Optimising multistage dairy cattle breeding schemes including genomic selection using decorrelated or optimum selection indices

Background

The prediction of the outcomes from multistage breeding schemes is especially important for the introduction of genomic selection in dairy cattle. Decorrelated selection indices can be used for the optimisation of such breeding schemes. However, they decrease the accuracy of estimated breeding values and, therefore, the genetic gain to an unforeseeable extent and have not been applied to breeding schemes with different generation intervals and selection intensities in each selection path.

Methods

A grid search was applied in order to identify optimum breeding plans to maximise the genetic gain per year in a multistage, multipath dairy cattle breeding program. In this program, different values of the accuracy of estimated genomic breeding values and of their costs per individual were applied, whereby the total breeding costs were restricted. Both decorrelated indices and optimum selection indices were used together with fast multidimensional integration algorithms to produce results.

Results

In comparison to optimum indices, the genetic gain with decorrelated indices was up to 40% less and the proportion of individuals undergoing genomic selection was different. Additionally, the interaction between selection paths was counter-intuitive and difficult to interpret. Independent of using decorrelated or optimum selection indices, genomic selection replaced traditional progeny testing when maximising the genetic gain per year, as long as the accuracy of estimated genomic breeding values was ≥ 0.45. Overall breeding costs were mainly generated in the path "dam-sire". Selecting males was still the main source of genetic gain per year.

Conclusion

Decorrelated selection indices should not be used because of misleading results and the availability of accurate and fast algorithms for exact multidimensional integration. Genomic selection is the method of choice when maximising the genetic gain per year but genotyping females may not allow for a reduction in overall breeding costs. Furthermore, the economic justification of genotyping females remains questionable.     

Neutrophil Gelatinase-Associated Lipocalin (NGAL) Predicts Response to Neoadjuvant Chemotherapy and Clinical Outcome in Primary Human Breast Cancer

In our previous work we showed that NGAL, a protein involved in the regulation of proliferation and differentiation, is overexpressed in human breast cancer (BC) and predicts poor prognosis. In neoadjuvant chemotherapy (NACT) pathological complete response (pCR) is a predictor for outcome. The aim of this study was to evaluate NGAL as a predictor of response to NACT and to validate NGAL as a prognostic factor for clinical outcome in patients with primary BC. Immunohistochemistry was performed on tissue microarrays from 652 core biopsies from BC patients, who underwent NACT in the GeparTrio trial. NGAL expression and intensity was evaluated separately. NGAL was detected in 42.2% of the breast carcinomas in the cytoplasm. NGAL expression correlated with negative hormone receptor (HR) status, but not with other baseline parameters. NGAL expression did not correlate with pCR in the full population, however, NGAL expression and staining intensity were significantly associated with higher pCR rates in patients with positive HR status. In addition, strong NGAL expression correlated with higher pCR rates in node negative patients, patients with histological grade 1 or 2 tumors and a tumor size <40 mm. In univariate survival analysis, positive NGAL expression and strong staining intensity correlated with decreased disease-free survival (DFS) in the entire cohort and different subgroups, including HR positive patients. Similar correlations were found for intense staining and decreased overall survival (OS). In multivariate analysis, NGAL expression remained an independent prognostic factor for DFS. The results show that in low-risk subgroups, NGAL was found to be a predictive marker for pCR after NACT. Furthermore, NGAL could be validated as an independent prognostic factor for decreased DFS in primary human BC.     

Identification of residues important for NAD+ binding by the Thermotoga maritima alpha-glucosidase AglA,a member of glycoside hydrolase family 4

The NAD+-requiring enzymes of glycoside hydrolase family 4 (GHF4) contain a region with a conserved Gly-XXX-Gly-Ser (GXGS) motif near their N-termini that is reminiscent of the fingerprint region of the Rossmann fold, a conserved structural motif of classical nicotinamide nucleotide-binding proteins. The function of this putative NAD+-binding motif in the alpha-glucosidase AglA of Thermotoga maritima was probed by directed mutagenesis. The K(d) for NAD+ of the AglA mutants G10A, G12A and S13A was increased by about 300-, 5-, and 9-fold, respectively, while their K(m) for p-nitrophenyl-alpha-glucopyranoside was not seriously affected. The results indicate that the GXGS motif is indeed important for NAD+ binding by the glycosidases of GHF4.     

Transports of water,particulate and dissolved organic and inorganic matter between a salt marsh and the Ems-Dollard estuary,the Netherlands

Summary Transport processes were studied in a gully between a saltmarsh and an estuary. After storm tides, ebb currents in the gully reached high values. It is concluded that particulate matter (both obganic and inorganic) are imported into the marsh. Coarse organic debris is exported during storm tides, but this amount is low when compared with the primary production on the marsh. Exports are shown for dissolved organic carbon, ammonia, phosphate and silica, while nitrate and possibly nitrite are imported. Therefore, it seems warranted to conclude that the organic matter producedin situ and imported is mineralized in the marsh.     

Intravenous immunoglobulin in the treatment of primary trigeminal neuralgia refractory to carbamazepine: a study protocol[ISRCTN33042138]

Background  

We have recently reported successful treatment of patients with chronic pain syndromes using human pooled intravenous immunoglobulin (IVIG) in a prospective, open-label cohort study. A randomised, placebo controlled, double blinded study is needed to confirm these results. We chose to study patients with carbamazepine resistant primary Trigeminal Neuralgia (rpTN), as these had responded particularly well to IVIG.     

Re-assessing the ecology of rare flood-meadow violets (<Emphasis Type="Italic">Viola elatior,V. pumila</Emphasis> and<Emphasis Type="Italic">V. persicifolia</Emphasis>) with large phytosociological data sets

This study demonstrates how conventional ecological knowledge on species together with models resulting from functional traits can be tested and refined by tapping large data sources that have been made available through recent electronic compilations. The study is based on the comparison of three rare, closely related flood-meadow violet species, which have been supposed to have similar ecological behaviour and niche occupation. In contrast, the analysis of 335 Central European relevés using different methods of numerical ordination, classification and calibration revealed distinct differences in habitat preferences between the three species. Detrended correspondence analysis ordination, and multiple-response permutation procedures and TWINSPAN classification displayed the separation ofViola persicifolia fromV. elatior andV. pumila along a moisture and base-richness gradient, while the latter two differed mostly in terms of mowing compatibility. Although the three violets are considered to be weak competitors they may be found under nutrient-poor as well as nutrient-rich site conditions. The distribution of C-S-R strategy types in relevés supported the hypothesis that at more fertile sites the violets crucially depend on disturbance by management or flooding events that create gaps and weaken strong competitors, while at less productive sites they may persist for a long time even under fallow conditions. The S/R strategy is shared by all three violets. Problems and perspectives arising with the use of phytosociological databanks as a source of ecological information are discussed.     

Banana defence responses to Cosmopolites sordidus feeding and methyl jasmonate application

Each year 25–75% of banana and plantain yields are lost because of rhizome damages caused by banana weevil (Cosmopolites sordidus) in growing regions of sub‐Saharan Africa. However, the specific plant defence response of the rhizome tissue in relation to the C. sordidus attack is unknown. Consequently, in this study, we evaluated whether plant defence substances in the rhizome are correlated with the degree of larval damage and whether applications of methyl jasmonate (MJ) elicit a greater induction of the plant defence potential against C. sordidus. Moreover, we attempted to reveal cellular modifications in response to the root feeding herbivore through histochemical staining. The banana cultivars “Km5” and “Mbwazirume” with tolerance and susceptibility to C. sordidus, respectively, were used in a pot experiment to evaluate percent rhizome damage, leaf chlorophyll content, total phenolic content (TPC), antioxidant capacity and cell morphology in response to C. sordidus attack and/or MJ applications compared to untreated control plants. We found that C. sordidus‐induced rhizome damage was 30% in the susceptible cultivar but less than 5% in the tolerant cultivar. The percent rhizome damage was not related to leaf chlorophyll content but showed a significant negative linear relationship to both TPC and antioxidant capacity. Larvae feeding induced a considerably greater increase of polyphenolic defence compounds in Km5 than in Mbwazirume; however, this response was opposite in the MJ treatment, suggesting that the phytohormone induced the susceptible plant to invest more into the synthesis of defence chemicals that in turn lead to reduced C. sordidus damage. Tissue staining demonstrated a greater deposition of lignin and suberin in C. sordidus challenged rhizome, presumably to seal off healthy tissue with a physical barrier from continued pest attack. It is concluded that MJ induces polyphenolics in susceptible Mbwazirume banana that reduced C. sordidus damage.     

Epidemiological pattern of classical Borna disease and regional genetic clustering of Borna disease viruses point towards the existence of to-date unknown endemic reservoir host populations

Classical Borna disease (cBD), a non-purulent encephalitis of solipeds and sheep, is endemic in certain areas of central Europe. The etiologic agent is Borna disease virus (BDV), thus far the only member of the family Bornaviridae. Based on epidemiological patterns of cBD and recent phylogenetic findings this review hypothesizes the possible existence of yet unknown BDV reservoir host populations, and analyzes critically BDVs from outside endemic regions.