Networks of inbreeding coefficients in a selected population of rabbits

The correlation between pedigree and genomic-based inbreeding coefficients is usually discussed in the literature. However, some of these correlations could be spurious. Using partial correlations and information theory, it is possible to distinguish a significant association between two variables which is independent from associations with a third variable. The objective of this study is to implement partial correlations and information theory to assess the relationship between different inbreeding coefficients using a selected population of rabbits. Data from pedigree and genomic information from a 200K SNP chip were available. After applying filtering criteria, the data set comprised 437 animals genotyped for 114,604 autosomal SNP. Fifteen pedigree- and genome-based inbreeding coefficients were estimated and used to build a network. Recent inbreeding coefficient based on runs of homozygosity had 9 edges linking it with different inbreeding coefficients. Partial correlations and information theory approach allowed to infer meaningful associations between inbreeding coefficients and highlighted the importance of the recent inbreeding based on runs of homozygosity, but a good proxy of it could be those pedigree-based definitions reflecting recent inbreeding.     

Production of Galacto-oligosaccharides by the β-Galactosidase from Kluyveromyces lactis : comparative analysis of permeabilized cells versus soluble enzyme

The transgalactosylation activity of Kluyveromyces lactis cells was studied in detail. Cells were permeabilized with ethanol and further lyophilized to facilitate the transit of substrates and products. The resulting biocatalyst was assayed for the synthesis of galacto-oligosaccharides (GOS) and compared with two soluble β-galactosidases from K. lactis (Lactozym 3000 L HP G and Maxilact LGX 5000). Using 400 g/L lactose, the maximum GOS yield, measured by HPAEC-PAD analysis, was 177 g/L (44% w/w of total carbohydrates). The major products synthesized were the disaccharides 6-galactobiose [Gal-β(1→6)-Gal] and allolactose [Gal-β(1→6)-Glc], as well as the trisaccharide 6-galactosyl-lactose [Gal-β(1→6)-Gal-β(1→4)-Glc], which was characterized by MS and 2D NMR. Structural characterization of another synthesized disaccharide, Gal-β(1→3)-Glc, was carried out. GOS yield obtained with soluble β-galactosidases was slightly lower (160 g/L for Lactozym 3000 L HP G and 154 g/L for Maxilact LGX 5000); however, the typical profile with a maximum GOS concentration followed by partial hydrolysis of the newly formed oligosaccharides was not observed with the soluble enzymes. Results were correlated with the higher stability of β-galactosidase when permeabilized whole cells were used.     

Functional and Bioactive Properties of Peptides Derived from Marine Side Streams

In fish processing, a great amount of side streams, including skin, bones, heads and viscera, is wasted or downgraded as feed on a daily basis. These side streams are rich sources of bioactive nitrogenous compounds and protein, which can be converted into peptides through enzymatic hydrolysis as well as bacterial fermentation. Peptides are short or long chains of amino acids differing in structure and molecular weight. They can be considered as biologically active as they can contribute to physiological functions in organisms with applications in the food and pharmaceutical industries. In the food industry, such bioactive peptides can be used as preservatives or antioxidants to prevent food spoilage. Furthermore, peptides contain several functional qualities that can be exploited as tools in modifying food ingredient solubility, water-holding and fat-binding capacity and gel formation. In the pharmaceutical industry, peptides can be used as antioxidants, but also as antihypertensive, anticoagulant and immunomodulatory compounds, amongst other functions. On the basis of their properties, peptides can thus be used in the development of functional foods and nutraceuticals. This review focuses on the bioactive peptides derived from seafood side streams and discusses their technological properties, biological activities and applications.     

Biochemical modulations in açaí palm (Euterpe oleracea Mart.) under vegetative stages in an agroforestry system of the Amazon

Background : The açaí palm (Euterpe oleracea Mart.) is a species native to the Amazon region, where the largest stock of these palms is located in the state of Pará, Brazil. This species occurs predominantly spontaneously in the plateau and plains areas of the Amazonian estuary. Water deficit is the main limiting factor of plants, negatively regulating the growth, metabolism and productivity of crops. Aim : This study aimed to deepen the ecophysiological and biochemical responses of Euterpe oleracea Mart. to a water deficiency condition in agroforestry systems. Methods : The study was carried out in a defined period of lowest rainfall in the region, which runs from July to October, averaging 58.6 mm for those months, such as location, age, uniformity, health, development, height and diameter of the stipe, in order to determine the biochemical variables. Responses to biochemical components under water deficit such as starch, sucrose and carbohydrates increased for rachis and fruits. Results : The concentrations of ammonia and proteins increased in stems and fruits. For amino acids, the structures that accumulated these organic compounds were fruits and arrow. One of the most representative amino acids against water deficiency is proline, and its increase in plant tissues is due to osmoprotein function, especially for structures such as rachis, fruit and petioles + rachis. Conclusions : Therefore, Euterpe oleracea Mart. presents excellent physiological plasticity to deal with stressful conditions as well as adaptive behavior to overcome this deficiency.     

A field study of reproductive performance and productivity of Pelibuey ewes in Southeastern Mexico

The objective was to evaluate the reproductive performance and productivity of Pelibuey ewes in two flocks in Southeastern Mexico. Animals grazed on irrigated star grass (Cynodon plectostachyus). In flock 1, lambs grazed with their mothers from 7 to 70 days of age (weaning age), whereas in flock 2, they were confined and offered chopped grass, a commercial concentrated and managed under restricted suckling until weaning at 60 days of age.. The statistical model included the fixed effects of flock, year and season of lambing, parity number, litter size at weaning, first order interactions and the random effects of ewe and the error term. The means ± SD for age at first lambing, prolificacy, lambing interval (LI), weaning weight, and productivity were 477?±?85.5 days, 1.41?±?0.51 lambs, 255.9?±?51.8 days, 16.5?±?4 kg, and 18.1?±?4.42 kg of lamb weaned, respectively. Repeatability estimates for the latter four traits were 0.09, 0.07, 0.11, and 0.13, respectively. All main effects in the models were significant (P?<?0.001), except for year on LI. Prolificacy and productivity increased with parity number. The shortest LI was in the rainy season. Ewes with two or three lambs produced 8 and 14 kg of lamb more at weaning than single lamb ewes. In conclusion, reproductive performance and productivity could be improved, and the low repeatability estimates suggest that management should be used in a short term rather than genetic approaches.     

Postharvest harpin or Bacillus thuringiensis treatments suppress citrus black spot in ‘Valencia’ oranges

Citrus black spot (CBS) caused by Guignardia citricarpa represents an important threat to citriculture in Brazil. Limited information is available regarding potential biological control agents and new alternative compounds that may provide protection of orange fruits against the disease. In this study, the effects of commercial products based on Bacillus thuringiensis var. kurstaki (Bt) bacterium, Bt pure isolates and Harpin protein (Messenger^®) on the postharvest control of CBS, were evaluated in ‘Valencia’ sweet orange fruits harvested for three consecutive years in a citrus grove. The fruits were sprayed with the following products: DiPel^® WP (Bt, subspecies, kurstaki strain HD-1, 16,000 International Units mg⁻¹, 32 g active ingredient kg⁻¹) (1, 20 and 50 mg ml⁻¹), Dimy Pel^® WP (Bt, subspecies, kurstaki, strain HD-1, 17,600 IU mg⁻¹, 26 g active ingredient l⁻¹) (2, 20 and 50 mg ml⁻¹), Messenger^® (3% harpin protein) (1 and 2 mg ml⁻¹) and fungicide Tecto^® Flowable SC (thiabendazole, 485 g l⁻¹) (0.8 g active ingredient l⁻¹), besides the Bt isolates, Bt- HD-567, Bt- DiPel and Bt- Dimy (9 × 10⁸ CFU ml⁻¹). Ten days after treatment, the number of newly developed CBS lesions and pycnidia produced were evaluated using fifty fruits per treatment. The Dimy Pel^® and Messenger^® reduced the number of new developed CBS lesions on fruits in up to 67% and 62%, respectively. All applied treatments drastically decreased the number of pycnidia produced in the CBS lesions on orange fruits with 85% to 96% reductions compared to the untreated control. Volatile compounds produced by the isolates Bt- HD-567, Bt- Dimy and Bt- DiPel, reduced the number of lesions on treated fruits by 70%, 65% and 71% compared to the control, respectively. In addition, the survival of Bt isolates on orange fruit surfaces were evaluated by recovering and quantifying the number of CFU every seven days for up to 28 days. The declines in survival rates on orange fruit surfaces were drastic for the three strains of Bt in the first week. The CFU numbers of all applied isolates declined by 4 to 5 orders of magnitude after storage at room temperature for 28 days. In vitro assays revealed that the Bt isolates significantly reduced the mycelial growth of the pathogen, ranging from 32% to 51%, compared to the control, whereas no inhibitory effect was observed in the presence of Messenger^®.     

Optimal Immobilization of Acidic Proteases from Monterey Sardine (Sardinops sagax caeurelea) on Partially Deacetylated Chitin from Shrimp Head Waste

ABSTRACT

Response surface methodology was employed to optimize the immobilization yield of acidic proteases from Monterey sardine (Sardinops sagax caeurelea) using partially deacetylated chitin as immobilization support. A rotatable central composite design was applied to evaluate the effects of immobilization conditions such as enzyme loading (X₁), immobilization pH (X₂), and tripolyphosphate concentration (X₃) on the immobilization yield. The analysis of variance revealed that the established model was significant (p < 0.05), and the adjustment of the quadratic model with the experimental data was satisfactory. Under optimal conditions (X₁ = 0.05 mg/mL, X₂ = 3.16, and X₃ = 0.75%), an immobilization yield of 79.1% was achieved; a value that was in accordance with the predicted one.     

Ontogenetic variation of food intake and gut evacuation rate in larvae of the doncella Pseudoplatystoma punctifer,as measured using a non‐destructive method

Food intake (FI) and gut evacuation (Rg) were measured in larvae of Pseudoplatystoma punctifer (4.5–18.4 mm SL) fed Artemia nauplii, taking advantage of the translucence of their abdominal region to achieve this in a non‐destructive way, using digital photographs and mathematical reconstruction of gut volume content (ellipsoidal and cylindrical models for stomach and intestine respectively). The inaccuracy of the method, with reference to counts of nauplii following fish dissection, was low (2.9 ± 1.5%) and independent of fish size (P = 0.6153). Pigmentation hampered measurement in fish >18–19 mm SL. Anaesthesia was needed in fish >9.5 mm SL, thereby preventing the measurement of Rg in individual fish. The FI increased rapidly during the ontogeny, passing from <7% M at 0.6 mg, to 14% M at 1 mg and 21% M at 15–40 mg, and then decreased slightly in larger fish. At 28.5°C, Rg (% M h^?1) was modelled as Rg = ?8.22 + 12.11 log FI + 6.30 log M – 12.67 (log M)² (R² = 0.904, d.f. = 27, with FI in% M and M in mg). Extrapolations of Rg over 24 h gave estimates of daily food rations that fit well with those measured in cannibalistic P. punctifer.     

Diversity of endophytes across the soil-plant continuum for Atriplex spp. in arid environments

Endophytes are hypothesized to be transferred across the soil-plant continuum, suggesting both the transfers of endophytes from environment to plant and from plant to soil. To verify this hypothesis and to assess the role of locality, we evaluated the similarity of microbial communities commonly found both in soils and endophytic communities in three arid regions, i.e. the Jornada LTER(Long Term Ecological Research) site in New Mexico, USA, and the research station of Jordan University of Science and Technology(JUST) and Khanasri research station in Badia region of Jordan. Rhizosphere and non-rhizosphere soils, leaves and seeds of Atriplex spp. were sampled. Diversity and distribution of bacteria and fungi across the soil-plant continuums were assessed by tag-encoded FLX amplicon pyrosequencing and sequence alignment. Of the total bacterial OTUs(operational taxonomic units), 0.17% in Khanasri research station, 0.16% in research station of JUST, and 0.42% in Jornada LTER site were commonly found across all the plant and soil compartments. The same was true for fungi in two regions, i.e. 1.56% in research station of JUST and 0.86% in Jornada LTER site. However, in Khanasri research station, 12.08% of total fungi OTUs were found in at least one soil compartment and one plant compartment. Putative Arthrobacter, Sporosarcina, Cladosporium and members of Proteobacteria and Actinobacteria were found across all the soil-plant continuums. Ascomycota, mainly including Didymellaceae, Pleosporaceae and Davidiellaceae were present across all the soil-plant continuums. Microbial communities in two regions of Jordan were similar to each other, but both of them were different from the Jornada LTER site of USA. SIMPER(similarity percentage) analysis of bacterial and fungal taxa for both soil and endophyte communities revealed that dissimilarities of two bacterial genera(Arthrobacter and Sporosarcina) and two fungal genera(Cladosporium and Alternaria) are very high, so they play key roles in the soil-plant continuums. A weighed Pearson correlation analysis for the specific bacterial OTUs in the soil-plant continuums only showed high similarity between the two regions of Jordan. However, fungal groups showed higher similarities among all regions. This research supports the hypothesis of continuity of certain bacterial and fungal communities across the soil-plant continuums, and also explores the influences of plant species and geographic specificity on diversity and distribution of bacteria and fungi.