Events
Ancient DNA Beyond Allele Frequencies
Conference 29-31 July 2024
Meeting Rationale:
Ancient DNA has transformed our understanding of the past, revealing the otherwise-hidden history of human, animal, plant, and microbial populations, and how they have been intertwined throughout time. The advent of large scale ancient population datasets, high coverage genomes and low coverage-optimised imputation algorithms now allow for a new phase of ancient genomic analysis, stepping beyond conventional allele-sharing approaches. These novel analyses exploit the power inherent to haplotypes and allow for a fine-scaled understanding of ancient relationships and demographies to be reconstructed.
Meeting Rationale:
Ancient DNA has transformed our understanding of the past, revealing the otherwise-hidden history of human, animal, plant, and microbial populations, and how they have been intertwined throughout time. The advent of large scale ancient population datasets, high coverage genomes and low coverage-optimised imputation algorithms now allow for a new phase of ancient genomic analysis, stepping beyond conventional allele-sharing approaches. These novel analyses exploit the power inherent to haplotypes and allow for a fine-scaled understanding of ancient relationships and demographies to be reconstructed.
Seminar by Prof Dan Longley, Queen's University Belfast
Prof. Dan Longley is Professor of Cancer Biology and Director of the Patrick Johnston Cancer Centre at Queen's University, Belfast and leads a group exploring drug resistance in cancer therapy. Dan's work was originally focused on resistance to standard-of-care chemotherapy in colorectal cancer and this has now broadened to include mechanisms of drug resistance in multiple cancers. Work from the Longley lab has focused primarily on the role of cFLIP—an important regulator of apoptosis initiated by death receptors—as a regulator of chemotherapy. Dan's work has shown that cFLIP is a key mediator of drug resistance, especially in colorectal cancer, as well as a biomarker of poor prognosis and a potential therapeutic target for cancer. He is currently working on the development of small-molecule cFLIP inhibitors for use in clinical settings where cFLIP is an important mediator of therapy resistance and/or where cFLIP is a major driver of tumour development and progression. Dan is a graduate of Brasenose College Oxford and a PhD graduate of the Dept. of Genetics, at Trinity College Dublin.
Seminar by Dr Rosa Fernández, Institute of Evolutionary Biology (CSIC) in Barcelona
Science (fiction) stories of hopeful monsters.
Talk Abstract:
The colonization of land by animals - the origin of animal terrestrial biodiversity - is one of the most fascinating episodes in the animal evolutionary chronicle. From marine ancestors, animals needed to reshape their genomes to 'learn' new ways of breathing, excreting, reproducing or protecting their DNA from UV light-induced damage. Terrestrialization occurred multiple times in several animal phyla, such as vertebrates, arthropods, mollusks, tardigrades or nematodes, among others. In today's talk, I will discuss how massive genomic rearrangements (to the point of losing any traces of macrosynteny) gave rise to the origin of a new annelid lineage, potentially facilitating their 'out-of-the-sea' transition towards freshwater and terrestrial environments. Be ready for some thought-provoking ideas about animal genome evolution that could seem to have been borrowed from a science fiction story.
Talk Abstract:
The colonization of land by animals - the origin of animal terrestrial biodiversity - is one of the most fascinating episodes in the animal evolutionary chronicle. From marine ancestors, animals needed to reshape their genomes to 'learn' new ways of breathing, excreting, reproducing or protecting their DNA from UV light-induced damage. Terrestrialization occurred multiple times in several animal phyla, such as vertebrates, arthropods, mollusks, tardigrades or nematodes, among others. In today's talk, I will discuss how massive genomic rearrangements (to the point of losing any traces of macrosynteny) gave rise to the origin of a new annelid lineage, potentially facilitating their 'out-of-the-sea' transition towards freshwater and terrestrial environments. Be ready for some thought-provoking ideas about animal genome evolution that could seem to have been borrowed from a science fiction story.
Seminar by Prof Roderick (Roddy) O'Sullivan, University of Pittsburgh School of Medicine Hillman Cancer Center, USA
Epigenetic and DNA Repair pathway crosstalk at human telomeres
Seminar by Dr Ed Gilbert, Royal College of Surgeons Ireland
Haplotypes and History: Insights from Irish population genetics
Seminar by Dr Andrew Lin, University of Sheffield
Sparse coding for odour-specific memories through homeostatic plasticity
Seminar by Dr Carolina Rezaval, University of Birmingham
Is love blind? Mating proximity gates threat perception
Seminar by Dr Kevin Daly, Trinity College Dublin
Footprints From The Past: Using ancient genomes to understand livestock domestication
Bio:
Dr Kevin Daly is currently an SFI-IRC Pathway Fellow within Prof. Daniel Bradley's group at TCD, and from February 2024 will be an UCD Ad Astra Lecturer/Assistant Professor. Dr. Daly completed his undergraduate at the Smurfit Institute, where he first had the opportunity to work in palaeogenomics - recovering thousands of years old DNA from the extinct Giant Irish Deer. Leading from this, Dr. Daly completed his PhD studies with Prof. Bradley on "Ancient Goat Genomics" and was responsible for producing one of the world's first large-scale ancient livestock genome datasets, spanning millennia . Subsequently, his research has expanded into ancient sheep genomics and detailing demography at the dawn of domestication. Dr. Daly was recently included in the inaugural cohort of the Young Academy of Ireland, and will lead a research team on Ruminant Palaeogenomics from UCD's School of Agriculture and Food Science, continuing his SFI Pathway's project "Herd Health" which is exploring the interplay between domestication, livestock diversity, and pathogen evolution.
Bio:
Dr Kevin Daly is currently an SFI-IRC Pathway Fellow within Prof. Daniel Bradley's group at TCD, and from February 2024 will be an UCD Ad Astra Lecturer/Assistant Professor. Dr. Daly completed his undergraduate at the Smurfit Institute, where he first had the opportunity to work in palaeogenomics - recovering thousands of years old DNA from the extinct Giant Irish Deer. Leading from this, Dr. Daly completed his PhD studies with Prof. Bradley on "Ancient Goat Genomics" and was responsible for producing one of the world's first large-scale ancient livestock genome datasets, spanning millennia . Subsequently, his research has expanded into ancient sheep genomics and detailing demography at the dawn of domestication. Dr. Daly was recently included in the inaugural cohort of the Young Academy of Ireland, and will lead a research team on Ruminant Palaeogenomics from UCD's School of Agriculture and Food Science, continuing his SFI Pathway's project "Herd Health" which is exploring the interplay between domestication, livestock diversity, and pathogen evolution.
Seminar by Dr Laetitia Chauve, Trinity College Dublin
Is there an advantage to polyploidy in animals? C. elegans tetraploids resist severe cold stress at the gravid adult stage, by escaping cold-induced death.
Talk Abstract:
Whole Genome Duplication (WGD), or polyploidization, is an important evolutionary event and considered instrumental in the generation of genetic innovation. In plants, WGD is recognized as a major evolutionary force, and is linked to speciation and the ability to resist periods of stress and of environmental upheaval. In animals, examples of current polyploid species are rarer, but we know of several ancient events of WGD: for instance, two rounds of WGD occurred during early vertebrate evolution. Those events are usually followed by gene loss and diploidization, processes which reshape the genome and channel evolutionary outcomes. The reason for the success of polyploidy in animals is unclear. Stressful conditions (heat or cold) can generate WGD and one debated hypothesis states that polyploidy is adaptive on the short-term, however this has never been studied in animals. We are using the microscopic worm C. elegans, where tetraploidy can be artificially constructed, as a model to study the effects of WGD on physiology and its potential adaptive consequences. Our results reveal that, although tetraploidy reduces fitness under regular conditions, tetraploid animals exhibit altered resistance to temperature-related stresses, especially upon severe cold, where tetraploids exhibit a dramatic increase in recovery at the gravid adult stage.
Talk Abstract:
Whole Genome Duplication (WGD), or polyploidization, is an important evolutionary event and considered instrumental in the generation of genetic innovation. In plants, WGD is recognized as a major evolutionary force, and is linked to speciation and the ability to resist periods of stress and of environmental upheaval. In animals, examples of current polyploid species are rarer, but we know of several ancient events of WGD: for instance, two rounds of WGD occurred during early vertebrate evolution. Those events are usually followed by gene loss and diploidization, processes which reshape the genome and channel evolutionary outcomes. The reason for the success of polyploidy in animals is unclear. Stressful conditions (heat or cold) can generate WGD and one debated hypothesis states that polyploidy is adaptive on the short-term, however this has never been studied in animals. We are using the microscopic worm C. elegans, where tetraploidy can be artificially constructed, as a model to study the effects of WGD on physiology and its potential adaptive consequences. Our results reveal that, although tetraploidy reduces fitness under regular conditions, tetraploid animals exhibit altered resistance to temperature-related stresses, especially upon severe cold, where tetraploids exhibit a dramatic increase in recovery at the gravid adult stage.
Seminar by Prof Dan Macqueen, University of Edinburgh
All things fish: genomic perspectives from food security to evolution
Talk Abstract:
Fish are important to humans for many reasons, perhaps most crucially as a food source that billions rely on daily. In this regard, fish farming (i.e. aquaculture) has a major and increasing role in supporting rising food demands across the globe. Fish are also remarkably diverse at the phenotypic and genetic levels, offering interesting study systems for tackling a range of evolutionary questions. Technology advances are opening up new ways to address a range of key applied challenges and fundamental questions in fish biology. Focussing on the societally important salmonid family, I will showcase how genomics is unlocking new types of data and strategies to address key challenges facing the aquaculture sector, while at the same time providing novel insights into evolutionary processes encoded by genome sequences.
Talk Abstract:
Fish are important to humans for many reasons, perhaps most crucially as a food source that billions rely on daily. In this regard, fish farming (i.e. aquaculture) has a major and increasing role in supporting rising food demands across the globe. Fish are also remarkably diverse at the phenotypic and genetic levels, offering interesting study systems for tackling a range of evolutionary questions. Technology advances are opening up new ways to address a range of key applied challenges and fundamental questions in fish biology. Focussing on the societally important salmonid family, I will showcase how genomics is unlocking new types of data and strategies to address key challenges facing the aquaculture sector, while at the same time providing novel insights into evolutionary processes encoded by genome sequences.
Seminar by Áine Niamh O'Toole, University of Edinburgh
APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016
Talk Abstract:
Historically, mpox has been characterized as a zoonotic disease, primarily transmitted through contact with the reservoir rodent host in West and Central Africa. However, in May 2022, human cases of mpox were identified spreading internationally beyond regions with established endemic reservoirs. Upon sequencing the first cases from 2022, it was found that they exhibited 42 nucleotide differences from the closest previously sampled mpox virus (MPXV). Nearly all these mutations are characteristic of the action of APOBEC3 deaminases, host enzymes with antiviral function.
Assuming that APOBEC3 editing is a hallmark of human MPXV infection, we developed a dual-process phylogenetic molecular clock. This clock, estimating a rate of approximately six APOBEC3 mutations per year, suggests that MPXV has been circulating in humans since at least 2016. These findings, demonstrating sustained transmission of MPXV, represent a significant departure from the traditional understanding of MPXV epidemiology as a zoonosis. They underscore the importance of re-evaluating public health communication related to MPXV and adjusting strategies for outbreak management and control.
Talk Abstract:
Historically, mpox has been characterized as a zoonotic disease, primarily transmitted through contact with the reservoir rodent host in West and Central Africa. However, in May 2022, human cases of mpox were identified spreading internationally beyond regions with established endemic reservoirs. Upon sequencing the first cases from 2022, it was found that they exhibited 42 nucleotide differences from the closest previously sampled mpox virus (MPXV). Nearly all these mutations are characteristic of the action of APOBEC3 deaminases, host enzymes with antiviral function.
Assuming that APOBEC3 editing is a hallmark of human MPXV infection, we developed a dual-process phylogenetic molecular clock. This clock, estimating a rate of approximately six APOBEC3 mutations per year, suggests that MPXV has been circulating in humans since at least 2016. These findings, demonstrating sustained transmission of MPXV, represent a significant departure from the traditional understanding of MPXV epidemiology as a zoonosis. They underscore the importance of re-evaluating public health communication related to MPXV and adjusting strategies for outbreak management and control.
Seminar by Inés T. Marin Moreno (Scientific Officer, European Research Council)
The European Research Council – funding opportunities for excellent research in the Life Sciences
Seminar by Prof Juliette de Meaux, University of Cologne
Polygenic selection and the evolution of gene expression in Arabidopsis lyrata ssp. petraea
Talk Abstract:
Gene expression is presumably the first manifestation of gene function. Its variation is thus evidently shaped by natural selection. Patterns of gene expression variation, unlike other complex phenotypes, have the advantage that they can directly inform us on the molecular basis of physiological and morphological adaptation. I will review what the analysis of gene expression taught us about adaptation in the outcrossing plant species Arabidopsis lyrata, which evolved to withstand drought better than its relatives while also adapting to local conditions. We will discuss the role of gene expression in the polygenic adaptation of natural populations.
Biographical Information:
The fundamental goal of Juliette's research is to elucidate ecological adaptations at the genetic and genomic level, and reveal the molecular basis of ecological performance in natural populations. She first worked on reconstructing the recent history of molecular variants associating with lifetime fitness in the weedy annual and model plant species Arabidopsis thaliana. Progressively, her research has incorporated genomics and systems biology approaches to characterize ecological adaptations, while still maintaining a strong trait-based perspective. As it shifts from single gene to polygenic approaches, the work of her team explores all questions related to the adaptive potential of natural populations. In a context of global climate change and widespread biodiversity erosion, understanding and interpreting natural variation has become an urgent matter.
Talk Abstract:
Gene expression is presumably the first manifestation of gene function. Its variation is thus evidently shaped by natural selection. Patterns of gene expression variation, unlike other complex phenotypes, have the advantage that they can directly inform us on the molecular basis of physiological and morphological adaptation. I will review what the analysis of gene expression taught us about adaptation in the outcrossing plant species Arabidopsis lyrata, which evolved to withstand drought better than its relatives while also adapting to local conditions. We will discuss the role of gene expression in the polygenic adaptation of natural populations.
Biographical Information:
The fundamental goal of Juliette's research is to elucidate ecological adaptations at the genetic and genomic level, and reveal the molecular basis of ecological performance in natural populations. She first worked on reconstructing the recent history of molecular variants associating with lifetime fitness in the weedy annual and model plant species Arabidopsis thaliana. Progressively, her research has incorporated genomics and systems biology approaches to characterize ecological adaptations, while still maintaining a strong trait-based perspective. As it shifts from single gene to polygenic approaches, the work of her team explores all questions related to the adaptive potential of natural populations. In a context of global climate change and widespread biodiversity erosion, understanding and interpreting natural variation has become an urgent matter.
Seminar by Dr. Colin Adrain, Queen's University, Belfast
The Role of the ADAM17 'sheddase complex' in Inflammation and Metabolic regulation
Biographical Information:
Dr. Colin Adrain is a Senior Lecturer with the Patrick Johnston Centre for Cancer Research at Queen's University, Belfast. The Adrain laboratory works on trafficking and shedding of cytokines, such as TNF, and in particular the role of molecules that regulate the ADAM17/TACE 'sheddase complex' that regulates TNF secretion. Colin obtained his PhD in the Martin Laboratory with the Dept. of Genetics at Trinity College and then undertook post-doctoral training at Trinity and then at The LMB, University of Cambridge, UK in the Freeman laboratory. Colin then set up his research group at The Gulbenkian Institute, Portugal, where he remained for 10 years, before moving to Queen's University Belfast in 2020.
Biographical Information:
Dr. Colin Adrain is a Senior Lecturer with the Patrick Johnston Centre for Cancer Research at Queen's University, Belfast. The Adrain laboratory works on trafficking and shedding of cytokines, such as TNF, and in particular the role of molecules that regulate the ADAM17/TACE 'sheddase complex' that regulates TNF secretion. Colin obtained his PhD in the Martin Laboratory with the Dept. of Genetics at Trinity College and then undertook post-doctoral training at Trinity and then at The LMB, University of Cambridge, UK in the Freeman laboratory. Colin then set up his research group at The Gulbenkian Institute, Portugal, where he remained for 10 years, before moving to Queen's University Belfast in 2020.
Seminar by Prof Baskar Bakthavachalu, Indian Institute of Technology Mandi, India
How structured and disordered domains in the SCA-2 and ALS associated protein Ataxin-2 control Ribonucleoprotein granule condensation
Baskar Bakthavachalu is an Assistant Professor at the Indian Institute of Technology Mandi, India. He is also an EMBO Global Investigator and a Wellcome-DBT India Alliance Intermediate fellow. Within his lab, Baskar focuses on intricate cellular mechanisms underlying neurodegeneration, with a particular emphasis on RNA binding proteins, RNP granules, and the misregulation of translation.
Baskar Bakthavachalu is an Assistant Professor at the Indian Institute of Technology Mandi, India. He is also an EMBO Global Investigator and a Wellcome-DBT India Alliance Intermediate fellow. Within his lab, Baskar focuses on intricate cellular mechanisms underlying neurodegeneration, with a particular emphasis on RNA binding proteins, RNP granules, and the misregulation of translation.
Seminar by Prof Ian Chambers, The Institute for Stem Cell Research, University of Edinburgh
Transcription factor control of identity in pluripotent and germline cells
Special lecture by Prof. Douglas R. Green, Chair of Immunology at St. Jude Children's Research Hospital, Memphis, USA
Persister Act: Near Death Experiences in Cancer Cells
The Martin laboratory would like to invite you to a special lecture that will be held in the atrium of the Smurfit Institute of Genetics on Thursday 9th of March at 2pm.
Doug will discuss his latest work (Kalkavan et al., Cell, 2022) exploring the non-genetic factors that regulate the escape of cancer cells from chemotherapy and can even make such cells more invasive and resistant to therapy. Doug Green is a world authority on Cell Death control, is an elected member of the US National Academy of Sciences, an Honorary Fellow of Trinity College, and is a highly engaging speaker. This should be a fantastic talk and all are welcome to attend.
The Martin laboratory would like to invite you to a special lecture that will be held in the atrium of the Smurfit Institute of Genetics on Thursday 9th of March at 2pm.
Doug will discuss his latest work (Kalkavan et al., Cell, 2022) exploring the non-genetic factors that regulate the escape of cancer cells from chemotherapy and can even make such cells more invasive and resistant to therapy. Doug Green is a world authority on Cell Death control, is an elected member of the US National Academy of Sciences, an Honorary Fellow of Trinity College, and is a highly engaging speaker. This should be a fantastic talk and all are welcome to attend.
Seminar by Prof. Janet Browne, Aramont Professor of the History of Science, Harvard University
Darwin Day Lecture
Janet Browne’s interests range widely over the history of the life and earth sciences and natural history. She came to Harvard in 2006 and teaches a variety of courses on evolutionary history and the history of natural history. After a first degree in zoology she studied for a PhD in the history of science at Imperial College London, published as The Secular Ark: Studies in the History of Biogeography (1983). She has spent many years studying the context of Charles Darwin’s work, first as associate editor of the early volumes of The Correspondence of Charles Darwin, and then in a biography of Darwin that integrated his science with his life and times. A leading intention of the book was to explore the ways in which scientific knowledge was created, distributed and accepted, moving from private to public, as reflected in the two-volume structure of the work. The biography was received generously both in the UK and USA, and awarded several prizes, including the James Tait Black award for non-fiction in 2004, the W. H. Heinemann Prize from the Royal Literary Society, and the Pfizer Prize from the History of Science Society. She is currently exploring the history of Darwin’s impact on popular culture from the time of his death to today. She was based for many years at the Wellcome Trust Centre for the History of Medicine at University College London where she taught in the MA, MSc and undergraduate programs in the history of science, biology, and medicine. She has been president of both the British Society for the History of Science and the History of Science Society - curiously, not the first person to do so, but the first woman. She has an Honorary degree from her alma mater, Trinity College Dublin, 2009.
Janet Browne’s interests range widely over the history of the life and earth sciences and natural history. She came to Harvard in 2006 and teaches a variety of courses on evolutionary history and the history of natural history. After a first degree in zoology she studied for a PhD in the history of science at Imperial College London, published as The Secular Ark: Studies in the History of Biogeography (1983). She has spent many years studying the context of Charles Darwin’s work, first as associate editor of the early volumes of The Correspondence of Charles Darwin, and then in a biography of Darwin that integrated his science with his life and times. A leading intention of the book was to explore the ways in which scientific knowledge was created, distributed and accepted, moving from private to public, as reflected in the two-volume structure of the work. The biography was received generously both in the UK and USA, and awarded several prizes, including the James Tait Black award for non-fiction in 2004, the W. H. Heinemann Prize from the Royal Literary Society, and the Pfizer Prize from the History of Science Society. She is currently exploring the history of Darwin’s impact on popular culture from the time of his death to today. She was based for many years at the Wellcome Trust Centre for the History of Medicine at University College London where she taught in the MA, MSc and undergraduate programs in the history of science, biology, and medicine. She has been president of both the British Society for the History of Science and the History of Science Society - curiously, not the first person to do so, but the first woman. She has an Honorary degree from her alma mater, Trinity College Dublin, 2009.
Seminar by Prof. Suresh Jesuthasan, Associate Professor of Behavioural Neuroscience in Lee Kong Chian School of Medicine, Nanyang Technological University
The slippery slope from fear to anxiety and depression: insights from zebra fish
Emotions are integral to life. They colour our experience, provide the impetus for action, and influence thinking. Strikingly, emotional responses are usually well suited to the needs of the moment, reflecting anticipated needs as well as current sensory stimuli. Here, using a combination of brain imaging, behaviour and genetic manipulation of zebrafish, I examine brain mechanisms that enable this precision in response. The focus is on systems that enable optimal defensive responses, as failure in this leads to conditions such as anxiety.
Emotions are integral to life. They colour our experience, provide the impetus for action, and influence thinking. Strikingly, emotional responses are usually well suited to the needs of the moment, reflecting anticipated needs as well as current sensory stimuli. Here, using a combination of brain imaging, behaviour and genetic manipulation of zebrafish, I examine brain mechanisms that enable this precision in response. The focus is on systems that enable optimal defensive responses, as failure in this leads to conditions such as anxiety.