Selecting the hologenome to breed for an improved feed efficiency in pigs—A novel selection index

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect of the microbiota composition on the breeding value of an animal is the conditional expectation of its breeding value, given the vector with microbiota frequencies, that is The breeding value of an animal can therefore be decomposed into a heritable contribution that arises from an altered microbiota composition and a heritable contribution that arises from altered metabolic pathways within the animal, so Instead of selecting for breeding value , an index comprising the two components and with appropriate weights, that is , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.     

Equine conidiobolomycosis: A review and case study

Conidiobolus coronatus is one of the most commonly identified upper respiratory fungal pathogens in horses. This article includes a review of clinical signs, diagnostics, treatment and outcomes in previously reported cases of equine conidiobolomycosis, as well as six additional cases seen at our hospital. Each of the six horses presented with a complaint of serosanguinous or haemorrhagic nasal discharge and conidiobolomycosis was confirmed by histopathology and fungal culture. Five horses recovered after administration of antifungal drugs alone (n = 4) or in combination with extensive nasal septum resection (n = 1). Surgical treatment alone was ineffective. One horse was euthanised without treatment because of the extent of the disease.     

ACTH stimulation test in the captive cheetah (Acinonyx jubatus)

Serum cortisol response was assessed in 8 captive cheetahs, of varying ages, after the intravenous administration of 500 microg of tetracosactide (Synacthen Depot, Novartis, Kempton Park) while maintained under general anaesthesia. In addition, 8 cheetahs were anaesthetised and given an equal volume of saline in order to establish baseline cortisol concentrations at similar stages of anaesthesia. A significant difference in the median cortisol concentration measured over time was found following ACTH administration in the ACTH group (P < 0.001). There was no difference between the median cortisol concentrations in the ACTH group at time-points 120, 150 and 180 min after ACTH stimulation (P = 0.867). Thus it appears appropriate to collect serum 120 to 180 min after tetracosactide administration to assess maximal stimulation of the adrenal in the cheetah. No statistically significant rise was seen in the anaesthetised control group following the injection of saline (P = 0.238).     

Neuronal ceroid lipofuscinosis: clinical and morphologic findings in nine affected Polish Owczarek Nizinny (PON) dogs

OBJECTIVE: The aim of this study was to characterize the clinical and morphologic features of neuronal ceroid lipofuscinosis (NCL) in the Polish Owczarek Nizinny (PON) breed of dog. ANIMALS: Nine Swedish PON dogs of both sexes were included in the study. PROCEDURE: All dogs underwent a detailed clinical evaluation, with emphasis on ophthalmic exams. Histopathology and electron microscopy were performed on the eyes, brain and various internal organs. Immunohistochemical staining for detection of sphingolipid activator proteins (SAPs) and mitochondrial ATP synthase (SCMAS) was performed on the eyes and brain. RESULTS: The dogs showed behavioral abnormalities, motor disturbances and visual impairment or blindness. Pupillary responses were abnormal while fundus changes varied from normal to severe retinal atrophy. Electroretinography (ERG) showed variable changes, from slight alterations in the process of dark adaptation to severely reduced or nonrecordable ERG a- and b-wave amplitudes. Histopathology revealed intracytoplasmic storage bodies within neurons of the brain and in retinal cells, especially the retinal pigment epithelium (RPE). Round to oval granular type of inclusion bodies, known as granular osmiophilic dense deposits (GRODS), were found in neuronal cells in the brain and in the retina. Immunohistochemistry identified the storage material in the brain and retina as consisting of SAPs. CONCLUSION: The presently described NCL disease in PON dogs shows similarities to previously recorded cases in the Miniature Schnauzer. The closest human equivalent to this disease is infantile NCL (CLN1), in which the major stored proteins are SAPs and the ultrastructure of the inclusion bodies of neuronal cells is granular.     

Genetic and non-genetic factors influencing KLH binding natural antibodies and specific antibody response to Newcastle disease in Kenyan chicken populations

This study aimed at investigating the influence of genetic and non-genetic factors on immune traits to inform on possibilities of genetic improvement of disease resistance traits in local chicken of Kenya. Immune traits such as natural and specific antibodies are considered suitable indicators of an individual's health status and consequently, used as indicator traits of disease resistance. In this study, natural antibodies binding to Keyhole Limpet Hemocyanin (KLH-NAbs) was used to measure general disease resistance. Specific antibodies binding to Newcastle disease virus (NDV-IgG) post vaccination was used to measure specific disease resistance. Titers of KLH-NAbs isotypes (KLH-IgM, KLH-IgG and KLH-IgA) and NDV-IgG were measured in 1,540 chickens of different ages ranging from 12 to 56 weeks. A general linear model was fitted to determine the effect of sex, generation, population type, phylogenetic cluster, line, genotype and age on the antibody traits. A multivariate animal mixed model was fitted to estimate heritability and genetic correlations among the antibody traits. The model constituted of non-genetic factors found to have a significant influence on the antibody traits as fixed effects, and animal and residual effects as random variables. Overall mean (±SE) concentration levels for KLH-IgM, KLH-IgG, KLH-IgA and NDV-IgG were 10.33 ± 0.04, 9.08 ± 0.02, 6.00 ± 0.02 and 10.12 ± 0.03, respectively. Sex, generation and age (linear covariate) significantly (p < 0.05) influenced variation across all the antibody traits. Genotype effects (p < 0.05) were present in all antibody traits, apart from KLH-IgA. Interaction between generation and line was significant (p < 0.05) in KLH-IgM and NDV-IgG while nesting phylogenetic cluster within population significantly (p < 0.05) influenced all antibody traits, apart from KLH-IgA. Heritability estimates for KLH-IgM, KLH-IgG, KLH-IgA and NDV-IgG were 0.28 ± 0.08, 0.14 ± 0.06, 0.07 ± 0.04 and 0.31 ± 0.06, respectively. There were positive genetic correlations (0.40–0.61) among the KLH-NAbs while negative genetic correlations (−0.26 to −0.98) were observed between the KLH-NAbs and NDV-IgG. Results from this study indicate that non-genetic effects due to biological and environmental factors influence natural and specific antibodies and should be accounted for to reduce bias and improve accuracy when evaluating the traits. Subsequently, the moderate heritability estimates in KLH-IgM and NDV-IgG suggest selection possibilities for genetic improvement of general and specific immunity, respectively, and consequently disease resistance. However, the negative correlations between KLH-NAbs and NDV-IgG indicate the need to consider a suitable approach that can optimally combine both traits in a multiple trait selection strategies.     

Historical spatial baselines in conservation and management of marine resources

Increased knowledge on the spatial distribution of marine resources is crucial for the implementation of a true ecosystem approach to management and the conservation of marine organisms. For exploited fish species characterized by aggregation behaviour during spawning time, the identification and tracking of spawning areas is essential for a correct assessment of their productivity and population abundance. To elucidate this concept, we reconstructed the spatio‐temporal distribution of adult plaice (Pleuronectes platessa, Pleuronectidae) during spawning time along the 20^th century. Historical data reveal that not only the abundance but also the former population richness was much higher than previously estimated and has declined because of protracted over‐exploitation during the last 30 years. We conclude that forecast of stock recovery to former levels of abundance neglecting spatial reorganizations might be over‐optimistic and shaded by a lost memory of the past population richness. These results reinforce the importance of managing exploited marine resources at a greater spatial resolution than has been carried out in the history of fishery management.     

Patterns of SSR variation in bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) seeds under ex situ genebank storage and accelerated ageing

Maintaining seed viability and germplasm integrity is a challenging task in conservation of plant genetic resources, as seeds under storage will lose viability and genetic changes will occur. Attempt was made to analyze the patterns of genetic changes in wheat germplasm under ex situ genebank storage and accelerated ageing treatments. A set of 16 naturally aged wheat accessions under ex situ genebank storage since 1994 were sampled. Four recently regenerated wheat accessions were selected, four random seed samples were chosen from each accession, and three of them were exposed to three different accelerated ageing treatments. These 32 seed samples in two germplasm sets displayed a range of germination rates from 4 to 98 %. Thirty-seven microsatellite markers representing 21 wheat chromosomes were applied to screen 12 seeds of each sample and 449 SSR alleles were scored. Large SSR variation was found in each germplasm set. There was 73.1 % of the total SSR variation present among the naturally aged samples and 78.2 % present among the accelerated ageing samples. Several analyses for genetic association consistently revealed no clear genetic separations among samples of high or low germination rates in both germplasm sets. Samples under different accelerated ageing treatments did not show much genetic differentiations from the original sample of each accession. Mantel tests revealed non-significant associations between SSR variability and sample germination rates for both germplasm sets. These findings are useful for understanding seed deterioration under different ageing conditions and suggest that genome-wide SSR variability may not provide sensitive markers for the monitoring of wheat seed viability.     

Species composition of arbuscular mycorrhizal fungi in two mountain meadows with differing management types and levels of plant biodiversity

Species composition of arbuscular mycorrhizal fungi (AMF) was analysed in two differently managed mountain grasslands in Thuringia (Germany). Arbuscular mycorrhizal fungi were studied in the roots of 18 dominant plant species from a total of 56 (32%). Additionally, spores of AMF were isolated from soil samples. Arbuscular mycorrhizal fungi species composition was analysed based on 96 sequences of the internal transcribed spacer of the nuclear ribosomal DNA, 72 originated from mycorrhizal roots, and 24 originated from AMF spores. Phylogenetic analyses revealed a total of 19 AMF species representing all genera of the Glomeromycota except Scutellospora and Pacispora. Despite a different farming intensity, resulting in remarkable differences concerning their plant species diversity (27 against 43 plant species), the diversity of AMF was found to be similar with 11 species on the intensively farmed meadow and ten species on the extensively farmed one. Nevertheless, species composition between both sites was clearly different. It thus seems likely that the AMF species composition, but not necessarily the species number, is related to above ground plant biodiversity in the system under study.     

Odor thresholds of microbially induced off-flavor compounds in apple juice

Microbially derived off-flavor is a major problem in apple juice production as it diminishes the sensory quality of the juice significantly. Fifteen relevant off-flavor compounds that are formed in apple juice, for example, by the strains Alicyclobacillus acidoterrestris and Actinomycetes (Streptomyces ssp.) were investigated with respect to their sensory relevance. The odor threshold values (i.e., detection and recognition values) were determined for all compounds in the matrix apple juice. Odor threshold values for fenchyl alcohol are reported here for the first time. The obtained values were set in relation to the limits of detection and quantification of a previously published GC-MS method. Eight tainted apple juice samples were analyzed for the presence of the 2 strains and the 15 off-flavor compounds. Both strains could be found in the samples; the presence of Streptomyces ssp. as spoilage bacteria of apple juice is reported for the first time. In samples with distinct off-flavor, 2-isopropyl-3-methoxypyrazine, 2-isobutyl-3-methoxypyrazine, 2-methylisoborneol, 1-octen-3-ol, fenchyl alcohol, geosmin, and guaiacol as well as 2,6-dibromophenol were determined in concentrations higher than the detection threshold.     

Influence of mycotoxin producing fungi (Fusarium, Aspergillus, Penicillium) on gluten proteins during suboptimal storage of wheat after harvest and competitive interactions between field and storage fungi

Cereals contaminated by Aspergillus spp., Penicillium spp., and Fusarium spp. and their mycotoxins, for example, ochratoxin A (OTA) and deoxynivalenol (DON), are not only a risk to human and animal health but can also show poor technological properties and baking quality. The influence of these genera on the sulfur speciation of low molecular weight (LMW) subunits of glutenin was characterized by investigating suboptimally stored wheat samples in situ by X-ray absorption near edge structure (XANES) spectroscopy and baking tests. Field fungi of the genus Fusarium have hardly any influence on both the sulfur speciation of wheat gluten proteins and the baking properties, whereas storage fungi of the genera Aspergillus and Penicillium have a direct influence. An increased amount of sulfur in sulfonic acid state was found, which is not available for thiol/disulfide exchange reactions in the gluten network, and thus leads to a considerably reduced baking volume. From changes of the composition of the mould flora during suboptimal storage of wheat and from the mycotoxin contents, it can be concluded that microbial competitive interactions play an important role in the development of the mould flora and the mycotoxin concentrations during (suboptimal) storage of wheat.