Genome-wide association studies of preweaning growth and in vivo carcass composition traits in Esme sheep

Sheep are considered as a major contributor of global food security. Moreover, sheep preweaning growth traits as well as in vivo carcass composition traits such as ultrasonic measurements of Longissimus dorsi muscle depth (UMD) and back-fat thickness (UFD) are crucially important indicators of meat yield and hot carcass composition. Despite their relative importance for productivity and profitability of a sheep production system, detected QTL for these traits are quite scarce. Therefore, we implemented GWAS for these traits using animal mixed model-based association approach provided by GenABEL in Esme sheep. Three genome-wide and 14 individual chromosome-wide associated SNPs were discovered. As a result, ESRP1, LOC105613082, ZNF641, DUSP5, TEAD1, SMOX, PTPRT, RALYL, POM121C, PHIP, LOC101106051, ZIM3, PEG3, TRPC7, FBXL4, LOC105610397, LOC105616489 and DNAAF2 were suggested as candidates. Some of the discovered genes and involved pathways were already annotated to contribute growth and development in various species including human, mice and cattle. All in all, the results of this study are expected to strongly contribute to shed a light on the underlying molecular mechanisms behind growth and carcass composition traits, with potential implications on studies aiming faster genetic improvement, targeted low-resolution SNP panel designs and genome-editing studies.     

Assessment of compost and three biochars associated with Ailanthus altissima (Miller) Swingle for lead and arsenic stabilization in a post-mining Technosol

The elevated presence of metal(loid)s in the environment significantly impacts ecosystems and human health and is generally largely due to industrial and mining activities. Thus, in the current study, we investigated and proposed an environmentally friendly method (phytomanagement) aimed at reducing the negative impacts associated with metal(loid) pollution through the use of soil amendments (biochar and compost) to permit Ailanthus altissima growth on a highly contaminated mining Technosol, with arsenic (As) and lead (Pb) contents of 539.06 and 11 453 mg kg^-1, respectively. The objective was to examine the impacts of three biochars and compost on i) the physicochemical characteristics of soil, ii) metal(loid) immobilization in soil, and iii) A. altissima growth. We revealed that the application of biochar as a soil amendment improved soil conditions by increasing soil electrical conductivity, pH, and water-holding capacity. Moreover, concomitantly, we observed a large reduction (99%) in Pb mobility and availability following application of the hardwood biochar in combination with compost (HBCP). Thus, this combined soil amendment was most effective in promoting A. altissima growth. In addition, the HBCP treatment prevented As translocation in the upper parts of plants, although soil pore water As concentration was not diminished by amendment application.     

Effect of cultural practices on the development of arabica coffee berry disease,caused by <Emphasis Type="Italic">Colletotrichum kahawae</Emphasis>

In the high altitude regions of Africa, coffee berry disease (CBD), caused by Colletotrichum kahawae, is the main constraint for arabica coffee (Coffea arabica) production. However, certain agricultural practices can reduce losses caused by the disease and thereby promote optimum production. On small family farms in Cameroon, mixed cropping with fruit trees, intercropping with food crops and maintenance pruning of coffee trees are very widespread agricultural practices that can affect CBD epidemics. Consequently, an epidemiological study was conducted to assess how cultural practices affected the disease in an arabica coffee smallholding in Cameroon. The disease was monitored on a weekly basis over four successive years (2002–2005) on coffee trees in diverse cultural situations. Cultural practices likely to reduce losses due to CBD were identified. The infection rate was significantly lower on coffee trees grown intensively than on coffee trees grown in the traditional manner. Coffee trees located under the shade of fruit trees were significantly less attacked than those located in full sunlight. In addition, berries on the leafless parts of branches, near the main trunk of the coffee tree, were less infected than those on leafy sections. These results show that maintenance pruning, removal of mummified berries, and mixed cropping with shade plants are cultural practices which create environmental conditions that limit CBD development.     

Multiplex real-time PCR for the detection and differentiation of equid herpesvirus 1 (EHV-1) and equid herpesvirus 4 (EHV-4)

A multiplex real-time PCR was designed to detect and differentiate equid herpesvirus 1 (EHV-1) and equid herpesvirus 4 (EHV-4). The PCR targets the glycoprotein B gene of EHV-1 and EHV-4. Primers and probes were specific to each equine herpesvirus type and can be used in monoplex or multiplex PCRs, allowing the differentiation of these two closely related members of the Alphaherpesvirinae. The two probes were minor-groove binding probes (MGB) labelled with 6-carboxy-fluorescein (FAM) and VIC for detection of EHV-1 and EHV-4, respectively. Ten EHV-1 isolates, six EHV-1 positive clinical samples, one EHV-1 reference strain (EHV-1.438/77), three EHV-4 positive clinical samples, two EHV-4 isolates and one EHV-4 reference strain (EHV-4 405/76) were included in this study. EHV-1 isolates, clinical samples and the reference strain reacted in the EHV-1 real-time PCR but not in the EHV-4 real-time PCR and similarly EHV-4 clinical samples, isolates and the reference strain were positive in the EHV-4 real-time PCR but not in the EHV-1 real-time PCR. Other herpesviruses, such as EHV-2, EHV-3 and EHV-5 were all negative when tested using the multiplex real-time PCR. When bacterial pathogens and opportunistic pathogens were tested in the multiplex real-time PCR they did not react with either system. The multiplex PCR was shown to be sensitive and specific and is a useful tool for detection and differentiation of EHV-1 and EHV-4 in a single reaction. A comprehensive equine herpesvirus disease investigation procedure used in our laboratory is also outlined. This procedure describes the combination of alphaherpesvirus multiplex real-time PCR along with existing gel-based PCRs described by other authors.     

Alleviation of alternate bearing phenomenon in mango (Mangifera indica L.) trees using boron and nitrogen fertilization

Abstract

This investigation was conducted during two successive seasons (2014/2015) and (2015/2016) using 15?years old productive mango (Mangifera indica) trees cv. Zebda. The trees were grown at AlMalak Valley Farm, El-Sharkeya Governorate- Egypt (30–51° North; 32–53° East). Trees were planted 8?×?8 meter within and between rows in sandy soil under drip irrigation system using the Nile water. The objective of this study is to alleviate alternate bearing in cv. Zebda using mineral nutrients (nitrogen in the on year and boron in the off year). Treatments included three concentrations of nitrogen (1000, 1250, 1500?g/tree/year) and three concentrations of boron (0.0, 250, 500?mg L^?1). Nitrogen was applied to the soil as ammonium sulfate and boron was applied as foliar spray of boric acid. The extra amount of nitrogen fertilizer (250 and 500?g N/tree) was applied at three installments in (May, June and July). Treatment was arranged in a factorial Completely Randomized Block Design with three replicates for each treatment. Results show that the on-year nitrogen fertilization significantly increased mango tree vegetative growth (number of shoot/branch, shoot length, shoot thickness, number of leaves/meter and leaf area) and yield. The average yield in the on year is 85.5?kg/tree at 1250?g N/tree but 67.4?Kilogram/tree at 1000?g N/tree (the control treatment). While in the off year boron foliar application resulted in a significant increase in flowering, initial fruit set, final fruit set and fruit yield. The average yield in the off year is 47?kg/tree at 250?mg L^?1 boron but 9?kg/tree at 0.0?mg L^?1 boron rate (the control treatment).The interaction treatment of 250?mg L^?1 boron + 1500?g nitrogen/tree is the best treatment as it resulted in the highest values for all the tested parameters. The average yield of this treatment is 53.5?kg/tree. This treatment helps alleviate alternate bearing phenomenon by 41% and obtain the highest economic yield in the off-year, i.e. increased yield by 5.9 fold.     

MicroRNA-21 expression,serum tumor markers,and immunohistochemistry in canine mammary tumors

Background

Canine mammary tumors (CMTs) are one of the most common malignancies in dogs and are associated with significant mortality. Serum tumor markers and non-coding microRNAs have gained widespread popularity in human oncology studies. The present study has two aims, first one is to investigate the miR-21 expression compared with changes in serum tumor markers (CEA and CA15-3) in CMT. The second aim is to detect the immunohistochemistry markers as vimentin, P63, and -SMA in CMT.

Methods

This study enrolled 17 female dogs: 10 with mammary tumors and seven controls without tumors. Blood samples were collected to measure miR-21, CEA, and CA 15-3, and histological samples were prepared for histological grading and immunohistochemistry.

Results

CA 15-3 was elevated in all animals, whereas CEA levels showed no change compared with controls. miR-21 was upregulated 12.84-fold in animals with CMT. The most frequently recorded CMT was the mixed type. Myoepithelial cells were identified by P63 immunoreactivity, but not SMA. High expression of miR-21 was observed with positive vimentin immunoreactivity, indicating the mesenchymal origin of the tumor cells.

Conclusion

The present study showed that miR-21 was elevated to a greater extent than CA 15-3 (12.84-fold vs. threefold). Tumors that was positive for vimentin immunoreactivity was also associated with an elevation in the levels of miR-21, showing that miR-21 is released from mesenchymal cells. These findings support the hypothesis that miR-21 may be a more sensitive, noninvasive indicator for CMT.

     

Improvement of functional properties of egg white protein through phosphorylation by dry-heating in the presence of pyrophosphate

Egg white protein (EWP) was phosphorylated by dry-heating in the presence of pyrophosphate at pH 3.0-7.0 and 85 degrees C for 1 and 5 days, and the functional properties of the phosphorylated EWP (PP-EWP) were investigated. The phosphorylation was accelerated with a decrease of pH from 7.0 to 3.0 and for heating times from 1 to 5 days. The phosphorus content of EWP increased approximately 1.05% by dry-heating at pH 4.0 and 85 degrees C for 5 days in the presence of pyrophosphate, which was higher than that of casein. The electrophoretic mobility of EWP increased with an increase in the phosphorylation level. The surface hydrophobicity of EWP increased by phosphorylation. The heat stability, emulsifying properties, and digestibility of EWP were improved by phosphorylation. The calcium phosphate-solubilizing ability of EWP was enhanced by phosphorylation. A firmer and transparent heat-induced gel of PP-EWP was obtained, and the water-holding capacity of heat-induced PP-EWP gel was higher that that of the control. These results suggest that phosphorylation by dry-heating in the presence of pyrophosphate is a useful method for improving the functional properties of EWP.     

Metabolic characterization of Brassica rapa leaves by NMR spectroscopy

The Brassica has been intensively studied due to the nutritional and beneficial effects. However, many species, varieties, and cultivars of this genus and the resulting large metabolic variation have been obstacles for systematic research of the plant. In order to overcome the problems posed by the biological variation, the metabolomic analysis of various cultivars of Brassica rapa was performed by NMR spectroscopy combined with multivariate data analysis. Discriminating metabolites in different cultivars and development stages were elucidated by diverse 2D-NMR techniques after sorting out different significant signals using (1)H NMR measurements and principal component analysis. Among the elucidated metabolites, several organic and amino acids, carbohydrates, adenine, indole acetic acid (IAA), phenylpropanoids, flavonoids, and glucosinolates were found to be the metabolites contributing to the differentiation between cultivars and age of Brassica rapa. On the basis of these results, the distribution of plant metabolites among different cultivars and development stages of B. rapa is discussed.     

Genetic variability and estimates of heritability in sorghum (Sorghum bicolor L.) genotypes grown in a semiarid zone of Sudan

A field experiment was conducted to evaluate nine genotypes of sorghum grown for two consecutive cropping seasons in 2006 and 2007 under rain-fed conditions in a semiarid zone at the Research Farm of El Fasher Research Station, Sudan. The objective of the study was to assess genetic variability and heritability among sorghum genotypes using phenotypic morphological traits. A randomized complete block design with four replications was used for the experiment. The grain yield (kg ha^?1), the number of heads/plant, followed by straw yield (kg ha^?1) had the highest genotypic coefficients of variation in both seasons. High heritability (above 95%) was shown for plant height in both seasons. High genetic advance was reported in straw yield, 1000-grain weight and days to flowering in both seasons. Highly significant differences among genotypes were found for all characters. The high-yielding genotype was Adv-Edo-CWS (E-9) with grain yields of 2780.6 kg ha^?1. Grain yield was significantly and positively correlated with straw yield (r = 0.91), number of heads/plant (r = 0.69), plant height (r = 0.53) and 1000-grain weight (r = 0.36). However, it was significantly and negatively correlated with days to 50% flowering (r = ?0.21). Based on their positive association with grain yield, the character’s straw weight, number of heads/plant, plant height and 1000-grain weight would be the preferable selection criteria for sorghum improvement program in the country.