PhD projects

Project 01 - n6/n3 Fatty acid (FA) ratio effect on piglet microbiome and immunity

Objectives

The aim of the project is to determine the impact of the n6/n3 fatty acid ratio in the diet of gestating and lactating sows on their performance and health, and on growth performance of the relative piglets.

Description of the project

The Early Stage Researcher (ESR) will first perform a trial on sows fed diets containing two different n6/n3 ratios throughout gestation and lactation. The effects on sow performance, milk fatty acids composition, and blood parameters will be evaluated. Piglets will be challenged with LPS from E. coli (serotype 055:B5), treated or not with exopolysaccharide (EPS) from Lactobacilli, characterized for immune modulation activity, received from the partner from the University of Kosice, and sampled for blood and faeces. At slaughter, liver and intestine will be sampled as well. The systemic and the intestinal immune status will be characterized using “classical” pathological and histological techniques. OMICs studies, including proteomics, metabolomics will be performed in serum and the microbiome will be determined for the sows and piglets in intestinal and faecal samples, the latter for the piglets only.

The ESR will be enrolled by the University of Milan (http://www.unimi.it/) under the supervision of Prof Giovanni Savoini and will be awarded a Double Doctorate degree in co-tutelle with the University of Glasgow, under the supervision of Dr Richard Burchmore at the University of Glasgow (https://www.gla.ac.uk/). The supervision team is completed by Dr Matilde Pinerio from Acuvet (http://acuvetbiotech.com/es/) at Zaragoza. The research will involve short secondments to the Autonomous University of Barcelona (http://www.uab.cat/) and MetLabs (http://metlabs.sk/) at Bratislava.

Project 02 - Nutrition and immunity: molecular approaches

Objectives

The aim of the project is to define the in vitro impact of molecules used in nutrition studies of other MANNA ESR studies.

Description of the project

The Early Stage Researcher (ESR) involves the characterization of the in vitro effects of M. cordata extract, exopolysaccharides (EPS), exosomes, polyunsaturated fatty acids (PUFA) and microRNA, in avian and mammalian immune defence. The ESR will apply (or develop where not available) protocols to purify and culture immune related cells in pigs, ruminants and chicken, that will be co-incubated with the molecules utilized by other ESR within the MANNA project (FA, carotenoids and M. cordata extracts, EPS, purified milk exosomes and xenoMiR present in milk exosomes. Main cell activities will be measured, including chemotaxis, degranulation, ROS production, phagocytosis for phagocytes, and cell proliferation and MHC presentation of lymphocytes. The secretome from cultures will be analysed by proteomics and microRNAomics. Expression of immune related microRNA and genes will be carried out by means of open array™ or other technologies.

The ESR candidate student will carry out her/his PhD thesis study work in the Department of Veterinary Medicine at the University of Milan (http://www.unimi.it/) under the supervision of Prof. Fabrizio Ceciliani and the Autonomous University of Barcelona (http://www.uab.cat/), under the supervision of Prof. Armand Sanchez Bonastre. The supervision team is completed by Dr Muriel Bonnet (http://www.researcherid.com/rid/M-6265-2017), at INRA (http://www.ara.inra.fr/) in the Herbivores Unit (http://umrh-bioinfo.clermont.inra.fr/Intranet/web/UMRH/en).

The research will also involves short secondments at INRA (http://www.ara.inra.fr/) in Clermont Ferrand, France, and MetLabs (http://metlabs.sk/) at Bratislava, Slovakia.

The selected candidate will participate in the network’s training activities and work placements in the laboratories of the participating academic and industrial partners.

Project 03 - Chicken proteomic and metabolomics biomarkers for production, health and welfare

Objectives

The aim of the project is to determine the change in the proteome and metabolome of chicken following endotoxin challenge and the effect of diet on this response.

Description of the project

The Early Stage Researcher (ESR) will determine the effects of natural immunomodulatory compounds as supplements to the diet of chicken and the potential protection provided to challenge by bacterial endotoxin. Samples from control and challenged chicken will be analysed using OMICs (metabolomics, microbiomics, proteomics and transcriptomics) technologies. The ESR will subsequently identify candidate molecules for further investigation by developing appropriate assay systems. The ESR will evaluate growth performance of healthy and challenged chicken, define the protocol to use for proteomics and metabolomics for integrated tissue analysis in chicken, define the intestinal microbiome, demonstrate the effects of immunomodulatory molecules on proteins expressed in the microbiota, intestine, serum and muscle following challenge and finally identify biomarkers of nutritional status and for digestion of feed in chickens.

The ESR will be enrolled in the University of Glasgow (https://www.gla.ac.uk/) under the supervision of Prof Maureen Bain and will be awarded a Double Doctorate degree in co-tutelle with the University of Zagreb (http://www.unizg.hr/homepage/), under the supervision of Prof Vladimir Mrljak. The supervision team is completed by a non academic supervisor, Dr Geert Bruggeman, of Nutrition Science (http://www.nutrition-sciences.com/), Belgium.

The research will involve secondments to Metlabs (http://metlabs.sk/) at Bratislava, in Slovak Republic, and Life Diagnostics (https://lifediagnostics.com/) (UK).

The selected candidate will participate in the network’s training activities and work placements in the laboratories of the participating academic and industrial partners.

Project 04 - Protein synthesis rates, effect of diet, health and innate immune responses in chicken

Objectives

The aim of the project is to determine the rate of protein synthesis in tissues of chicken following endotoxin challenge and the effect of diet on this response.

Description of the project

The Early Stage Researcher (ESR) will study the fractional synthesis rate (FSR) of multiple target proteins in tissues from broiler chickens and assess the effects of using natural immunomodulatory compounds as supplements in their diet to the FSR under challenge by bacterial endotoxin. The ESR will focus on determining the FSR of selected target proteins by supplementing the diets with deuterium oxide (2H2O) and determining FSR by gas chromatography and mass spectrometry. The analytical spectrum will then be extended to OMIC analysis on selective proteins such as ovotransferrin, myosin, albumin and other plasma proteins with their relative synthesis rates determined during endotoxin challenge.

The ESR will be enrolled in the University of Glasgow (https://www.gla.ac.uk/) under the supervision of Professor Tom Preston, Scottish Universities Environmental Research Centre, and will be awarded a Double Doctorate degree in co-tutelle with the University of Veterinary Medicine and Pharmacy in Kosice (http://www.uvlf.sk/en), under the supervision of Professor Mangesh Bhide. The supervision team is completed by a non academic supervisor, Dr. Chris Chadwick, of Life Diagnostics (https://lifediagnostics.com/), UK.

The research will involve secondments to the University of Zagreb (http://www.unizg.hr/homepage/), Croatia, AB Agri (https://www.abagri.com/home) UK and MetLabs (http://metlabs.sk/), Slovak Republic.

The selected candidate will participate in the network’s training activities and work placements in the laboratories of the participating academic and industrial partners.

Project 05 - Assessment of the effects of increased intakes of the amino acid methionine (Met) during the first weeks of lactation and during early pregnancy in dairy cows

Objectives

The aim of the project is to evaluate the effects of increased Met intakes on metabolism and fertility in dairy cows during the first 140 d of lactation via characterizing the metabolome, the proteome and the microRNA-ome in blood serum.

Description of the project

The Early Stage Researcher (ESR) linked to the project will be involved in a large animal study with more than 1000 Holstein cows receiving a standard diet with or without Met supplementation from week 4 – 20 of lactation, and undergoing regular blood sampling. The ESR will use the performance (milk yield and composition), health and fertility data for identifying cows that are positively or negatively outstanding in terms of health, fertility and performance, to form 4 subgroups from which samples will be used. The analytical part comprises serum OMICS to characterize the metabolome, the phospho and the methyl-proteome and to assess miRNAs related to metabolic health and reproductive performance in blood serum from cows throughout the first 140 d of lactation. Besides, “classical” variables to describe the metabolic status and ovarian activity of the cows will be applied.

The ESR will be enrolled by the University of Bonn (https://www.uni-bonn.de/the-university) under the supervision of Prof. Helga Sauerwein and will be awarded a Double Doctorate degree in co-tutelle with the University of Glasgow (https://www.gla.ac.uk/) under the supervision of Dr Karl Burgess. The supervision team is completed by a non academic supervisor, Dr. Claudia Parys from Evonik Nutrition & Care GmbH (http://corporate.evonik.com/en), Germany.

The research will involve secondments to Porto Conte Ricerche (http://www.portocontericerche.it/), Italy, and MetLabs (http://metlabs.sk/) located in Bratislava, Slovak Republic.

The selected candidate will participate in the network’s training activities and work placements in the laboratories of the participating academic and industrial partners.

Project 06 - miRNomics, proteomics, and lipidomics of sow’s milk exosomes

Objectives

The aim of the project is to determine the miRN-ome, proteome, and the lipidome of sow’s milk exosomes at different stages of lactation, and to test the effects of feeding with different diets.

Description of the project

The Early Stage Researcher (ESR) linked to the project will characterize the miRN-ome, proteome, and the lipidome of sow’s milk exosomes derived from other MANNA projects: The ESR will receive milk samples and blood serum samples of sows and piglets from ESR1 for isolating and characterising milk exosomes by means of OMICS. The miRN-ome will be in focus to assess the miRNA composition of milk exosomes. The ESR will identify how the composition of milk exosomes is modified during the transition from the colostral until the weaning stage, and by different ratios of n-3:n-6 fatty acids in the diet, and will compare the miRNAs from milk exosomes with the one in sows’ and piglets’ serum samples. By relating the miRNA-omes to growth performance, immune response and microbiome of the piglets (ESR1), the miRNAs associated with health and growth performance will be identified opening the perspective of developing miRNA supplements e.g. by “exosome-mimetics”.

The ESR will be enrolled by the University of Zagreb (http://www.unizg.hr/homepage/) under the supervision of Prof. Vladimir Mrljak and will be awarded a Double Doctorate degree in co-tutelle with the University of Bonn (https://www.uni-bonn.de/the-university), under the supervision of Prof. Helga Sauerwein. The supervision team is completed a non academic supervisor from Dr Mike Salter, from AbAgri (https://www.abagri.com/home) UK.

The research will involve secondments to the University of Milan (http://www.unimi.it/), to Porto Conte Ricerche (http://www.portocontericerche.it/), and AbAgri (https://www.abagri.com/home), UK.

The selected candidate will participate in the network’s training activities and work placements in the laboratories of the participating academic and industrial partners.

Project 07 - Bacterial, fungal and archaeal components of the gut microbiota and their impact on animal nutrition

Objective

To characterize the microbiome (bacterial, fungal and archaeal) of porcine gut and faecal samples using Deep-sequencing techniques.

Description of the project

The project linked to the Early Stage Researcher (ESR) will characterize the microbiome (bacterial, fungal and archaeal) of porcine gut and faecal samples using Deep-sequencing techniques. The ESR will receive faecal and intestinal samples from pig reared in different conditions coming from studies done by ESR working on other MANNA projects and from additional pigs (2 different breeds) to compare 16S sequencing and deep sequencing for their informative value about the entire gut microbiome and to characterize the microbiome under the different feeding conditions applied in the pig experiments. Experiments on relatedness of gut and faecal samples profiles of the porcine microbiome will also be carried out. Besides metabolomics and proteomics will be applied and data will be evaluated to identify biomarkers for innovative breeding strategies.

The ESR will be enrolled by the Autonomous University of Barcelona (http://www.uab.cat/), Spain, under the supervision of Prof. Armand Sanchez Bonastre and will be awarded a Double Doctorate degree in co-tutelle with the University of Glasgow (https://www.gla.ac.uk/), UK, under the supervision of Dr Mark McLaughlin. The supervision team is completed a non academic supervisor, Prof Filippa Addis, from Porto Conte Ricerche (http://www.portocontericerche.it/). The research will involve secondments to Life Diagnostics (https://lifediagnostics.com/), UK, Porto Conte Ricerche, Italy and MetLabs (http://metlabs.sk/) at Bratislava, Slovak Republic.

The selected candidate will participate in the network’s training activities and work placements in the laboratories of the participating academic and industrial partners.

Project 08 - Effect of dietary lipids on porcine meat quality (intramuscular fat content and composition)

Objective

The project linked to the ESR will study the effects dietary lipid composition on meat quality of the pig and associate this finding to the genetics of the pig.

Description of the project

In a first experiment, changes in the muscular miRNOme and transcriptome from pigs fed with diets enriched with either saturated or unsaturated fatty acid will be determined by RNAseq. The Early Stage Researcher (ESR) will also characterize the intramuscular fat content with a near-infrared transmittance device and muscle fat by gas chromatography, and will participate in an in vitro study carried out with other MANNA ESR projects. Metabolomics and proteomics will also be carried out on serum and muscle samples. Results will be compared with phenotypic and genomic data obtained in previous projects performed at UAB in different breeds and translated into commercial products and innovative breeding strategies.

The ESR will be enrolled by the Autonomous University of Barcelona (http://www.uab.cat/), Spain, under the supervision of prof. Armand Sanchez Bonastre and will be awarded a Double Doctorate degree in co-tutelle with the University of Milan (http://www.unimi.it/), Italy, under the supervision of Prof. Giovanni Savoini. The supervision team is completed a non academic supervisor from Harriet Scott, from RAFT Solutions. The research will involve secondments to University of Glasgow (https://www.gla.ac.uk/), to RAFT Solutions, UK, (https://raftsolutions.co.uk/), and MetLabs (http://metlabs.sk/) at Bratislava, Slovak Republic.

The selected candidate will participate in the network’s training activities and work placements in the laboratories of the participating academic and industrial partners.

Project 09 - Establishing novel in vitro intestinal epithelial cell models in animal nutrition

Objectives

The aim of the project is to determine the use of in vitro models of intestinal epithelial cells in order to test the effects of different bioactive and immunomodulatory molecules such as carotenoids and M. cordata extract, PUFA, as well as EPS and LPS.

Description of the project

In the first part of

This project has received funding from the European Union’s Horizon 2020 research and innovation programme H2020-MSCA- ITN-2017- EJD: Marie Skłodowska-Curie Innovative Training Networks (European Joint Doctorate) – Grant agreement nº: 765423