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.     

Effect of triploidization on juvenile African catfish (<Emphasis Type="Italic">Clarias gariepinus</Emphasis>)

Triploid African catfish (Clarias gariepinus) produced through cold shock 3 min post fertilization were compared to diploid offspring of the same parentage at 66 days of age. Triploid fish were significantly shorter (11%) and weighed less (18%) than diploids but showed no significant difference in mortality or cannibalism, which can be an important source of losses under aquaculture conditions. Erythrocytes of triploid fish were more oval shaped than the normal spherical shape of diploid erythrocytes, were significantly larger (38%) and had nuclei that were significantly larger (25%) than observed in diploid fish. Erythrocyte morphological characteristics show potential as an indicator for the detection of triploidy in African catfish.     

Agricultural zinc fluxes into soils and crops of central Iran at regional scale

Mass flux assessment can provide information that is essential for a sustainable management of elements in agricultural soils. In this article, we present an assessment of regional-scale averages of zinc (Zn) fluxes into agricultural soils and crops of central Iran for the period 1997–2011, using available databases such as regional agricultural statistics. The basic units of the balances were 15 townships of the provinces Qom, Isfahan and Fars. Averaged over the entire study region, the net Zn input into arable soil resulting from all fertilizer inputs – Zn removal with harvested crops was 1515 g ha^?1 yr^?1 across the entire region, with a range of 438–3009 g ha^?1 yr^?1 among townships. Estimated average Zn inputs with manure, mineral fertilizers, sewage sludge and compost were 1254, 531, 19 and 7 g ha^?1 yr^?1, respectively. The input-to-output ratio of these fluxes ranged from 1.8 to 12.9 among townships and averaged 6.1 for the entire study area. Considering that outputs other than with crop harvests are minor, Zn stocks are rapidly building up in the soils of the study region. Uncertainties in the manure and crop removal data were the main sources of estimation uncertainty in this study.     

Chrysin Reduced Acrylamide-Induced Neurotoxicity in Both in vitro and in vivo Assessments

Background: Acrylamide (ACR) is a well-known industrial toxic chemical that produces neurotoxicity, which is characterized by progressive central and peripheral neuronal degeneration. Chrysin is a natural, biologically active flavonoid compound, which is commonly found in many plants. The antioxidant and neuroprotective properties of chrysin have been demonstrated. Methods: In this study, the possible effect of chrysin on ACR-induced toxicity was evaluated in both in vitro and in vivo experiments. PC12 cells were used as a suitable in vitro model. Cells were exposed to chrysin (0.5-5 µM) for 12 and 24 h, and then ACR in IC₅₀ concentration was added to the cells. Finally, cell viability was determined using (4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium assay. For in vivo assay, Wistar rats were treated with ACR (50 mg/kg i.p. for 11 days) alone or in combination with chrysin (12.5, 25, and 50 mg/kg). At the end of treatment, behavioral index was evaluated. Results: ACR decreased cell viability and pre-treatment with chrysin (0.5-5 µM) significantly decreased ACR-induced cytotoxicity in the time- and dose-dependent manner. In Wistar rats, exposure to ACR significantly induced severe gait abnormalities, but treatment with chrysin (50 mg/kg) reduced ACR-induced neurotoxicity in animals. Conclusion: In the current study, chrysin exhibited neuroprotective effect on PC12 cells as an in vitro model and also on Wistar rats. Iran. Key Words: Acrylamide, Chrysin, Neurotoxicity, Antioxidant     

Effect of sucrose concentrations on somatic embryogenesis in carnation (Dianthus caryophyllus L.)

The effect of sucrose concentration on callus induction followed by differentiation of embryogenic callus derived from petal explants of four carnation cultivars (Nelson, Sagres, Spirit and Impulse) was investigated. Embryogenic calli were produced on Murashige and Skoog [Murashige, T., Skoog, F.A., 1962. Revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol. Plant 154, 73–479] basal medium (MS) culture medium containing six concentrations of sucrose (3, 6, 9, 12, 15 and 18%, w/v) all supplemented with 9 μM 2,4-dichlorophenoxyacetic acid (2,4-D) and 0.8 μM 6-benzyladenine (BA). Maximum frequency of embryogenic callus was obtained from the media containing 9 and 12% sucrose. Somatic embryos were induced on a hormone-free MS media containing the seven concentrations of sucrose. Development of somatic embryos was enhanced by increasing sucrose concentration from 1.5 to 12%, while it was reduced in higher concentrations of 15 and 18%. However, normal embryos were not developed in the media containing 1.5 and 3% sucrose. Ninety-five percent of somatic embryos were regenerated to form the entire plantlets when they transferred onto the half-strength hormone-free MS culture medium containing 3% sucrose. Plantlets were also continued to grow normally under greenhouse condition.     

Quantitative trait loci (QTL) associated with resistance of rainbow trout Oncorhynchus mykiss against the parasitic ciliate Ichthyophthirius multifiliis

The parasitic ciliate Ichthyophthirius multifiliis has a low host specificity eliciting white spot disease (WSD) in a wide range of freshwater fishes worldwide. The parasite multiplies rapidly whereby the infection may reach problematic levels in a host population within a few days. The parasite targets both wild and cultured fish but the huge economic impact of the protozoan is associated with mortality, morbidity and treatment in aquacultural enterprises. We have investigated the potential for genetic selection of WSD-resistant strains of rainbow trout. Applying the DNA typing system Affymetrix^® and characterizing the genome of the individual fish by use of 57,501 single nucleotide polymorphisms (SNP) and their location on the rainbow trout chromosomes, we have genetically characterized rainbow trout with different levels of natural resistance towards WSD. Quantitative trait loci (QTL) used for the selection of breeders with specific markers for resistance are reported. We found a significant association between resistance towards I. multifiliis infection and SNP markers located on the two specific rainbow trout chromosomes Omy 16 and Omy 17. Comparing the expression of immune-related genes in fish—with and without clinical signs—we recorded no significant difference. However, trout surviving the infection showed high expression levels of genes encoding IgT, T-cell receptor TCRβ, C3, cathelicidins 1 and 2 and SAA, suggesting these genes to be associated with protection.     

Gill amoebae from freshwater rainbow trout (Oncorhynchus mykiss): In vitro evaluation of antiparasitic compounds against Vannella sp.

Gill parasitic infections challenge farming of rainbow trout (Oncorhynchus mykiss, Walbaum) in freshwater facilities. Apart from flagellates (Ichthyobodo, (Pinto) and ciliates (Ichthyophthirius (Fouquet), Ambiphrya (Raabe), Apiosoma (Blanchard), Trichodinella (Sramek-Husek) and Trichodina (Ehrenberg)), we have shown that amoebae are prevalent in Danish trout farms. Gills were isolated from farmed rainbow trout in six fish farms (conventional and organic earth pond and recirculated systems) and placed on non-nutrient agar (NNA) moistened with modified Neff's amoeba saline (AS) (15°C). Gill amoebae from all examined fish colonized the agar and were identified based on morphological criteria showing species within the genera Trinema (Dujardin) (family Trinematidae), Vannella (Bovee) (family Vannellidae). In addition, hartmannellid amoebae were recorded. We established a monoculture of Vannella sp., confirmed the genus identity by PCR and sequencing and performed an in vitro determination of antiparasitic effects (dose–response studies) of various compounds including sodium chloride (NaCl), hydrogen peroxide, peracetic acid, formalin, aqueous garlic and oregano extracts and a Pseudomonas H6 surfactant. All amoebae were killed in concentrations of 16.90 mg/ml (garlic), 17.90 mg/ml (oregano), NaCl (7.5 mg/ml), hydrogen peroxide (100 µg/ml), peracetic acid (0.03 µg/ml), formaldehyde (25 µg/ml) and the Pseudomonas H6 surfactant (250 µg/ml).     

Appropriateness of farmers’ adoption of irrigation methods: The application of the AHP model

This paper explores the use of analytic hierarchy process (AHP) for selecting an appropriate irrigation method. A sample of farmers was separated into four groups using cluster analysis. A panel of experts utilized AHP to determine the priority of three irrigation methods (border, basin and sprinkler) for each group of farmers. The findings indicated that the highest priority of irrigation methods differed with respect to farmers groups. The appropriateness of the decision of each farming group, regarding selection of irrigation methods, was determined. In 74% of cases, experts confirmed the farmer’s decision in selection of irrigation methods, but questioned the appropriateness of the decision for 26% of farmers. Recommendations are made for future use of decision tools to improve extension programs and farmers decision-making process.