INTEGRATED ANALYSIS OF TRANSCRIPT-LEVEL REGULATION OF METABOLISM AND DISEASE-ASSOCIATION OF GENES UNDER HIGH REGULATORY LOAD
Mafalda Galhardo, EnvMetaGen Project, CIBIO-InBIO/UPorto | November 25, 2016 – 15h00 | CIBIO-InBIO’s Auditorium, Campus de Vairão
WELCOME SEMINAR IN BIODIVERSITY AND EVOLUTION
In this presentation, I will show an integrated analysis of human adipocyte differentiation, focusing on transcript-level regulation and its impact on the metabolic network. Diverse data types including gene expression microarrays, target gene identification for 3 down-regulated microRNAs, genome-wide binding profiles of 3 key adipogenic transcription factors and profiling of the active transcription mark H3K4me3, were used together with constraint-based metabolic modelling to obtain a global and concerted view of the regulatory and metabolic events occurring during adipogenesis. Such integrated analysis revealed the convergence of microRNAs and TFs on disease-associated genes from metabolic pathways predicted to change activity throughout differentiation. In order to test the hypothesis that genes under higher regulation are associated to a disease more often than expected, we analyzed a large set of public data from diverse tissues and cell types, from the genome-wide profiling of transcription factor binding or the location of active enhancers, revealing an enrichment for disease-associated genes among genes with the highest regulatory load. Further analysis taking into account diseases and their associated genes (based on DisGeNET) highlights the association of diseases relating to a particular cell type or function to the genes with the highest regulatory load on that particular cell type, such as the case of genes associated to Parkinson’s disease being enriched among the genes with more enhancers in samples from the substantia nigra (brain). Overall, integrated analyses can be very useful in understanding relationships and dependencies within biological processes or systems, as well as potentiate new testable hypotheses which are otherwise difficult to grasp using single methodologies.
Mafalda Galhardo has recently joined CIBIO-InBIO as a post-doc in the EnvMetaGen project, to work on data analysis and integration on topics such as epigenetics. She studied Biochemistry (BSc) in Lisbon (FCUL) and continued with Systems Biology (MSc) in Luxembourg (FSTC), where she also did her PhD. Her interests include genome regulation, epigenetics and metabolism.
Image credits: Mafalda Galhardo
]]>ENVMETAGEN – Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics
Joana (http://cibio.up.pt/people/details/jcpauper)
Mafalda (https://cibio.up.pt/people/details/mgalhardo)
Bastian (https://cibio.up.pt/people/details/egeterbas)
DNA BASED DIET ANALYSIS OF SEABIRDS
Julie McInnes (University of Tasmania, Australia) | September 13, 2016 – 11h00 | CIBIO-InBIO’s Auditorium, Campus de Vairão
Many seabird species are highly susceptible to marine threats, including interactions with commercial fisheries and climate change. Understanding their prey requirements and dietary flexibility in this context is important for effective conservation and management. However, current methods used to identify seabird prey items are often only available during certain stages of the breeding season and can be limited to certain prey groups. Small or soft-bodied items, such gelatinous and larval prey, are often under-estimated and hard-bodied prey are often over-represented, due to retention of hard-parts.
DNA metabarcoding of food in animal scats provides a non-invasive dietary analysis method for vertebrates. This method can be applied to all stages of the breeding season for seabirds and can detect soft-bodied prey. This talk will provide you with an overview of what DNA dietary analysis is, the varying approaches used and discuss my current albatross dietary work. We have developed field and laboratory methodologies for albatross diet analysis and used these techniques to establish range-wide prey information for the globally distributed Black-browed Albatross (Thalassarche melanophrys).
Julie has worked on numerous seabirds over the last ten years, which has included remote field work on albatross in the sub-Antarctic and penguins in the Antarctic, Australia and New Zealand. She is currently a PhD student at the University of Tasmania researching albatross diet analysis by DNA analysis of scats. Her work involves developing field protocols to ensure high quality dietary data is obtained and refining laboratory methods to detect all albatross prey items. This has then been applied to two case studies, firstly a broad collaborative study on the broadly distributed black-browed albatross; and secondly on the Tasmanian endemic shy albatross.
[Host: Simon Jarman, ERA-Chair in Environmental Metagenomics]
Image credits: Julie McInnes
]]>
Details available here.
]]>I have a strong current interest in age-related changes in DNA methylation of specific genes as a biomarker for age. This allows cross-sectional sampling of animal populations to obtain age information and has great potential to provide information on the age structure of wild animal populations that are not under intense longitudinal study. Epigenetic biomarkers have untapped potential as biomarkers for physiological status of wild animals other than age and I intend to investigate this further.
I studied Genetics at the University of Aberdeen, Scotland and then did postgraduate research on genetics of the Antarctic krill at the University of Tasmania. I spent fourteen years working for the Australian Antarctic Division in Kingston, Tasmania, Australia where I was developing DNA-based diet analysis and age estimation methods for a range of Southern Ocean animal species. I was recently appointed as the ERA chair in Environmental Genomics at CIBIO-InBIO, University of Porto, where my team and I have the exciting opportunity to expand the field of Environmental Metagenomics and establish a local centre of expertise in this area.
Details available here.
Image credits: Simon Jarman
]]>ENVIRONMENTAL METAGENOMICS
Simon Jarman (ERA Chair in Environmental Metagenomics, CIBIO-InBIO/UP) | June 15, 2016 | 12h00 | CIBIO-InBIO’s Auditorium, Campus de Vairão
WELCOME SEMINAR IN BIODIVERSITY AND EVOLUTION
Environmental Metagenomics is the study of genetic material taken from communities or single organisms in their natural environment. Research in this area allows ecological questions to be answered that cannot be addressed by other methods. I am fortunate to have recently been appointed as the ERA chair in Environmental Metagenomics based at CIBIO. The EnvMetaGen project that funds this and several other positions, provides an opportunity to build a world class team that will apply existing DNA metabarcoding and other environmental metagenomics methods to a range of ecological questions. It will also allow us to expand and refine Environmental Metagenomic methodologies and establish CIBIO as an internationally recognised centre of excellence in this area. I have worked extensively on dietary DNA metabarcoding for wild animals since this area was established. In my introductory seminar, I will describe some of the dietary analysis work I have done on penguins, whales and Antarctic krill in the past. I will give an overview of the field of dietary DNA metabarcoding and talk about future ideas and plans for expanding research in this area at CIBIO-InBIO. The chronological age of wild animals is a key ecological characteristic that is often hard to determine. I have worked on novel molecular approaches for estimating the age of animals such as humpback whales and long-lived seabirds. Age can be estimated from changes in DNA methylation at specific regions of genes in DNA from samples of skin or feathers. This allows the age structure of animal populations to be determined from cross-sectional sampling. I will talk about applications for these technologies and about the potential for analysing other physiological states of animals such as reproductive status or health condition from molecular biomarkers like DNA methylation and micro RNAs. Environmental Metagenomics can be applied to analysing biodiversity within any taxonomic group and at any spatial scale from viruses to whales. Existing research at CIBIO covers a great range of organisms from diverse environments. This provides excellent opportunities for integration of molecular biodiversity assessments from different environments to research the underlying processes that affect biodiversity in all places.
Simon Jarman studied Genetics at the University of Aberdeen, Scotland and then did postgraduate research on genetics of Antarctic krill at the University of Tasmania. He spent fourteen years working for the Australian govenment’s Antarctic research programme, where he was developing DNA-based diet analysis and age estimation methods for a range of Southern Ocean animal species. Simon was recently appointed as the ERA chair in Environmental Genomics at CIBIO-InBIO, University of Porto, where he and his team have the exciting opportunity to expand the field of Environmental Metagenomics and establish a centre of expertise in this area. Simon was born in England, but he moved to Australia when he was very young. He likes to explore the natural world in other ways when he is not working. He likes walking and climbing rock and ice in remote areas; he likes surfing, sailing and kayaking and h has paddled a sea kayak from mainland Australia to Tasmania. Simon’s main hobby in recent years has been walking to the sources of remote rivers in Tasmania with small inflatable rafts (‘packrafts’) and descending the rivers by packraft to get back home.
Image credits: Simon Jarman
]]>