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.     

Genetic and phenotypic aspects of early reproductive performance in Raeini Cashmere goats

This study used pedigree information and data collected from 1979 to 2012 at the Raeini Cashmere goat breeding station, located in Baft City in Kerman Province in southeastern Iran. Genetic and phenotypic parameters for early reproductive traits of breeding does, including total numbers of kids born at first kidding (LSB1), total numbers of kids weaned at first kidding (LSW1), total birth weight of all kids born at first kidding (LWB1), total weaning weight of all kids weaned at first kidding (LWW1), and age at first kidding (AFK), were estimated using a Bayesian approach via Gibbs sampling. Posterior means for heritability estimates of LSB1, LSW1, LWB1, LWW1, and AFK were statistically significant, with values of 0.12, 0.23, 0.17, 0.15, and 0.46, respectively. Low-to-moderate additive genetic variation was present for the studied reproductive traits. Estimated genetic correlations among LSB1, LSW1, LWB1, and LWW1 were statistically significant and ranged from 0.12 between LWB1 and LWW1 to 0.72 between LSB1 and LSW1. Corresponding phenotypic correlation estimates were also statistically significant and ranged from 0.04 between LWB1 and LWW1 to 0.55 between LSB1 and LSW1. Posterior means of genetic and phenotypic correlations between AFK and other studied traits were statistically significant only for LSB1 and LWB1. For LSB1, LSW1, LWB1, and LWW1, we conclude that genetic and phenotypic improvement in any of these traits in Raeini Cashmere does would favorably influence all of the other traits. However, does that first kidded at younger ages have smaller litters at birth and lower litter birth weights at their first parity.

     

DNA vaccine-encoded glycoprotein B of HSV-1 fails to protect chronic morphine-treated mice against HSV-1 challenge

The use of morphine has been demonstrated to increase susceptibility to infections. Herpes simplex virus type 1 (HSV-1) is a highly successful pathogen among immunocompromised individuals. In the present study, due to the importance of HSV vaccination in morphine abusers, the effects of chronic morphine exposure on the host response to a HSV-1 gB DNA-based vaccine have been investigated. The study is addressing an important aspect of vaccine development among the susceptible (immunocompromised) hosts. BALB/c mice were exposed to morphine over 11 days. They were then vaccinated with DNA vaccine or KOS strain as a live vaccine. The findings showed that the morphine-treated animals failed to respond to DNA vaccination evaluated by the anti-HSV gB antibody titer, delayed type hypersensitivity (DTH) and lethal HSV-1 challenge. Under the same conditions, the KOS vaccine showed a reduced Ab titer and DTH response in morphine-treated mice, but could protect mice against the lethal challenge and was safe for vaccination of morphine-treated animals.     

Serum biochemistry and hematology values and hemoglobin electrophoresis in Persian squirrels (Sciurus anomalus)

BACKGROUND: Serum biochemical and hematologic parameters are important in the management of game species in Iran, such as Persian squirrels. OBJECTIVE: The purpose of this study was to establish baseline serum chemistry and hematology values in Persian squirrels (Sciurus anomalus) and describe blood cell morphology and the electrophoretic pattern of hemoglobin. METHODS: Blood samples were collected from 30 Persian squirrels (Sciurus anomalus) maintained in captivity in the Tehran Zoo. Blood was placed into EDTA and serum clot tubes and analyzed using standard manual hematology and biochemical techniques. Hemoglobin electrophoresis was done on cellulose acetate paper strips. RESULTS: Minimum, maximum, and median values were obtained for 11 hematologic and 12 serum chemistry parameters. Hypersegmented neutrophils were observed frequently. We did not find basophils or band neutrophils. Hemoglobin electophoresis resulted in a band slightly anodal to that of human hemoglobin A. CONCLUSION: Biochemical and hematologic values in Persian squirrels were comparable to those of related species, and may be used as a standard profile for healthy Persian squirrels kept in captivity.     

Antibacterial activities of a new combination of essential oils against marine bacteria

The antibacterial activities of essential oils and herbal extracts have been demonstrated against a range of bacterial species. In this study, the antibacterial effects of a new combination of essential oils from the herbs Thymus vulgaris, Salvia officinalis, Eucalyptus globulus and Mentha piperita were assayed against common bacterial isolates (Staphylococcus aureus, Escherichia coli and Pseudomonas aeroginosa) and fifteen novel marine bacteria isolates. The sensitivity of different isolates to antibacterial activity of the essential oils was determined using well diffusion assays. Minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) were quantified by micro dilution assays. The data demonstrate that the combination of essential oils had potent antibacterial effects and marine bacteria were more sensitive to growth inhibition (P < 0.05). MIC rates were 0.77–6.18 mg/ml, and MBC rates were 1.67–12.30 mg/ml. This indicates that the combined essential oils (CEO) can be a new source of antibacterial agents for use in marine aquaculture.     

Effects of prebiotic mannan oligosaccharide on the growth,survival, and anxiety-like behaviors of zebrafish (Danio rerio)

A study was designed to investigate the possible positive prebiotic effects of mannan oligosaccharides (MOS) on growth and reduction of anxiety behaviors in zebrafish (Danio rerio). The experimental diets were supplemented with 0, 2, 4, 6, or 8 g MOS kg^?1 and were fed to juvenile fish (0.47 ± 0.017 g) in triplicates for six weeks. Significant differences were found in the final body weight, body weight intake, percent body weight intake, and specific growth rate among treatments. The regression analyses showed that the optimum MOS level was 4–4.1 g MOS kg^?1 diet. Fish fed 4 g MOS kg^?1 feed showed higher survival than the other treatments. Also, using the novel tank test, fish fed with 4 g MOS kg^?1 diet showed lower anxiety by swimming in the upper portion of the tank. The other behavior parameters remained unaffected by the prebiotic. The results indicated the beneficial effect of the prebiotic MOS on growth and partly on welfare of zebrafish juveniles.     

Assessment of the Antibacterial Effect of Chitosan Coated with Heracleum persicum Oil on Rainbow Trout Quality

Today, due to the rapid spoilage of fish, the use of natural preservatives is a priority over those of synthetic varieties. Also, the natural antimicrobial effects of essential oils can help to increase shelf life. There are very few studies concerning the use of essential oils in this regard. In the present study, the antibacterial effect of chitosan coated with Heracleum persicum oil was investigated on the quality of rainbow trout. The control and the coated fish samples were analyzed periodically by generalized estimating equation (GEE) for total viable count (TVC), psychrophilic bacteria, total volatile base nitrogen (TVB-N), polyunsaturated fatty acids (PUFA), texture, taste, odor, and overall acceptance parameters. The results showed that by increasing the amount of chitosan, TVC, psychrophilic bacteria, and TVB-N decreased while PUFA, texture, taste, odor, and overall acceptance parameters increased.     

The effect of maternal size on larval characteristics of Persian sturgeon Acipenser persicus

The objective of this work was to study the relationship between female size (weight) and variables of egg and larval stage of Persian sturgeon Acipenser persicus . In this study, 19 female breeders were captured in Caspian Sea and fertilized by routine methods. Positive significant correlations ( P <0.05) were established between female weight and ovulated eggs per female, time of second mitosis division and volume of yolk-sac at hatching. There was not significant correlation ( r =0.33, P =0.161) between female weight and egg diameter. Female weight was not affected weight of larvae at hatching time ( r =0.37, P =0.119), as well as larval length ( r =−0.14, P =0.558) and larval weight at the end of the experiment (48 hours after first feeding) ( r =0.16, P =0.491). Mortality rate during yolk-sac absorption was higher with increased female weight but their correlation was not significant ( r =0.40, P =0.076). During the first feeding stage, mortality rate was 13.39% and there was no significant correlation between mortality rate in this period and female weight ( r =−0.12, P =0.613). Conclusively, as a result female size influenced fecundity, time of second mitosis division and yolk-sac volume at hatching time without affecting mortality rate during yolk-sac absorption and first feeding stage in Persian sturgeon. Thus, smaller female broods do not cause more mortality than larger ones in larval production and they can be used in reproduction procedure.     

Evaluation of dietary natural mineral materials as an antibiotic replacer on growth performance,non‐specific immune responses and disease resistance in rainbow trout,Oncorhynchus mykiss

We evaluated the effects of some dietary natural mineral materials as an antibiotic replacer based on growth performance, non‐specific immune responses and disease resistance in juvenile and subadult rainbow trout, Oncorhynchus mykiss. First experiment, juvenile rainbow trout averaging 2.7 ± 0.02 g (mean ± SD) were fed one of the six experimental diets; a basal commercial diet as a control (CON), CON with oxytetracycline (OTC), with yellow loess (YL), with Macsumsuk^® (MS), with Song‐Gang^® stone (SG) and with barley stone (BS) at 0.4% of each diet. At the end of 8‐week feeding trial, weight gain (WG), specific growth rate (SGR), feed efficiency (FE) and protein efficiency ratio (PER) of fish fed YL diet were significantly higher than those of fish fed CON diet. Non‐specific immune responses such as superoxide dismutase (SOD), myeloperoxidase (MPO), lysozyme (LYS) activity and oxidative radical production of fish fed YL diet were higher than those of fish fed CON diet. At the end of 15 days of challenge test with Aeromonas salmonicida, average cumulative survival rate of fish fed YL diet was significantly higher than that of fish fed BS and CON diets. However, there were no significant differences among fish fed YL, SG and OTC diets. Second experiment, subadult rainbow trout averaging 261.5 ± 3.5 g (mean ± SD) were fed one of the four experimental diets for 22 weeks: CON, and CON with OTC, YL or SG at 0.4% of each diet. At the end of feeding, growth performance of fish fed SG and YL diets was significantly higher than that of fish fed CON diet. Non‐specific immune responses in terms of SOD, MPO, LYS and NBT of fish fed SG and YL diets were significantly higher than those of fish fed CON diet. However, there were no significant differences among the fish fed YL, SG and OTC diets. The results indicate that dietary yellow loess or Song‐gang^® stone at 0.4% of diet could replace oxytetracycline in juvenile and subadult rainbow trout.     

Growth and economic analysis of freshwater prawn,Macrobrachium rosenbergii (de Man), produced with feeds substituting sunflower cake for fish meal,soya bean meal and mustard oil cake

A feeding trial with Macrobrachium rosenbergii was carried out to test the effectiveness of sunflower cake (SFC) as a replacement for conventional protein sources. Four isonitrogenous (~30% crude protein) and isocaloric (388–402 kcal) diets were formulated. Diet‐1 was a control made with conventional ingredients including fish meal, soya bean meal and mustard oil cake. Diet‐2, Diet‐3 and Diet‐4 were made with 30%, 40% and 50% SFC, respectively, replacing the usual protein sources used in Diet‐1. After 100 days, diets with SFC inclusion showed favourable growth and economic performance trends compared to control diet‐1, but without significant differences (p > .05). Better production (572.89 ± 62.99 kg/ha) was observed with Diet‐4 followed by Diet‐2, Diet‐3 and Diet‐1. Diet‐4 revealed the best feed conversion ratio (2.56 ± 0.24), specific growth rate (1.18 ± 0.05) and protein efficiency ratio (1.14 ± 0.10) among these diets. Whole carcass composition analysis revealed highest crude protein (18.19%) and lipid (4.43%) content in prawns fed Diet‐3 followed by Diet‐4. Highest total income, gross margin and benefit cost ratio (BCR) per hectare from prawns were US$5,759, US$2,623 and 1.84, respectively, found in Diet‐4. This study demonstrates that 30%–50% inclusion of SFC has favourable impacts on productivity and profitability compared with controls, with 50% SFC inclusion as the most cost‐effective diet for prawns without apparent compromise in growth, flesh quality or economics. The performances of the diets suggest that SFC may be a suitable substitute for fishmeal, soya bean meal and mustard oil cake in prawn feed. The effectiveness of higher SFC concentrations should also be investigated.