Genome 10K and Genome Science Conference
Tuesday 29 August
Friday 1 September 2017
Norwich Research Park
Federica Di Palma, Amanda Chong, Wilfried Haerty, Emily Angiolini, Dawn Turnbull
Early Bird Registration deadline 31 May 2017. Registration closes 31 July 2017.
Standard Early Bird £250; Standard Late £330; Student Early Bird £150; Student Late £200; Day Delegate Early Bird £70 (per day); Day Delegate Late £100 (per day)
We are delighted to host both the Genome 10K 2017 conference and the Genome Science 2017 conference in parallel here in Norwich.
About the event.
For the first time, Norwich, UK will host two distinguished conferences - Genome 10K 2017; the biannual conference exploring critical topics essential for understanding how complex animal life evolved through changes in DNA and how we can use this to help save dying species; and Genome Science 2017 - an annual meeting exploring advances in genomics technology and computational methodologies as well as innovation in its application.
The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in a major tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.
The mission of the Genome 10K COS is to assemble a genomic zoo of some 10,000 vertebrate species to help to understand how complex animal life evolved through changes in DNA and use this knowledge to become better stewards of the planet.
The Genome 10K Project was founded by David Haussler, Oliver Ryder, and Stephen O'Brien, who launched the project in April 2009 at a three-day meeting at the University of California, Santa Cruz.
The Genome Science meeting started out life in 2011 as the UK Next Generation Sequencing meeting, hosted by the DeepSeq facility at the University of Nottingham. Since then it has evolved and grown to be a successful event attracting in the region of 250 delegates each year. This meeting represents a fantastic opportunity for both academia and industry to engage, sharing advances, innovations and challenges in working with -omics data.
In addition to a programme packed full of interesting sessions, we have some fantastic invited speakers who will epitomise the prestige and strength of these conferences. There will also be plenty of networking opportunities, such as the social mixer and conference dinner, as well as the poster sessions. We believe training is crucial to the success of all research projects, including the G10K project and its long-term attainment of objectives. Alongside training for early career researchers we will also include parallel Special Interest Group sessions, which will monitor progress in the sector and set new milestones of the G10K project.
|Open/close||G10K||Genome Science||Shared Sessions||Training/EI Led||Breaks|
Day 1 Tuesday 29 August
|08:30 - 09:00||Registration|
|12:30 - 13:00||Lunch|
|13:00||Welcome: Neil Hall and Federica Di Palma|
|13:30 - 14:15|| Keynote 1|
Towards the gapless assembly of complete vertebrate genomes
Dr Adam M. Phillipy
|14:15 - 15:00|| Keynote 2|
Saving the Tasmanian devil from extinction
Prof Kathy Belov
|15:00 - 15:30||Coffee Break|
|15:30 - 17:45|
|18:00||Social Mixer, EI|
Day 2 Wednesday 30 August
|08:30 - 09:00||Registration|
|09:00 - 10:30|
Clinical and Translational Genomics
|10:30 - 11:00||Coffee Break|
|11:00 - 12:30|
|12:30 - 13:30||Lunch and Poster Session|
|13:30 - 15:00|
Session 4: Sequencing Technology & Developments
Chairs: Mike Quail
|15:00 - 15:30||Coffee Break|
|15:30 - 17:45|
Session 5: Genome Informatics
Chair: Rob Davey
|18:00||Conference Dinner, The Halls, Norwich|
Day 3 Thursday 31 August
|08:30 - 09:00||Registration|
|09:00 - 10:30|
|10:30 - 11:00||Coffee Break|
|11:00 - 12:30|
|12:30 - 13:30||Lunch and Poster Session|
|13:30 - 14:15|
Plenary 2: Homeobox genes and animal evolution: from duplication to divergence
Prof Peter Holland
|14:15 - 15:00|
Plenary 2: Genomics in healthcare: the challenges of complexity
|15:00||Close of Conference|
|15:30 - 16:45||Working Group 1|
Day 4 Friday 1 September
|08:30 - 09:00||Registration|
|09:00 - 10:30|
Working Group 2
Training: De novo assembly
Training: Introduction to Galaxy
|10:30 - 11:00||Coffee Break|
|11:00 - 12:30|
Working Group 3
|12:30 - 13:30||Lunch|
|13:30 - 15:00|
Working Group 4
|15:00 - 15:30||Coffee Break|
|15:30 - 17:00|
Working Group 5
To understand the evolution of animals, we must understand genomes and development. One of the most important discoveries in 20th century biology was the finding that widely different animal species use similar genes, such as homeobox genes, to build their embryos. But if the genes are conserved, why do animal species look so different? Does evolution subtly change the regulation of key genes, or change the number of genes, or change their protein coding sequences? Examples of all three routes have been revealed through comparative genomics, including some surprising examples of how evolution changed the number and function of homeobox genes in mammalian evolution.
About Professor Peter Holland
Peter Holland is the Linacre Professor of Zoology at the University of Oxford, UK. After a degree in Zoology from Oxford and a PhD in Genetics from London, he has held academic posts at the Universities of Reading and Oxford. His research into animal genomes and evolution, spanning marine invertebrates, fish, insects and mammals, has been recognized by award of the Kowalevsy Medal, De Snoo Medal, Linnean Medal, Frink Medal and Genetics Society Medal. He was elected to Fellowship of the Royal Society in 2003.
Kathy’s research team have demonstrated that Tasmanian devils have extremely low levels of genetic diversity at the Major Histocompatibility Complex (MHC) providing an opportunity for Tasmanian Devil Facial Tumour Disease (DFTD), a rare contagious cancer, to spread through devil populations without encountering histocompatibility barriers. They continue this research by studying the relationship between MHC type and disease susceptibility in devil populations, as well as the impact of the emergence and evolution of DFTD strains using genomics technologies.
About Professor Kathy Belov
Professor Kathy Belov is based in the Faculty of Veterinary Science at the University of Sydney. Kathy’s research expertise covers comparative genomics and immunogenetics of Australian wildlife. As well as core research into the Tasmanian Devil Facial Tumour Disease and the genetic management of the Tasmanian devil insurance programme, Kathy’s research team have participated in the opossum, platypus and wallaby genome projects where they have gained insights into genes involved in immunity and defense.They are now working on the koala and echidna genomes. Kathy has received two Eureka awards, the Crozier medal and the Fenner medal for her research.
Genomic technologies have greatly enhanced our understanding of health and disease. Sequencing has become cheaper and quicker, whilst our increasing ability to interpret the data using huge computer power and very big databases, means that genomic testing can now influence clinical decisions in many areas of medicine. Whilst new possibilities continue to escalate, moving from scientific research to tried, tested and routine healthcare is not straightforward.
In this presentation I will outline some of the many dimensions of genomics in healthcare including disease prevention, making a precise diagnosis in rare and more common diseases, choosing drug treatments and assessing reproductive risk. I will explore some of the challenges facing health systems, which arise in part from the complexity of genomic information and the fast-moving nature of the technologies, but also include organisational and professional challenges: for example, the regulatory and practical difficulties of sharing personal data in health systems, or the educational programmes required to ensure that all healthcare professionals can use genetic testing appropriately and safely in their practice.
As health systems face the demands of an ageing population, a constant stream of emerging technologies and raised public expectations, I will suggest that using genomics effectively can be part of the solution. Together with other biomedical and even digital technologies, it can enable a move towards more personalised healthcare and a shift from end-stage ‘rescue’ to prevention and earlier diagnosis.
About Hilary Burton
Dr Hilary Burton is the Director and one of the founder members of the PHG Foundation and a Fellow of Hughes Hall, Cambridge. The PHG Foundation is a not for profit organisation with a special focus on how genomic and other technologies can provide more effective personalised healthcare and improve population health http://www.phgfoundation.org/. Qualified in medicine at Oxford University, Hilary subsequently trained in public health in the Eastern Region and worked as a consultant in Cambridge.
Since 1997 at the PHG Foundation Hilary has focused on the genomics context for population health, and, in particular, has led national work on the implementation of new technologies in mainstream UK health services. As a member of the Joint Committee on Medical Genetics, she was the main author of a report looking at the service implications of introducing genomics across a wide range of clinical specialties. In pursuing this further she is currently chairman of a national RCP Steering Group, which aims to promote increased awareness and competence in genomics amongst UK physicians http://www.phgfoundation.org/project/mainstream_medicine/.
Hilary has also written about the importance of genomic technologies in enabling personalised healthcare and prevention. In 2011/2 she sat on the UK Government Human Genomics Strategy Group and is currently a member of the UK Genetic Testing Network Clinical and Scientific Advisory Group and the Joint Committee on Genomic Medicine of the Medical Royal Colleges.
Genome-wide association studies (GWAS) have long been a staple of human genetics. In the simplest case a population-matched cohort of unrelated individuals with and without a disease or trait is genotyped, and then every marker (SNP) is tested for association with the phenotype. The ease of design has allowed very large cohorts to be recruited to these studies, yielding excellent power for linking genotype to phenotype. With the recent availability of populations hundreds or thousands of sequenced bacterial isolates interest has developed in applying the same technique to relevant pathogen phenotypes such as drug resistance and invasive potential. However, the highly variable pan-genome and potentially confounding strong population structure of bacteria make GWAS difficult to apply in the same way. In this talk I will describe Sequence Element Enrichment analysis (SEER), a method we have published which overcomes these issues by using k-mers as a generalised sequence variant along with appropriate population structure corrections. SEER is freely available and scales to thousands of genomes, and has been used to discover variants affecting invasive potential of S. pyogenes and region specific patterns of B. pseudomallei. Finally, I will describe recent work which pushes the limits of GWAS, testing the contribution of rare and structural variants to bacterial phenotypes.
About John Lees
John Lees is a PhD student, primarily studying the integration of sequencing data from both host and pathogen in cases of bacterial meningitis. He is also interested in phylogenetics and methods for genotype-phenotype association in bacteria.
How is it possible that severe early-onset disorders are mostly genetic in origin, even though the disorders are not inherited because of their effect on fitness? Genomic studies in patient-parent trios have recently indicated that most of these disorders are caused by de novo germline mutations, arising mostly in the paternal lineage.
In this presentation I will discuss our research on the causes and consequences of de novo mutations using novel genomic approaches. I will illustrate all of this using severe intellectual disability as a model, for which we are making rapid progress and now have the opportunity to provide medically relevant information to the majority of patients and families involved.
Synthetic biology applies engineering principles to biology for the construction of novel biological systems designed for useful purposes. It advocated for standards and foundational technologies to facilitate biological engineering. Defining standards for plants has enabled us to automate parallel DNA assembly at nanoscales, removing research bottlenecks and providing the international plant community access to reusable, interoperable, characterized, standard DNA parts. We are applying these principles to programmable genome engineering tools for multiplexed targeted mutagenesis and for the development of tunable, orthologous regulatory elements, synthetic transcription factors and genetic logic gates.
About Nicola Patron
Nicola is a molecular and synthetic biologist interested in the natural and engineered transfer of genetic material between genomes of different species. Her lab is focused on engineering photosynthetic organisms for industrial biotechnology and crops that are healthier to consume and less environmentally damaging to cultivate.
The adaptive radiations of haplochromine cichlid fish in the East African great lakes provide paradigmatic systems to study the dynamics of species formation, and of natural and sexual selection. The most extensive radiation is in Lake Malawi, where in the last million years or so one or a few ancestral populations have given rise to a flock of more than 500 species, filling almost all piscine ecological niches in the lake.
Over the past few years we have collected with collaborators over 2500 samples and sequenced the whole genomes of over 300 fish from over 100 species of Lake Malawi cichlids. All species are genetically close, with pairwise divergence typically between 0.1 and 0.25%, compared to heterozygosity between 0.05 and 0.15%. In addition to extensive incomplete lineage sorting, we see strong signals of gene flow between clades at different levels in the radiation, based on PCA, F statistics and related methods. There appear to be several long chromosomal regions exhibiting unusual phylogeny, perhaps indicative of a role for large inversions in species separation.
At a finer scale, although for close species pairs Fst can be under 20%, we also see local spikes or “islands” of high differentiation that are statistically significant under simple models of population separation, suggestive of loci under selection. Finally, at a functional level, we see higher non-synonymous to synonymous differences between species in genes involved in retinal processing, the innate immune system, oxygen transport, and a number of other pathways.
About Richard Durbin
Richard Durbin is a Senior Group Leader at the Wellcome Trust Sanger Institute, where he has been since its founding in 1992. He has been involved in a succession of large scale genome sequencing projects, including co-leading the 1000 Genomes Project. His current research is focused on studying genome variation and genome evolution, and methods for processing population scale whole genome sequencing data. He has also made many contributions to biological sequence analysis, including developing methods for sequence alignment using Hidden Markov models and suffix array methods, and developing genomic databases including Pfam, Ensembl, and TreeFam. Richard is an Honorary Professor in Computational Genomics at Cambridge University, a Member of EMBO and a Fellow of the Royal Society.
Beth Shapiro*, Nedda Saremi, Megan Supple, Gemma Murray, Richard E. Green, Eduardo Eisirik and the puma genome sequencing consortium
Human land-use changes, including deforestation and establishment of roads and highways, can obstruct natural dispersal and migration corridors, leading to population isolation and inbreeding. Among the most affected species in North America by human land-use changes is the mountain lion, Puma concolor. Once distributed across North America, mountain lions are today found only in southern Florida and the western part of the continent.
To explore the genomic consequences of increasing isolation between mountain lion populations, we sequenced and assembled a chromosome-scale de novo genome from a mountain lion from the Santa Cruz mountains, 36M, and generate high coverage resequencing data from mountain lions from populations across North America and Brazil. Using these data, we investigated the relative timing of onset and duration of inbreeding within potentially distinct mountain lion populations. North American mountain lions contain significantly less genomic diversity than Brazilian mountain lions, but show varying levels of inbreeding that does not correspond directly to present-day barriers between them. Finally, we explore the selective consequences of inbreeding on North American mountain lions, and identify genomic changes that may have evolved as a consequence of increased interaction with humans.
About Beth Shapiro
My research aims to better understand how populations and species change through time, in particular in in response to environmental and other changes to their habitat. To address this, my group uses the latest experimental and computational approaches to analyze genetic information isolated from fossil and archived remains. I am particularly interested in learning what drives two particularly important evolutionary processes: speciation and extinction.
The domestication of animal species was essential for the emergence of complex human societies. Despite its importance there is much about the domestication process that we still do not know. Domesticated species tend to share a suite of phenotypic traits referred to as the ‘domestication syndrome’. However, whether these phenotypic similarities are the result of convergence at the genetic level remains unclear. We generated whole-genome sequences from experimentally domesticated Norway rats and American mink, and identified genes and putatively functional variants that may underlie the phenotypic differences seen in the domesticated animals.
When we combine these data with whole-genome sequences from multiple pairs of domestic animals and their wild sister species we find biological pathways that appear to be recurrently affected by the domestication process across all domesticated animal species. One of these is the ErbB signalling pathway, involved in the development of the reproductive system and neural crest migration.
About Alex Cagan
Alex Cagan investigates evolutionary processes in somatic tissue. His research focuses on characterising mutation and selection in healthy tissues and how this relates to cancer and ageing.
Evolution is often considered to be an almost imperceptibly slow process. However, the cells that compose our own bodies are constantly acquiring mutations. Some of these mutations may influence cellular phenotypes, such as growth, resulting in clonal expansions. Over time the body may become a patchwork of clones. These processes may have profound implications for cancer progression and ageing. Due to technical limitations this evolutionary landscape has remained almost totally unexplored. I work with laser capture microdissection and genome sequencing to describe and understand processes of somatic evolution. I seek to adapt methods from comparative evolutionary genomics to gain new insights into evolution within the body.
- Andrea Harper | Using Associative Transcriptomics to predict tolerance to ash dieback disease in European ash trees
Associative Transcriptomics (AT) is a potent method, first developed in the crop plant Brassica napus, enabling rapid identification of gene sequence and expression markers associated with trait variation in diversity panels. It can be effective even when advanced genomic resources are unavailable, making it a valuable tool for studying traits in non-model species. Most recently, we applied AT to the problem of ash dieback disease, a fungal disease affecting ash trees which was first discovered in the UK in 2012.
Using a Danish ash diversity panel varying for susceptibility to the disease, we discovered expression-based markers that could be used to identify trees with high levels of tolerance to the disease. In addition, information about the genes in which the markers are located, is revealing clues to the mechanisms underlying the ability of some trees to tolerate the disease.
About Andrea Harper
Dr Harper's lab is focused on utilising next-generation sequencing data for the development of statistical genetic and systems biology methods, such as associative transcriptomics, to identify the underlying genetic control of important traits in plants.
- Aaron McKenna | Information storage and recovery using the diversity of second-generation sequencing technologies
Second-generation sequencing has been traditionally seen in terms of a key trade-off: a huge increase in information recovery at the cost of information fragmentation. Here we show that such weaknesses can be overcome by leveraging a series of inventive techniques developed by the field at large. First, we demonstrate that second-generation sequencing can be used to recover chromosomal level contiguity in the de novo genome assembly of a previously unsequenced Muridae species. In addition, we demonstrate it's utility in recovering the 'orthogonal genome': human engineered information storage within the genomes of single living cells, and its application to tracing whole-organism lineage.
- Kristin Tessmar-Raible | Genomic and transcriptomic approaches for the study of daily, monthly and seasonal timing
Life is controlled by multiple rhythms. While the interaction of the circadian clock with environmental stimuli is well documented, its relationship to endogenous oscillators with other periods, as well as natural timing variation between individuals of the same species is little understood.
The marine bristle worm Platynereis dumerilii harbors a light-entrained circadian, as well as a monthly (circalunar) clock. Our first studies suggest that the circalunar clock persists even when circadian clock function is disrupted as evidenced by the complete absence of molecular and behavioral circadian oscillatory patterns. However, the circalunar clock impacts on the circadian clock on two levels:
a) It regulates the level of a subset of core circadian clock genes.
b) In addition to its molecular input, we furthermore find that the circalunar clock changes the period and power of circadian behavior, although the period length of the daily transcriptional oscillations remains unaltered.
In order to study the molecular and cellular nature of its circalunar clock, as well as its interaction with the circadian clock, we have established transient and stable transgenesis, inducible specific cell ablations, chemical inhibitors, as well as TALEN-mediated genome engineering. We have been investigating the extent of transcript changes in the brain caused by the circalunar clock and compare these changes to other major conditions (sex determination, maturation) occurring during the life of the worm, as well as to the known extent of transcript changes caused by the circadian clock.
The marine midge Clunio marinus possesses a circadian clock, and in addition acquired a circalunar clock during the past 20.000 years. Strains of different geographic origins exhibit differences in their circalunar and circadian timing (“chronotypes”), which are genetically encoded and map to 3 quantitative trait loci (QTLs). We sequenced and assembled the 90Mbp genome of the midge and mapped the QTLs to the molecular map. Based on subsequent single nucleotide polymorphism (SNP) analyses differentially fixed in different timing strains, and molecular studies, we suggest that circadian chronotypes in Clunio are caused by activity variants in the enzyme CaMKII.
Given its evolutionary conservation and prominent role in the mammalian brain, it is tempting to speculate, that CaMKII could play a similar role in mammals, and could thus provide a molecular link between extreme chronotypes and frequently co-occurring neuropsychological diseases.
About Kristin Tessmar-Raible
The main interest of my lab is to investigate how solar and lunar light are sensed by the nervous system and how this light information impacts on the animals' information processing and endogenous clocks.
In particular, we aim to decipher the neuron types and molecules underlying fundamental, yet unexplored monthly oscillators (so-called circalunar clocks), using the bristle worm Platynereis dumerilii and the midge Clunio marinus.
Understanding evolution of plant immunity is necessary to inform rational approaches for genetic control of plant diseases. The plant immune system is innate, encoded in the germline, yet plants are capable of recognizing diverse rapidly evolving pathogens. Availability of plant genomes plant species allowed us to elucidate evolutionary history of plant immune receptors of Nucleotide-Binding Leucine Rich Repeat class (NLRs) that provide genetic diversity to recognize pathogens and induce signaling cascade. We identified the ‘core’ and highly variable sub-clades of NLRs from across 60 plant species, including previously understudied monocots and uncovered sub-family clade expansions. A recent paradigm in NLR-based recognition of pathogens involves NLRs with exogenous gene fusions, called integrated domains (NLR-IDs) that can serve as baits for pathogen-derived effectors. We have shown that NLR-IDs are prevalent across flowering plants and identified their ID repertoires. We uncovered a clade of NLRs that is undergoing repeated independent integration events that produces diverse NLR fusions to other genes. This NLR clade is ancestral in grasses with members often found on syntenic chromosomes while integrated domains are exchanged from different genomic locations. Sequence analyses revealed that DNA transposition or ectopic recombination are most likely mechanisms of NLR-ID formation. The identification of a subclass of NLRs that is naturally adapted to new domain integration can inform biotechnological approaches for generating synthetic receptors with novel pathogen ‘traps’.
About Ksenia Krasileva
Ksenia is a Group Leader at the Earlham Institute and The Sainsbury Laboratory. Dr. Krasileva has expertise in bioinformatics and genomics, plant biology and plant-microbe interactions. She holds both Bachelors of Science and PhD degrees from University of California, Berkeley where she studied plant innate immunity in Arabidopsis and got her training in Genomic and Computational Biology. For the past four years she has focused on wheat, first as a post-doctoral fellow with Jorge Dubcovsky (University of California Davis and Howard Hughes Medical Institute) where Dr. Krasileva was awarded a prestigious USDA NIFA Fellowship “Developing Functional Genomics for Wheat” and now with her own team at EI/TSL.
Dr. Krasileva is a co-developer of wheat exome capture and one of the leads on generating wheat reverse genetic resource "in silico TILLING". She maintains her research interests in the biology of wheat genome, evolution of plant innate immunity and functional analyses of plant immune receptors. Her group rapidly adopts new technologies and successfully combines fundamental and translational research to better understand plants and to generate crops with durable resistance to pathogens.
Small subunit (SSU) ribosomal RNA (rRNA) genes have been the standard phylogenetic markers for the study of microbial evolution and diversity for decades. However, the essential reference databases of full-length rRNA gene sequences are underpopulated, ecosystem skewed, and subject to primer bias; which hampers our ability to study the true diversity. In this talk, I will present our latest method development that combines poly(A)-tailing and reverse transcription of SSU rRNA molecules with synthetic long-read sequencing, to generate millions of high quality, full-length SSU rRNA sequences without primer bias. We applied the approach to complex samples from seven different ecosystems and obtained more than 1,000,000 SSU rRNA sequences from all domains of life. The novel diversity is overwhelming and include several potentially new archaeal phyla of the deeply branching Asgard Archaea, which are previously suggested to bridge the gap between prokaryotes and eukaryotes. This approach will allow expansion of the rRNA reference databases by orders of magnitude and will enable a comprehensive census of the tree of life. With a fully populated SSU tree of life, it will be possible to prioritize efforts towards making a fully populated genome tree of life. To demonstrate the progress with these efforts, I will also discuss our recent progress on extraction of complete (closed) genomes from metagenomes using high-throughput long-read Nanopore.
About Mads Albertsen
Biog: Mads Albertsen is an Associate Professor at the Center for Microbial Ecology at Aalborg University, where he heads his own research group. The research of his group is focused on microbial ecology and method development within metagenomics in the interface of bioinformatics and molecular biology. At the age of thirty-one, he is an international recognized expert in the field of metagenomics and has developed novel approaches to retrieve complete genomes from metagenomes. He has received several awards for his work, including the 2016 “Rising Star” award from the ISME society, “Research result of the year in Denmark 2015” and the SparNord Fond research excellence award of 35.000 EUR. His current research projects are focused on populating the tree of life by developing new methods for high-throughput full-length rRNA sequencing and using high-throughput long-read metagenomics to enable genome extraction of complete genomes from metagenomes.
The Albertsen Lab is part of Center for Microbial Communities at Aalborg University. The Center has approx. 30 young scientist working with structure and function of microbial communities, primarily related to environmental biotechnology. The Center has state-of-the art equipment within DNA sequencing (Illumina MiSeq & HiSeq and Oxford Nanopore MinION & PromethION), proteomics, metabolomics and advanced microscopy.
Our research is focused on method development within DNA sequencing related topics including metagenomics, metatranscriptomics, amplicon sequencing and bioinformatic method development. A strong focus on new technologies related to novel applications, method and software development. Dedicated to make complex data, analysis and workflows simple and usable for the broader scientific community.
- Prof Emma Teeling | Growing old yet staying young: A genomic perspective on bats’ extraordinary longevity
Of all mammals, bat possess the most unique and peculiar adaptations that render them as excellent models to investigate the mechanisms of extended longevity and potentially halted senescence. Indeed, they are the longest-lived mammals relative to their body size, with the oldest bat caught being 41 years old, living approx. 9.8 times longer than expected. Bats defy the ‘rate-of-living’ theories that propose a positive correlation between body size and longevity as they use twice the energy as other species of considerable size, but live far longer. The mechanisms that bats use to avoid the negative physiological effects of their heightened metabolism and deal with an increased production of deleterious Reactive Oxygen Species (ROS) is not known, however it is suggested that they either prevent or repair ROS damage.
Bats also appear to have resistance to many viral diseases such as rabies, SARS and Ebola and have been shown to be reservoir species for a huge diversity of newly discovered viruses. This suggests that their innate immunity is different to other mammals, perhaps playing a role in their unexpected longevity. Here the potential genomic basis for their rare immunity and exceptional longevity is explored across multiple bat genomes and divergent ‘ageing’ related markers. A novel blood based population-level transcriptomics approach is developed to explore the molecular changes that occur in an ageing wild population of bats to uncover how bats ‘age’ so slowly compared with other mammals. This can provide a deeper understanding of the causal mechanisms of ageing, potentially uncovering the key molecular pathways that can be eventually modified to halt, alleviate and perhaps even reverse this process in man.
About Emma Teeling
Prof. Emma Teeling established the Laboratory of Molecular Evolution and Mammalian Phylogenetics in 2005 and is the Founding Director of the Centre for Irish Bat Research at University College Dublin (UCD). She has been awarded a prestigious European Research Council Starting grant (2012) and a Science Foundation Ireland, President of Ireland Young Researcher Award (2006). Her integrative research in the fields of zoology, phylogenetics, genomics and conservation biology uncovers the genetic signatures of survival that enables species to adapt to an ever-changing environment. The two mains goals of her research are: (1) study unique model species to enable a better understanding of the structure and function of the human genome to inform medicine and molecular biology; (2) understand and therefore conserve, natural populations and environments to promote ecosystem well-being and functioning. She successfully leads a prolific, internationally renowned research team of typically 10 people and has secured over 4.4M in research funding. She is listed in top 100 female Irish scientists (2014) and gave a TEDx talk (2012) > 340,000 downloads.
Porcine Reproductive and Respiratory Syndrome (PRRS) is arguably the most important infectious disease for the world-wide pig industry. The effects of PRRS include late-term abortions and stillbirths in sows and respiratory disease in piglets. The causative agent of the disease is the positive-strand RNA PRRS virus (PRRSV). PRRSV has a narrow host cell tropism, targeting cells of the monocyte/macrophage lineage. One of the host proteins involved in facilitating viral entry is CD163 which has been described as a fusion receptor for PRRSV. CD163 is expressed at high levels on the surface of macrophages, particularly in the respiratory system. The scavenger receptor cysteine-rich domain 5 (SRCR5) region of CD163 has been shown to interact with virus in vitro.
We used CRISPR/Cas9 gene editing technology to generate pigs with a deletion of the CD163 exon 7 which encodes the SRCR5 domain. Deletion of SRCR5 showed no adverse effects in pigs maintained under standard husbandry conditions with normal growth rates and complete blood counts observed. Pulmonary alveolar macrophages (PAMs) and peripheral blood monocytes (PBMCs) were isolated from the animals and assessed in vitro. Both PAMs and macrophages obtained from PBMCs by CSF1 stimulation (PMMs) show the characteristic differentiation and cell surface marker expression of macrophages of the respective origin.
Expression and correct folding of the SRCR5 deletion CD163 on the surface of macrophages and biological activity of the protein as hemoglobin-haptoglobin scavenger was confirmed. Both PAMs and PMMs were challenged with PRRSV genotype 1, subtypes 1, 2, and 3 and PMMs with PRRSV genotype 2. PAMs and PMMs from pigs homozygous for the CD163 exon 7 deletion showed complete resistance to viral infections assessed by replication. Confocal microscopy revealed the absence of replication structures in the SRCR5 CD163 deletion macrophages, indicating an inhibition of infection prior to gene expression, i.e. at entry/fusion or unpacking stages.
About Alan Archibald
Professor Alan L. Archibald FRSE is Deputy Director and Head of Division of Genetics and Genomics at The Roslin Institute, R(D)SVS, University of Edinburgh. Alan's research focuses on understanding the genetic control of complex traits, including responses to infectious disease, in farmed animals, primarily pigs and cattle.
Registration is now open, you can secure your place by clicking the button below.
- Access to all lectures
- Access to poster sessions
- Access to a choice of special interest groups, training and CPD sessions
- Conference Dinner
- Optional transport to the conference venue from UEA accommodation (15 minutes’ walk)
Please note: Accommodation is not included in the registration fee. Accommodation at Paston House, UEA is optional at registration and will be added to the registration fee if selected.
Registration opens: 1 February 2017
Early Bird registration closes: 31 May 2017
Abstract submission deadline: 31 May 2017
Late registration closes: 31 July 2017
|Early Bird Registration (1 Feb 2017 - 31 May 2017)||Late Registration (1 May 2017 - 31 Jul 2017)|
|Day Delegate (per day)||£70||£100|
Deadline for submission of abstracts is 31 May 2017.
1 February - 31 May 2017
You may submit an abstract during early bird registration only. You will be permitted to submit your abstract for consideration for:
- Oral presentation
- Poster presentation
- Oral and poster presentation
During submission, you will be required to identify the most appropriate theme aligned to the session topics. The chair persons for that session will form the reviewers panel for your abstract.
- Peer review of your work
- A track record of your successes for your CV
- Opens opportunities for networking
- Can support manuscript preparation
Eligible abstracts will be subject to selection to receive travel bursaries to allow individuals to attend the conference (details to follow).
Hosted at the Earlham Institute (EI), a cutting edge, contemporary research institute and registered charity, working in an area of rapid technological development and innovation. Established in 2009, EI is strategically funded by the BBSRC to lead the development of a skill base in bioinformatics and a genomics technology platform for UK bioscience.
The Institute is located on the Norwich Research Park, together with its partners: the John Innes Centre, the Institute of Food Research, The Sainsbury Laboratory, the University of East Anglia and the Norfolk and Norwich University Hospital. The Research Park has an excellent reputation for research in plant and microbial sciences, interdisciplinary environmental science and food, diet and health, to which EI contribute strengths in genomics and bioinformatics.
Close links exist between the NRP partners and new opportunities for collaboration in exciting new initiatives are under development. The NRP recently received £26M of government investment to facilitate innovation and further develop infrastructure to attract science and technology companies to the Park to enhance the vibrant environment and realise economic impact from research investment.
The JIC Conference Centre.
Earlham Institute at night
Accommodation is reserved at Paston House, University of East Anglia (UEA), a short 15-20 minute walk from the conference venue. The cost of this is £34.00 per night, including breakfast. This is en-suite student accommodation on the UEA campus with access to shops as well as buses to Norwich city centre.
Earlham Institute has also negotiated rates at the following hotels and facilities. When booking a room, please mention that you are attending the ‘Genome 10K Conference’ to ensure that you receive our negotiated rates:
Park Farm Hotel, Hethersett is 4 miles from Earlham Institute to the south of Norwich. This hotel has leisure facilities including a pool and the preferential rate is £90 per night bed and breakfast. A taxi would be required and costs approx. £12, but could be shared at this price.
Maid’s Head Hotel, Norwich is 4.6 miles from Earlham Institute in the centre of Norwich, next to the Cathedral. Here we also attract a beneficial rate of £90 per night bed and breakfast. A taxi, if pre-ordered, would cost around £10.
Transport is arranged to take you from the conference to the conference dinner venue on Wednesday evening at 18:00 for pre-dinner reception at 19:00
Limited transport operating on a first-come, first-served basis is available from the accommodation at UEA to the conference venue.
The conference dinner will be held on 30 August 2017 at 19.30pm in St. Andrew's Hall which is the centrepiece of The Halls and is the name by which many people refer to the whole complex of buildings.
It has a fine, high-beamed ceiling, beautiful stained glass windows, limestone columns and a large polished maple floor. It was originally the nave of the friary and was completed in 1449. The size and beauty of its proportions are impressive without elaborate decoration in keeping with the friars' rule of simplicity.
The stained glass, stone carving and deeply-coloured portraits add richness to the simple backdrop of the building, adding a contemporary feel to this incredibly historical building of civic tradition - the best of both worlds.
Coaches will take you from the conference venue at 18:00 to St Andrews Hall for the conference dinner which is in the very heart of the City of Norwich.
The Norwich Arcade, in the heart of the city centre.
Norwich as a city has a lot to offer with high street shops, two shopping centres, restaurants, bars, pubs, cinemas, a bowling alley, theatres and much more. The city is also known for Norwich Cathedral (Church of England) and the Cathedral of St John the Baptist (Catholic Church) as well as Norwich Castle which is now an art gallery and museum.
You can find more information about Norwich here.
Just a short journey out of the City and you can also enjoy the Norfolk coast which spans 93 miles with a variety of beaches and coastal landscapes.
You can find more information about what Norfolk has to offer here.
Scientific Organising Committee
Local Organising Committee
Genome 10K Organising Committee
Erich Jarvis - Contact
Steve O'Brien - Contact
David Haussler - Contact
Tomas Marques (UPF) – Contact
Jenny Graves – Contact
Byrappa Venkatesh – Contact
Richard Durbin - Contact
Oliver Ryder – Contact
Harris Lewin – Contact
Kerstin Lindblad-Toh – Contact
Klaus Koepfli (Centre for Species Survival, Smithsonian National Zoo) – Contact
Benedict Paten – Contact
Beth Shapiro – Contact
Warren Johnson – Contact
Emma Teeling – Contact
Tandy Warnow – Contact
Federica Di-Palma – Contact
Guojie Zhang – Contact
Elinor Karlsson – Contact
Adam Phillippy (NIH/NHGRI) – Contact
Gene Myers – Contact
Rebecca Johnson – Contact
Olivier Fedrigo – Contact
Genome Science Organising Committee
This year the Microbiology Society is pleased to be sponsoring two awards (cash prizes and society memberships) for the best and runner-up Microbial Genomics posters. The Microbiology Society is a membership organisation for scientists who work in all areas of microbiology. See more on the benefits of membership here https://www.microbiologysociety.org/ or follow us on twitter @MicrobioSoc
De novo Assembly Training Workshop.
Hosted by Earlham Institute on the Norwich Research Park, UK, enjoy world-class facilities at both EI and the John Innes Conference Centre. We also welcome you to Norwich, a city steeped in history and culture set in the middle of East Anglia.
Become a sponsor.
Address and map.
John Innes Conference Centre
Norwich Research Park