Evaluation and development of animal breeding in Ireland

End of project reportThe primary objectives of this study were: 1) to annually evaluate the pertinence of the Irish dairy cattle breeding index, the Economic Breeding Index (EBI) and where necessary modify, 2) to evaluate the potential of do-it-yourself milk recording as an alternative to current supervised methods of milk recording, and 3) to estimate the level and rate of accumulation of inbreeding in Irish dairy and beef cattle, to quantify its effects on traits of economic importance, and to develop remedial measures to minimise the future accumulation of inbreeding in Ireland

The effect of Holstein-Friesian genotype and feeding system on selected performance parameters of dairy cows on grass-based systems of milk production in Ireland

End of project reportThe overall objective of this project was to assess, the effect of strain of Holstein-Friesian dairy cow, pasture-based feed system (FS) and their interaction on animal performance in terms of milk productivity and lactation profile, body weight (BW), body condition score (BCS), feed intake and energy balance (EB), reproductive performance and overall economic profitability

Autophagy participates in the unfolded protein response in Toxoplasma gondii

Environmental and genetic perturbations of endoplasmic reticulum (ER) function can lead to the accumulation of unfolded proteins. In these conditions, eukaryotic cells can activate a complex signaling network called the unfolded protein response (UPR) to reduce ER stress and restore cellular homeostasis. Autophagy, a degradation and recycling process, is part of this response. The parasitic protist Toxoplasma gondii is known to be able to activate the UPR upon ER stress, and we now show that this pathway leads to autophagy activation, supporting the idea of a regulated function for canonical autophagy as part of an integrated stress response in the parasites

Genetic and transcriptional analysis of phosphoinositide-specific phospholipase C in Plasmodium

Phosphoinositide-specific phospholipase C (PI-PLC) is a major regulator of calcium-dependent signal transduction, which has been shown to be important in various processes of the malaria parasite Plasmodium. PI-PLC is generally implicated in calcium liberation from intracellular stores through the action of its product, inositol-(1,4,5)-trisphosphate, and is itself dependent on calcium for its activation. Here we describe the plc genes from Plasmodium species. The encoded proteins contain all domains typically found in PI-PLCs of the δ class but are almost twice as long as their orthologues in mammals. Transcriptional analysis by qRT-PCR of plc during the erythrocytic cycle of P. falciparum revealed steady expression levels that increased at the late schizont stages. Genetic analysis in the P. berghei model revealed that the plc locus was targetable but that plc gene knock-outs could not be obtained, thereby strongly indicating that the gene is essential during blood stage development. Alternatively, we attempted to modify plc expression through a promoter exchange approach but found the gene to be refractory to over-expression indicating that plc expression levels might additionally be tightly controlled

Development of an index to rank dairy females on expected lifetime profit

peer-reviewedThe objective of this study was to develop an index to rank dairy females on expected profit for the remainder of their lifetime, taking cognizance of both additive and nonadditive genetic merit, permanent environmental effects, and current states of the animal including the most recent calving date and cow parity. The cow own worth (COW) index is intended to be used for culling the expected least profitable females in a herd, as well as inform purchase and pricing decisions for trading of females. The framework of the COW index consisted of the profit accruing from (1) the current lactation, (2) future lactations, and (3) net replacement cost differential. The COW index was generated from estimated performance values (sum of additive genetic merit, nonadditive genetic merit, and permanent environmental effects) of traits, their respective net margin values, and transition probability matrices for month of calving, survival, and somatic cell count; the transition matrices were to account for predicted change in a cow’s state in the future. Transition matrices were generated from 3,156,109 lactation records from the Irish national database between the years 2010 and 2013. Phenotypic performance records for 162,981 cows in the year 2012 were used to validate the COW index. Genetic and permanent environmental effects (where applicable) were available for these cows from the 2011 national genetic evaluations and used to calculate the COW index and their national breeding index values (includes only additive genetic effects). Cows were stratified per quartile within herd, based on their COW index value and national breeding index value. The correlation between individual animal COW index value and national breeding index value was 0.65. Month of calving of the cow in her current lactation explained 18% of the variation in the COW index, with the parity of the cow explaining an additional 3 percentage units of the variance in the COW index. Females ranking higher on the COW index yielded more milk and milk solids and calved earlier in the calving season than their lower ranking contemporaries. The difference in phenotypic performance between the best and worst quartiles was larger for cows ranked on COW index than cows ranked on the national breeding index. The COW index is useful to rank females before culling or purchasing decisions on expected profit and is complementary to the national breeding index, which identifies the most suitable females for breeding replacements

Temporal analysis of the autophagic and apoptotic phenotypes in Leishmania parasites

The leishmaniases are worldwide neglected tropical diseases caused by parasitic protozoa of the Leishmania genus. Different stimuli induce Leishmania cell death, but the proteins involved remain poorly understood. Furthermore, confusion often appears between cell death and the cell survival process autophagy, whose phenotype is not clearly defined. In this article, we present a comprehensive and temporal analysis of the cellular events occurring during miltefosine-induced cell death and autophagy in L. major. We also provide a list of features in order to clearly identify apoptotic cells, autophagic cells and to distinguish both processes. Furthermore, we demonstrate that autophagy is followed by apoptosis in the absence of nutrients. Finally, we show that cells treated with the generic kinase inhibitor staurosporine express apoptotic as well as autophagic markers and therefore cannot be used as an apoptosis inducer in Leishmania. These descriptions lead to a better recognition and understanding of apoptosis and autophagy, enabling their targeting in the development of new anti-leishmanial drugs. These researches also make it possible to better understand these processes in general, through the study of an ancestral eukaryote

A proteomic analysis unravels novel CORVET and HOPS proteins involved in Toxoplasma gondii secretory organelles biogenesis

Apicomplexans use the endolysosomal system for the biogenesis of their secretory organelles, namely, micronemes, rhoptries, and dense granules. In Toxoplasma gondii, our previous in silico search identified the HOPS tethering but not the CORVET complex and demonstrated a role of Vps11 (a common component for both complexes) in its secretory organelle biogenesis. Herein, we performed Vps11‐GFP‐Trap pull‐down assays and identified by proteomic analysis, not only the CORVET‐specific subunit Vps8 but also a BEACH domain‐containing protein (BDCP) conserved in eukaryotes. We show that knocking‐down Vps8 affects targeting of dense granule proteins, transport of rhoptry proteins, and the localization of the cathepsin L protease vacuolar compartment marker. Only a subset of micronemal proteins are affected by the absence of Vps8, shedding light on at least two trafficking pathways involved in microneme maturation. Knocking‐down BDCP revealed a restricted and particular role of this protein in rhoptry and vacuolar compartment biogenesis. Moreover, depletion of BDCP or Vps8 abolishes parasite virulence in vivo. This study identified BDCP as a novel CORVET/HOPS‐associated protein, playing specific roles and acting in concert during secretory organelle biogenesis, an essential process for host cell infection. Our results open the hypothesis for a role of BDCP in the vesicular trafficking towards lysosome‐related organelles in mammals and yeast

Substrate Suppression of Thermal Roughness in Stacked Supported Bilayers

We have fabricated a stack of five 1,2-dipalmitoyl-sn-3-phosphatidylethanolamine (DPPE) bilayers supported on a polished silicon substrate in excess water. The density profile of these stacks normal to the substrate was obtained through analysis of x-ray reflectivity. Near the substrate, we find the layer roughness and repeat spacing are both significantly smaller than values found in bulk multilayer systems. The reduced spacing and roughness result from suppression of lateral fluctuations due to the flat substrate boundary. The layer spacing decrease then occurs due to reduced Helfrich repulsion.This work was partially supported by NSF Grants No. DMR-0706369 and No. DMR-0706665. Use of the Advanced Photon Sourcewas supported by theUSDepartment of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. SKS and ANP wish to acknowledge support from the Office of Basic Energy Sciences, US Department of Energy, via Grant No. DE-FG02- 04ER46173. We would also like to thank Suresh Narayanan for his support of the experimental work at Sector 8-ID

Deriving economic values for national sheep breeding objectives using a bio-economic model

peer-reviewedThe economic value of a trait in a breeding objective can be defined as the value of a unit change in an individual trait, while keeping all other traits constant and are widely used in the development of breeding objectives internationally. The objective of this study was to provide a description of the development of economic values for the pertinent traits included in the Irish national sheep breeding objectives using a whole farm system bio-economic model. A total of fourteen traits of economic importance representing maternal, lambing, production and health characteristics were calculated within a whole farm bio-economic model. The model was parameterised to represent an average Irish flock of 107 ewes with a mean lambing date in early March, stocked at 7.5 ewes per hectare and weaning 1.5 lambs per ewe joined to the ram. The economic values (units in parenthesis) calculated for maternal traits were: €39.76 for number of lambs born (per lamb), €0.12 for ewe mature weight cull value (per kg), −€0.57 for ewe mature weight maintenance value (per kg), −€0.09 for ewe mature weight replacement value (per kg) and −€0.84 for ewe replacement rate (per%). The economic values calculated for lambing traits were: €54.84 for lamb surviving at birth (per lamb), −€0.27 and −€0.30 for direct lambing difficulty in single and multiple-bearing ewes, respectively (per%); the corresponding values for maternal single and multiple lambing difficulty (per%) were −€0.25 and −€0.27, respectively. The calculated economic values for production traits were: −€0.25 for days to slaughter (per day), €3.70 for carcass Conformation (per EUROP grade) and −€0.84 for carcass fat (per fat score). The economic values for health traits were: −€0.24 for ewe lameness (per%), −€0.08 for lamb lameness (per%), −€0.25 for mastitis (per%), −€0.34 for dag score (per dag score) and −€0.08 for faecal egg count (per 50 eggs/g). Within the two Irish breeding objectives, the terminal and replacement breeding objective, the greatest emphasis was placed on production traits across both the terminal (62.56%) and replacement (41.65%) breeding objectives. The maternal and lambing traits accounted for the 34.19% and 23.45% of the emphasis within the replacement breeding objective, respectively. Results from this study will enable the implementation of new economic values within the national terminal and replacement Irish sheep breeding objectives which highlights the traits of importance for increasing overall farm profitability

In Situ Surface-Enhanced Infrared Spectroscopy to Identify Oxygen Reduction Products in Nonaqueous Metal-Oxygen Batteries

We report on the detection of metastable, solvated, and surface adsorbed alkali metal–oxygen (M–O₂) discharge species using in situ attenuated total reflectance surface enhanced infrared absorption spectroscopy (ATR-SEIRAS). Oxygen–oxygen stretching bands (ν_O–O) of superoxide species formed during M–O₂ battery discharge have been challenging to observe by conventional infrared (IR) techniques, and because of this, there has been limited use of IR techniques for in situ monitoring of the discharge products at the cathode in metal–O₂ batteries. We explore SEIRAS technique to investigate lithium–oxygen and sodium–oxygen electrochemistry in acetonitrile (MeCN; a low Gutmann donor number solvent) as well as dimethyl sulfoxide (DMSO; a high Gutmann donor number solvent) in order to demonstrate the feasibility of our approach in the ongoing efforts toward the realization of M–O₂ battery technology. In situ IR spectroscopy studies, together with a coupled-cluster method including perturbative triple excitations [CCSD­(T)] calculations, establishes that certain M–O and O–O stretching bands (ν_M–O and ν_O–O) of metal superoxide and peroxide molecular species are IR active, although these vibrational modes are silent or suppressed in their crystalline forms. An in situ IR spectroscopy based approach to distinguish between “solution mediated” and “surface confined” discharge pathways in nonaqueous M–O₂ batteries is demonstrated