO but this was not dose dependent at the doses studied.     

Effect of lactation on functional and morphological echocardiographic variables in adult dairy cows

ObjectivesTo study the effect of pregnancy and lactation on echocardiographic parameters in Holstein dairy cows.AnimalsNine multiparous high milk producing (HMP) dairy cows (producing more than 40 kg of milk per day in peak production) and 9 low milk producing (LMP) cows (producing less than 30 kg or milk per day in peak production).MethodsEchocardiography was performed twice; one month before calving and two months after calving.ResultsThe heart rate of HMP cows in the early lactation period was significantly higher than in the dry period. In LMP cows, there was a significant increase in left ventricular dimension in the early lactation period as compared to the dry period, and the interventricular septum in systole (IVSs) in the dry period was significantly thicker than early lactation period. In HMP cows, there was an increase in the right ventricular diameter in systole in the early lactation period as compared to the dry period. Left ventricular and aortic dimensions in the dry period of HMP were significantly higher than those of LMP cows. When the data were corrected for body weight, comparison of values of the dry period of HMP and LMP cows showed that left ventricular volume in systole in HMP was significantly higher and that IVSs, left ventricular fractional shortening and ejection fraction were significantly lower than in LMP cows.ConclusionsThis study demonstrated that lactation influences the intracardiac dimensions. The amount of milk production can influence echocardiographic parameters in dairy cows.     

Experimental caprine coccidiosis caused by Eimeria arloingi: Morphopathologic and electron microscopic studies

The progressive morphohistopathologic changes, distribution pattern of lesions and ultrastructural characteristics in Eimeria arloingi infection were investigated in experimentally infected kids. The 18 newborn animals allocated to 3 equal groups. Two of groups, A, B were inoculated with a single dose of 1 × 10³ and1 × 10⁵ sporulated oocysts of E. arloingi, respectively. At 7, 14, 21, 28, 35, and 42 days postinoculation (DPI), 1 kid from each group was necropsied for pathologic and ultrastructural studies. Progressive lesions were present at 21, 28, 35 and 42 DPI in the jejunum, ileum, cecum with fewer in the duodenum and proximal colon. The oocysts shedding begin between 16 to 18 DPI. Grossly, minimal changes were observed at 21 DPI as few whitish plaques or nodules and advanced lesions at 42 DPI as pseudoadenomatous pattern in the mucosa and a cerebriform pattern on the serosal surface of jejunum and ileum. Early histopathologic lesions due to schizogony phase were including presence of intracytoplasmic developmental stages of the parasite such as trophozoites, immature to mature schizonts and mild infiltration of inflammatory cells. In late lesions due to various stages of gametogony, the histological pattern was mainly remarkable hyperplasia of the villi and crypts epithelial cells, eventually developed into papillary projections of reactive epithelium. The mesenteric lymph nodes showed a few numbers of large schizonts in the cortical lacteals. This study showed E. arloingi as a highly pathogenic species for kids, the incubation period was 16–18 days and the main target organ was jejunum with characteristic morphohistopathologic lesions.     

Rates of inbreeding and genetic diversity in Iranian Holstein Cattle

The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1 048 572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non‐founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non‐founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co‐ancestry and inbreeding, which would lead to better handling of the effective population size.     

A review of okara (soybean curd residue) utilization as animal feed: Nutritive value and animal performance aspects

Year by year, huge quantities of by-products are generated during the manufacturing process of soybean-based products. Okara is one of the by-products, and it is an insoluble portion of the soybean. It consists of high moisture (8.4–22.9%); on dry matter basis, it contains high metabolizable energy (9.0–14.2 MJ/kg) and other components that include crude protein (20.9–39.1%), crude fiber (12.2–61.3%), crude fat (4.9–21.5%), and ash (3.4–5.3%). Fermentation of okara improves its nutritional quality and reduces its anti-nutrient contents. Due to animals' palatability, okara can be used to replace the soybean meal/concentrate feed partially or completely in ruminant's diet and partially in nonruminant's diet. Okara feeding does not depress the intake, digestibility, growth, milk production, blood metabolic profiles, and meat quality of animals. However, this by-product decays quickly due to its high moisture content, and its heavy weight and sticky nature make it difficult to process and expensive to dry using conventional methods. This paper thoroughly summarizes the utilization of okara as animal feed in the cause of developing a general guideline with favorable levels of inclusion in the diets of animals for its exploitation and valorization. This review will encourage further research to develop eco-friendly and value added feed for animals.