Doctoral Research

Host: Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Co Meath, Ireland 

Main Supervisor: Prof David Kenny (Teagasc Animal & Grassland Research and Innovation Centre, Grange, Ireland; David.kenny@teagasc.ie); Prof Pat Lonergan (University College Dublin; pat.lonergan@ucd.ie)

Duration: 36 months starting July to September 2024

Profile: A candidate with a master’s degree in animal science, biological science or aligned field or a BSc in veterinary science. In-depth knowledge of the nutritional control of reproduction in cattle.  

Project Description: Metabolic acidosis arising from subacute ruminal acidosis (induced by feeding high grain diets) has been associated with altered metabolic function however, the latent effect on the musculoskeletal and reproductive systems are not clear. The objectives are (i) Clearly define the incidence and reasons for culling in natural service and AI bulls using data from the Irish Cattle Breeding Federation and AI industry databases, with specific emphasis on musculoskeletal disorders. (ii) Establish an in vivomodel of metabolic inflammatory pathology whereby peripubertal bulls are individually intensively fed on a high or moderate grain diet from 5 months and slaughtered at 15 months of age: 1. Characterise the concurrent and latent metabolic, physiological and immunological response. 2. Assess libido and conduct detailed semen quality analysis including computer assisted sperm assessment, in vitro functional assays etc. and 3. Conduct detailed morphological, histopathological and molecular analyses of key metabolic organs (i.e. liver) and musculoskeletal tissue.

Host: INRAE, Paris, France 

Main Supervisor: Dr Helene Kiefer (INRAE, France; helene.kiefer@inrae.fr)

Project Description: The epigenome of germ cells is sensitive to environmental variations but there is no data about the molecular changes occurring during spermatogenesis. We therefore hypothesise that the effects of high energy/grain diets during rearing on testicular function are partly mediated by epigenetic modifications. The objectives are (i) Isolate pure populations of spermatogenic male germ cells from mature testes. (ii) Describe the molecular variations that can be observed between the different spermatogenic stages. (iii) Investigate whether high energy diets offered during rearing affect these variations, and relate the diet-induced modifications to testicular function. (iv) Investigate whether high energy diets offered during rearing affect the sperm epigenome.

Host: Spanish National Research Council (CSIC – INIA), Madrid, Spain;

Main Supervisor: Dr Beatriz Fernandez-Fuertes (CSIC- INIA, Spain; beatriz.fernandez@inia.csic.es); Prof Sean Fair (University of Limerick; sean.fair@ul.ie)

Project Description: The sperm epigenome can be modified as they migrate through the epididymis of the bull and this can be altered by diet. The specific objectives are to (i) Determine the effect of bull sperm exposure to epididymal EVs on sperm function, miRNA cargo, embryo development and gene expression, as well as the regulation of the oviduct and uterine environments. (ii) Evaluate changes in epididymal EV cargo in response to different diets, with a focus on miRNA. (iii) Determine differences in maternal response and embryo development between sperm exposed to epididymal EVs isolated from bulls fed high or moderate grain diets.

Host: Université Clermont Auvergne, France

Main Supervisor: Prof. Joël Drevet (Université Clermont Auvergne, France; joel.drevet@uca.fr); Dr Fabrice Saez, Université Clermont Auvergne, France; fabrice.saez@uca.fr)  

Project Description: The modification of the sperm proteome during epididymal maturation in the bull is poorly understood. The objectives are to (i) Characterize the proteome of extracellular vesicles responsible for a large part of epididymal sperm protein maturation, i.e. epididymosomes. (ii) Characterize the proteome of seminal extracellular vesicles involved in post-ejaculatory sperm maturation. (iii) Correlate these data with the sperm proteome, both in epididymal and ejaculated cells, as a function of diet. (iv) Investigate the nutritional impact of different diets on epididymal and ejaculate sperm quality, focusing on sperm nuclear integrity (condensation, oxidation and fragmentation), as well as oxidative stress at post-testicular and systemic levels.

Host: Institute for Reproduction of Farm Animals Schönow, Germany

Main Supervisor: Prof Martin Schulze (Institute for Reproduction of Farm Animals Schönow, Germany; m.schulze@ifn-schoenow.de); Prof Gudrun Brockmann (Humboldt University Berlin, Germany; gudrun.brockmann@agrar.hu-berlin.de)

Duration: 36 months starting July to September 2024

Profile: A candidate with a master’s degree in animal science, veterinary science, biological science or aligned field. In-depth knowledge of microbiological, spermatology and molecular techniques is an advantage.   

Project Description: Bacterial killing activity of seminal fluid is known across several species, including the bull. However, to what extent the microbiome influences the occurrence of the bacterial killing activity against specific gram-negative and gram-positive bacteria in individual bulls has not been studied. The objectives are: (i) Collect seminal plasma (SP) from AI bulls (summer vs. winter), determine bacterial killing activity (BKA) & sort bulls based on the level of BKA (high or low) against gram+, gram- bacteria, or both (four groups, 1-4). (ii) Determine the microbiological profile of the test group ejaculates (16S rDNA sequencing). (iii) Analyze post-thaw sperm quality of the test groups using an extended spectrum of spermatological methods (e.g. thermo-resistance, mitochondrial activity, membrane integrity, multi-color assay, etc.) and relate it to BKA. (iv) Identify and isolate possible BKA-exerting components from SP samples (e.g. proteomics analyses, 2D SDS page, MALDI, etc.). (v) Characterize fertilizing capacity of ejaculates with low and high BKA (e.g. IVF, AI trials, non-return rate). 

Host: Institute for Reproduction of Farm Animals Schönow, Germany

Main Supervisor: Prof Martin Schulze (Institute for Reproduction of Farm Animals Schönow, Germany; m.schulze@ifn-schoenow.de); Prof Sean Fair (University of Limerick, Ireland; sean.fair@ul.ie)

Duration: 36 months starting July to September 2024

Profile: A candidate with a master’s degree in animal science, biological science or aligned field or a BSc in veterinary science.In-depth knowledge of spermatology and molecular techniques is an advantage.   

Project Description: Bulls vary in the cryotolerance of their semen for reasons that are not fully understood. The objectives are: (i) Characterise and interrogate the relationship between the lipidome, proteome, and exosome of undiluted and sex sorted semen from bulls categorised as ‘good’ or ‘bad’ freezers. (ii) Establish a predictive model of bull cryotolerance in both conventional and sex-sorted semen by using omics data in combination with pre-and post-freeze motility, antioxidant capacity, membrane integrity, fluidity, and stability. (iii) Investigate the effect of altering sperm cryopreservation media components including antioxidants (e.g Hydroxytyrasol) and membrane stabilizers (e.g. cholesterol, lecithin), and the effects of the deep interactions among these components and specific dilution, cooling and equilibration processing techniques on the cryotolerance of semen from bulls categorised as good and bad freezers. (iv) Assess temperature dependent volume response and osmotic tolerance in sperm from good and bad freezers, the effects of antioxidants and membrane stabilizers on these properties, and correlate these data with lipidome and proteome differences. Identify media components that should be used in cryopreservation medium to mitigate osmotic damage both during glycerol equilibration and during cooling for both good and bad freezers.

Host: University of Limerick, Limerick, Ireland

Main Supervisor: Prof Sean Fair (University of Limerick, Ireland; sean.fair@ul.ie)

Project Description: Bull sperm are immunogenic in the uterus and we have recently demonstrated that sperm from high fertility bulls have a more active transcriptomic response leading to more rapid clearing of the endometrium of sperm as well as priming the endometrium for implantation. The objectives are (i) Using an established in vitro uterine explant model characterise the physiological role for sperm subpopulations (motile and non-motile) on the uterine immune response using a panel of pro-inflammatory genes and proteins. (ii) Using an in vivo model, investigate the uterine exposure of sperm from high and low field fertility bulls on the modulation of cytokine signalling, inflammation and immune response pathways both locally in the uterus as well as regionally in the cervix, uterine horn and oviduct. (iii) Investigate the effect of uterine conditioning by sperm from high and low fertility bulls during oestrus, on the developmental competence of in vitro derived embryos transferred to heifers on Day 7 and recovered on Day 15. (iv) Assess if repeated exposure of the endometrium of heifers with sperm dampens the immune response and, if so, what cells are being dampened

Host: University College Dublin, Lyons Research Farm, Newcastle, Dublin, Ireland

Main Supervisor: Prof Pat Lonergan (University College Dublin; pat.lonergan@ucd.ie)

Project Description: Sperm can alter DNA methylation patterns, mRNAs, small non-coding RNAs, and proteins in the embryo after fertilisation. The objectives are to (i) Study the dynamics mRNAs/sncRNA expression in the early embryo at several key stages (blastocyst, elongating conceptus) (ii) Analyse the influence of sperm sncRNAs on embryonic gene expression (iii) Infer causal networks and disrupted pathways from these data (iv) Explore in-depth the role of some key networks involved in embryo development.

Host: University of Cologne, Germany

Main Supervisor: Prof Oya Beyan (University of Cologne; oya.beyan@uni-koeln.de); Prof. Stefan Wesner (wesner@uni-koeln.de), Prof Achim Tresch (University of Cologne; achim.tresch@uni-koeln.de)

Project Description: Analysing complex data sets, such as sperm quality data, requires the secure integration of heterogeneous and cost-intensive modification of data format. Moreover, lack of transparency about data quality and provenance is a cause for severe reproducibility and reusability issues. The objectives are to (i) Acquisition and curation of a high-quality data set that follows the FAIR principles (findable, accessible, interoperable, reusable) that serves as input to machine-learning algorithms. Introduction of standardized vocabularies and ontologies. (ii) Development of data connectors (software interfaces) to secure data access from every participating animal breeding centre. Improvements in existing workflows and data-processing pipelines, following compliance with domain standards and practices. (iii) Introduction of a data usage license management. Identify different license types, develop machine-readable versions of them. Automate validation of certificates. (iv) Create knowledge graph database by embedding heterogenous data sets (sperm quality, genomics, transcriptomics, microbiome, field fertility) and applying privacy preserving techniques to query the sensitive data without revealing the proprietary information.

Host: University of Cologne, Germany

Main Supervisor: Prof Achim Tresch (University of Cologne; achim.tresch@uni-koeln.de); Prof Oya Beyan (University of Cologne; oya.beyan@uni-koeln.de)

Duration: 36 months starting July to September 2024

Profile: A candidate with a master’s degree in machine learning, statistics, data analytics, applied mathematics or aligned field. In-depth knowledge of advanced machine-learning techniques is an advantage.   

Project Description: 

Most studies predicting the fertility of conventional semen only have field data at the bull level which is a major limitation. This project aims to relate in vitro sperm quality and molecular data of sex-sorted semen at the ejaculate level to field fertility. The objectives are to (i) Quantify the inter- and intra-ejaculate variability of sperm quality and its impact on fertility in a multi-centric study, using computer-assisted sperm analysis (CASA) and flow cytometry data from replicate samples from hundreds of bulls from each breeding centre used for sex sorting. (ii) Quantify the dependency of molecular data (sperm transcriptomics and microbiome datasets) and microscopically determined sperm parameters (CASA, flow cytometry). (iii) Use advanced machine-learning techniques and variable selection/dimension reduction to improve the prediction of the primary endpoints including cryotolerance and the fertility of sex-sorted and conventional semen. Data integration of further molecular covariates (16s rDNA, structural DNA variants, proteomics) and testing for their added predictive value. (iv) Establish an analysis workflow, together with a software tool for the selection of ejaculates/bulls by breeding centres.

Host: University of Zurich, Switzerland

Main Supervisor: Prof Heinrich Bollwein (University of Zurich; Switzerland; heinrich.bollwein@uzh.ch); Dr Eleni  Malana (University of Zurich; Switzerland; emalama@vetclinics.uzh.ch)

Project Description: It has been shown that heterospermic insemination doses, has improved post-thaw sperm quality characteristics compared to homospermic doses and here we hypothesis that exosomes contained in the seminal plasma mediate sperm-to-sperm interactions. The objectives are: (i) To establish a model of good vs. bad freezers (sires with good vs. suboptimal sperm cryotolerance) based on a combination of pre-freeze vs. post-thaw sperm quality parameters and the quantitative characteristics of extracellular vesicles (exosomes) identified in the seminal plasma (SP). (ii) To characterise the secretion/molecular content (miRNA/sncRNA) of seminal exosomes (SE) in sperm of good vs. bad freezers. (iii) To characterise and compare the effects of whole SP, SP depleted of SE (SPdSE) and SE collected from good vs. bad freezers on fertility-relevant sperm quality parameters and developmental rates of in vitro produced embryos. (iv) To explore the role of SE in sperm-to-sperm interaction by comparing the sperm quality traits, the profile and miRNA cargo of SE in heterospermic vs. homospermic semen samples.

Host: Swiss Federal Institute of Technology (ETH) of Zurich; Switzerland

Main Supervisor: Prof Hubert Pausch (Swiss Federal Institute of Technology of Zurich; Switzerland; hubert.pausch@usys.ethz.ch) 

Project Description: It is becoming increasingly evident (from species other than cattle), that structural variants are likely to have larger effects on phenotypes than SNPs and Indels but are not well captured by SNPs. The objectives are to (i) Identify structural variants (>50 bp) in the genome of bulls with low and high field fertility success (selected from ~3,500 genotyped AI bulls with field fertility data) from long sequencing reads mapped against a bovine pangenome. (ii) Derive structural variant genotypes from the pangenome and impute them into large and densely genotyped mapping cohorts with gene expression and fertility-related phenotypes. (iii) Association testing between structural variant genotypes and complex trait phenotypes (1300 Brown Swiss AI bulls with detailed semen quality records from ~70,000 ejaculates and field fertility data, as well as RNAseq-derived gene expression from testis, epididymis and vas deferens of 120 whole-genome sequenced bulls) to identify trait-associated structural variants. (iv) Partitioning of the heritability by variant annotations and transcriptome-wide association testing to quantify the contribution of structural variants to the genetic variation of traits relevant for male fertility.

Host: University of Nottingham, United Kingdom

Main Supervisor: Prof. Ravinder Anand-Ivell (University of Nottingham; ravinder.anand-ivell@nottingham.ac.uk); Prof Richard Ivell (University of Nottingham; richard.ivell@nottingham.ac.uk)  

Duration: 36 months starting July to September 2024

Profile: A candidate with a master’s degree in animal science, veterinary science, biological science or aligned field. In-depth knowledge of cell culture and molecular techniques is an advantage.   

Project Description: There is no published information on the development of the epididymal secretome through puberty, or whether this is synchronized to the appearance of sperm in the first ejaculates and hence to their fertility. The objectives are: (i) Develop a robust method to assess epididymal biomarkers of post-testicular sperm maturation in mature bulls comparing freshly ejaculated, diluted (with extender), and frozen-thawed preparations, as well as caudal epididymal and testicular sperm. (ii) Using a biomarker approach, compare the post-testicular (epididymal) sperm proteome from pubertal development to sexual maturity at bi-weekly intervals, and after nutritional modulation, thereby determining whether epididymal maturation develops synchronously with other sperm parameters. (iii) Characterise regulation of the mature bull epididymal secretome using primary cell culture. (iv) Monitor the role of INSL3, its receptor RXFP2, and related relaxin family hormones in the epididymis of the bull and assess their influence on semen quality.

Host: Queens University Belfast, United Kingdom

Main Supervisor: Prof Sharon Huws (Queens University Belfast, United Kingdom s.huws@qub.ac.uk); Prof David Kenny (Teagasc Grange, Ireland; David.kenny@teagasc.ie) 

Project Description: Bull semen has a rich microbiome but the origin and impact of this on sperm quality, cryotolerance and field fertility is unclear. The objectives are: (i) Characterise the diversity of the bull semen microbiome in neat semen and determine whether these microbiomes influence semen quality. (ii) Investigate the origin (lab, prepuce, epididymis testes, seminal glands) of semen microbiome and the effects of sperm processing and cryopreservation. (iii) Investigate the effects of key bacterial isolates isolated from (i) and (ii) on sperm quality and cryotolerance and field fertility after artificial insemination. (iv) Determine the effects of seminal exosomes on semen microbiomes in vitro.