My personal and professional adventure into Science

Archives for 2015

Reconstructing the universal tree and network of life

I would like to bring your attention to the following talk, which is tomorrow December 11th 2015 from 14-15 at Copenhagen University.

Place: Thorvaldsensvej 40, 3rd floor, rooms R322 + R323

Talk by invited speaker Professor Philip Hugenholtz. Director of Australian Centre for Ecogenomics at the University of Queensland, Australia.

Professor Philip HugenholtzShort biography:
From a PhD in 1994 at The University of Queensland, Phil Hugenholtz developed a career in microbiology and genomics in the USA and in Australia.
Phil’s last position in the USA was as Staff Scientist (2004-2010) at the DOE Joint Genome Institute. In late 2010 Phil returned home to establish the Australian Centre for Ecogenomics.
The Centre was founded around himself as Director, and ARC QEII Fellow and Deputy Director, Associate Professor Gene Tyson.
Phil has published over one hundred papers in molecular microbial ecology including several Science & Nature papers.
Currently, Phil’s research interests include the microbial ecology and evolution of host-associated ecosystems such as the termite hindgut and human microbiome,
and genomic mapping of the microbial tree of life. He has helped pioneer the use of culture-independent molecular methods to characterise microbial communities
including marker gene and shotgun (metagenomic) approaches.
In 2006, Phil received the Young Investigators Award from the International Society of Microbial Ecology (ISME), was elected in 2012 as a Fellow of the American Academy of Microbiology (AAM)
and more recently, in June 2015, was successful in receiving an Australian Research Council Laureate Fellowship.

Recent research topics include an Australian Research Council funded metagenomics project on “Evolution of the marsupial gut microbiome and adaptation to plant toxins”.
Based on a joint linkage grant obtained in 2015 from the Australian Research Council Phil Hugenholtz is now collaborating with Elizabeth Neilson, Mette Clausen and Birger Lindberg Møller
at the Plant Biochemistry Laboratory, UCPH and with Thomas Sicheritz-Ponten and his staff at the Center for Biological Sequence Analysis,
DTU on the project “Understanding the koala microbiome: unlocking the secrets of koala health and dietary specialisation, and successful husbandry and translocation”.

You are hereby invited to attend the lecture, a glass of wine is served

On behalf of Thomas Sicheritz-Ponten, Lizzie Neilson and Birger Lindberg Møller

 

Australian Centre for Ecogenomics

Adapting to -70 degrees in Siberia: a tale of Yakutian horses

I am proud to have been a part of the work described below. You can check out the paper Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments 🙂

From an evolutionary perspective it happened almost overnight. In less than 800 years Yakutian horses adapted to the extremely cold temperatures found in the environments of eastern Siberia. The adaptive process involved changes in the expression of a plethora of genes, including some also selected in human Siberian groups and the extinct wooly mammoth.

(Copyright Patrice Gérard-CNRS-MAFSO, Mission Archéologique Francaise en Siberie Orientale)

(Copyright Patrice Gérard-CNRS-MAFSO, Mission Archéologique Francaise en Siberie Orientale)

In a new scientific study, the comparison of the complete genomes of nine living and two ancient Yakutian horses from Far-East Siberia with a large genome panel of 27 domesticated horses reveals that the current population of Yakutian horses was founded following the migration of the Yakut people into the region in the 13-15th century AD. Yakutian horses, thus, developed their striking adaptations to the extreme cold climate present in the region in less than 800 years. This is one of the fastest examples of adaptation within mammals. The findings are reported in the PNAS early edition from November 23rd by an international team of researchers led by Dr. Ludovic Orlando from the Centre for GeoGenetics at the Natural History Museum of Denmark, University of Copenhagen.

A horse-centered lifestyle

Horses have been essential to the survival and development of the Yakut people, who migrated into the Far-East Siberia in the 13-15th century AD, probably from Mongolia. There, Yakut people developed an economy almost entirely based on horses. Horses were indeed key for communication and keeping population contact within a territory slightly larger than Argentina, and with 40 % of its surface area situated north of the Arctic Circle. Horse meat and hide have also revealed crucial for surviving extremely cold winters, with temperatures occasionally dropping below -70C.

Horses have been present in Yakutia for a long time as 30,000 year-old Late Pleistocene fossils from the region show. Yet, Dr. Ludovic Orlando and his team now reveal that ancient horses of this region were not the ancestors of the present-day Yakutian horses.

(Copyright Patrice Gérard-CNRS-MAFSO, Mission Archéologique Francaise en Siberie Orientale)

(Copyright Patrice Gérard-CNRS-MAFSO, Mission Archéologique Francaise en Siberie Orientale)

A divergence as deep as the origin of modern humans

The genome sequence obtained from the remains of a 5,200 year-old horse from Yakutia appears within the diversity of a now-extinct population of wild horses that the team discovered last year in Late Pleistocene fossils from the Taymir peninsula, Central Siberia. This new finding extends by thousands of kilometers eastwards the geographical range of this divergent horse population, which became separated from the lineage leading to modern horses some 150,000 years ago. It also extends its temporal range up to 5,200 years ago, a time when woolly mammoths also became extinct. Dr. Ludovic Orlando says:

– This population did not appear on any radar until we sequenced the genomes of some of its members. With 150,000 years of divergence with the lineage leading to modern horses, this makes the roots of this population as deep as the origins of our human species.

Interestingly, the new genome analyses show that the horses that Yakut people now ride and probably rode all along their history (as shown by the genome of a ~200 year-old horse), are not related with this now-extinct horse lineage, but rather with the domesticated horses from Mongolia. Dr. Ludovic Orlando says:

– We know now that the extinct population of wild horses survived in Yakutia until 5,200 years ago. Thus it extended from the Taymir peninsula to Yakutia, and probably all across the entire Holarctic region. In Yakutia, it may have become extinct prior to the arrival of Yakut people and their horses. Judging from the genome data, modern Yakutian horses are no closer to the extinct population than is any other domesticated horse.

The new genome analyses show that the founders of the modern Yakutian horse population probably entered into the region with Yakut horse-riders in the 13-15th Century AD.  Dr. Ludovic Orlando further adds:

– This is truly amazing as it implies that all traits now seen in Yakutian horses are the product of very fast adaptive processes, taking place in about 800 years. This represents about a hundred generations for horses. That shows how fast evolution can go when selective pressures for survival are as strong as in the extreme environment of Yakutia.

Reprograming gene expression: a key component of fast adaptation

The team leveraged on their large horse genome panel to identify the genes underlying such adaptations. Strikingly, they found that a large fraction of the selection signatures were not located within the coding region of genes, but within their upstream regulatory regions. It, thus, suggests that the adaptation of Yakutian horses to their environment took place through a massive reprograming of gene expression. Dr. Pablo Librado comments:

– The founder group of the current population was quite reduced in size. The genetic variation standing within gene bodies was, thus, probably limited in comparison to that present within regulatory regions. These regulatory variants probably offered as many possibilities to rapidly modify horse traits in a way that was compatible with their survival.

Focusing on the genes and their regulatory regions showing evidence of selection, the team identified key biological functions involved in the adaptive process. These concern morphological changes, hormonal responses involved in the regulation of thermogenic requirement and the production of anti-freezing compounds. The list of selective signatures also include genes, such as TGM3, which is involved in hair development and might be responsible for the extremely hairy winter coat of Yakutian horses. Dr. Librado adds:

– In addition to unveil their evolutionary origins, our approach helped narrow down the genetic basis of adaptations that are unique to Yakutian horses. In one word, their genetic makeup. We also found genes that were reported to have undergone selection in other Arctic populations, such as indigenous Siberian humans, and even the woolly mammoth. It provides a compelling example of evolutionary convergence, where unrelated groups exposed to similar environments end up independently developing similar adaptations.

Such genes showing convergent signals of adaptation include in humans PRKG1, which is involved in the shivering response to cold, and BARX2 in the woolly mammoth which is involved in hair development.

(Copyright Morgane Gibert-CNRS-MAFSO, Mission Archéologique Francaise en Siberie Orientale)

(Copyright Morgane Gibert-CNRS-MAFSO, Mission Archéologique Francaise en Siberie Orientale)

Dr. Clio Der Sarkissian concludes:

– Our work shows the power of ancient DNA, as we would have never been able to discover the existence of the now extinct ancient population of horses by analyzing the genome of modern horses. With ancient genomes, we can now understand the dynamics of past populations at unprecedented levels and track, through space and time, how these became adapted to changing environments. Applied to pre-industrial museum specimens, our approach can therefore help following how extant populations have been affected by ongoing climate changes and recent human activities. This can help develop tailor-made conservation programs, which will be ultimately essential for preserving endangered populations.

The group has already implemented such approaches for preserving the Przewalski’s horse, which represents the last truly wild horse living in the planet.

“Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments”. Librado P et al. PNAS 2015 ; published ahead of print November 23, 2015, doi:10.1073/pnas.1513696112

This work was developed at the Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, and was funded by the Danish National Research Foundation (DNRF94), the Danish Council for Independent Research, the Villum

Fonden, the Lundbeck Foundation, Marie Curie FP7 and H2020 initiatives, the International Research Group Program, Deanship of Scientific Research, King Saud University and the IDEX “Chaires d’attractivite” programme from University of Toulouse. It also involved 19 research groups around the planet, including the University of Copenhagen, the Technical University of Denmark, the Joint Genome Institute, the University Pompeu Fabra, the Swiss National Stud Farm, the University of Bern, the University of Toulouse, the King Saud University, the North-Eastern Federal University, the University of Minnesota, the Russian Academy of Sciences, the University of California, Berkeley, the Kurchatov Institute and the University of Eastern Finland.

Contact

Dr. Ludovic Orlando
Centre for GeoGenetics
Natural History Museum of Denmark
Head of the Paleomix research group
Lorlando@snm.ku.dk
+45 21 84 96 46

Dr. Pablo Librado
Centre for GeoGenetics
Natural History Museum of Denmark
Post-doctoral researcher
plibrado@snm.ku.dk
+45 52 65 99 62, +34 649 22 62 73

Dr. Clio Der Sarkissian
Centre for GeoGenetics
Natural History Museum of Denmark
Post-doctoral researcher
clio.dersarkissian@snm.ku.dk
+45 40 33 71 57

Uffe Wilken
Communications Officer
Centre for GeoGenetics
ugwilken@snm.ku.dk
+45 4018 5992

Martin Bertelsen
Communications Officer
Natural History Museum of Denmark
mlbertelsen@snm.ku.dk
+45 2448 2147

Day 1 summary of ICG-10 – the 10th International Conference on Genomics

ICG10 – The 10th International Conference on Genomics #DTUicg10

On Tuesday I will finally get some air under my wings again (It’s been almost 2 months since my last flight !!), as I will be heading towards Shenzhen, China. The occasion is the 10th International Conference on Genomics held by BGIGigaScience and China National Genebank. The aim of the conference is to:

… gather leaders, researchers and professionals in ‘omics’ research focusing on human health, animal and plant science, including agriculture and related fields, to share their thoughts and discuss the implications of the latest developments in genomics.

ICG-10

The conference is from October 22-25, 2015. With more than 80 speaker split over 16 sessions I am sure that it will be very interesting. The program can be found here: Sessions and workshops. Note that on Sunday we have a session, S16 AI, Big Data and Health. This session is chaired by Ramneek Gupta from CBS and consist of speakers from CBS, DTU and KU (see below).

If you have not signed up for the conference, I will do my best to Tweet using the hashtag #DTUicg10, and if the internet connection allows it I will also write a few blog posts, so make sure to signup for notifications from my blog as well. You can do that on the right side of this page.

If you are attending the conference, then send me a tweet, Twitter, so we can meet for a beer at the banquet 🙂

Below is the session Chaired by DTU which I can only recommend you to attend!

S16 AI, Big Data and Health (15:45-18:20)

Chair: Ramneek Gupta, Technical University of Denmark, Denmark
Introduction:

Life Sciences today easily fulfils the major tenets of the need for Big Data thinking: Volume of Data, Velocity of data accrual and Variability of data. Indeed, all of these offer opportunities in gathering unprecedented insights into living systems. However, how far up the Hype Curve is current Big Data thinking in Life Sciences? How do we translate insights to value in the life sciences domain ? For example, when big data approaches are mentioned for precision medicine, what kind of approaches will get closer to clinical implementation ? What kind of infrastructural developments are needed in software or hardware or organisationally to accomplish this ? How does artificial intelligence help ? What are some of the basic challenges faced by the hugely increased Volume, Velocity and Variability of data ?

This track aims to present case stories or ideas in this direction.

Speakers:

Ramneek Gupta15:45 – 15:55
Ramneek Gupta
Technical University of Denmark, Denmark
Track Introduction: What is Big Data, and Why is it Relevant to Life Sciences?
Søren Brunak15:55-16:20
Søren Brunak
Technical University of Denmark, Denmark
Topic: Creating Disease Trajectories from Big Biomedical Data Covering Millions of Patients
Laurent Gautier16:20-16:40
Laurent Gautier
Novartis Institute for Biomedical Research, USA
Topic: Handle Big Data in Drug Discovery and Health Care with Software Prototyping
Line Clemmensen16:40-17:00
Line Clemmensen
Technical University of Denmark, Denmark
Topic: Slimming Big Data
Thomas Sicheritz-Ponten17:00-17:20
Thomas Sicheritz-Ponten
Technical University of Denmark, Denmark
Topic: Big Planes, Big Risks and Big Data
Helle Krogh Pedersen17:20-17:40
Helle Krogh Pedersen
Technical University of Denmark, Denmark
Topic: Ranking Factors Involved in Diabetes Resolution after Bariatric Surgery: A Neural Network Approach for Integrating Clinical and Genomic Data
Ole Lund17:40-18:00
Ole Lund
Technical University of Denmark, Denmark
Topic: Genomic Epidemiology
Peter Løngreen18:00-18:20
Peter Løngreen
Technical University of Denmark, Denmark
Topic: Supercomputing and Cloud: Converging Technologies in Life Science

 

Impute.me – Get four times as much information from your genome

Are you one of the people who bought a 23andme kit, and then ever since “wanted more”? Lasse Folkersen, one of my colleagues from CBS, is one of those people, but instead of just thinking about it, he actually did something about, and now he needs help on his recent Kickstarter project to back his imputation server.

impute

Get four times as much information from your genome

Imputation is the name of a technology that is used in almost all major genetic studies today. Simply put it is a well-validated method of ‘guessing’ or imputing large parts of a non-measured genome, based on existing measurements from genotyping microarrays, as well as large reference databases such as the 1000 genomes project. From an input of 0.7M genotyped genetic variants, one typically gets knowledge of more than 4M new genetic variants.

However, the required command-line handling can be daunting to do this on a personal scale. That’s why an interesting new service called www.impute.me offers an easy interface to this technology. Upload your genome-data and get four times as much information back.That’s going from a large data file to an even larger data file.

But what can it then be used for? — the answer is broadly to get up-to-date with modern genetics research. Since most modern genetics studies use this technology, the majority of new findings are not available on basic direct-to-consumer microarrays, such as the ones offered by 23andme. So the second extension of the site is of course also to provide a selection of these novel analysis. A few basic analysis modes have already been implemented to show the added, benefit – such as for example a height-predictor, using the recent GIANT-consortiums findings on genetic variation of human height, as well as the ability to actually get the imputed data for this variation. However, the future idea is to provide many more of these modules – which are easily implementable, once the general imputation framework is in place.

Or – you could of course just enjoy your own personal 4 million extra data points in excel: the choice is yours, but there is no doubt that imputation is the way forward also for personal genomics.

You can see Lasses Impute.me kickstarter project here.

The last wild horses on Earth – Przewalski

Yesterday we got our story about the Przewalski horses published in Cell Current Biology. The article describes the world’s last remaining truly wild horses, which only comprises around 2,100 individuals worldwide. Eleven Przewalski horses were sequenced and compared to the genomes of 28 domesticated horses to provide a more detailed look at the endangered species which is shown to have diverged from Domesticated horses ~45.000 years ago. Finally the genomic impact of ∼110 years of captivity is also monitored, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%.

For a great Photo story check out the Discovery news website.

https://www.genomeweb.com/genetic-research/comparative-genomics-offers-clues-przewalskis-horse-conservation-efforts

http://horsetalk.co.nz/2015/09/25/study-reveals-genetic-ties-between-przewalskis-and-domesticated-horses/#axzz3mk41voq5

http://videnskab.dk/miljo-naturvidenskab/przewalski-heste-har-klaret-100-ars-fangenskab-overraskende-godt

 

 

Copyright: Ludovic Orlando

Copyright: Museum of domesticated animals, “Julius Kühn” at University of Halle-Wittenberg

Copyright: Ludovic Orlando

Copyright: Museum of domesticated animals, “Julius Kühn” at University of Halle-Wittenberg

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

DerSarkissian_media3

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Resumé of the Elixir Conference 27-28 august 2015

Remember to follow the Elixir conference on Twitter

The first annual danish Bioinformatics conference, arranged by the danish Elixir hub, is now ongoing in the old docks in Odense. If you are not already attending the conference, you can still follow it on Twitter by following the hashtag #elixirdk.

The program is very exciting and until now we have had talks in the subject of Systems Biology and Medical Informatics, Proteomics Informatics and RNA Bioinformatics.

Tomorrow the talks will be within the areas of Population Genetics, Medical Genomics and Industrial view on Danish Bioinformatics: Challenges and Opportunities. In the end of the conference there will also be a presentation about Computerome and Cloud computing which I am really looking forward to.

Stephen Hawking – ’Quantum Black Holes’

A few months ago I won a ticket through DTU Alumni to Stephen Hawking‘s Stephen Hawking public lecture – ’Quantum Black Holes’. So now I took and extra vacation day and flew to Stockholm to see his lecture. I know nothing about Quantum Black Holes, but it will be interesting to see Stephen Hawking live giving a lecture 🙂

 

Stephen Hawking

Stephen Hawking

Stephen Hawking, one of the greatest minds of the modern age and a cultural icon admired by millions worldwide, will present the public lecture “Quantum Black Holes” at the Stockholm Waterfront Congress Centre. Carol L. Folt, chancellor of the University of North Carolina at Chapel Hill, will provide opening remarks.

Hawking has dedicated his career to studying the basic laws that govern the universe. With Roger Penrose, he showed that Einstein’s General Theory of Relativity implied space and time would begin with a singularity at the Big Bang and end in a singularity in the center of black holes.

I will stay overnight as his lecture is at 19.00 and then fly home tomorrow morning and go straight to work. There will be a lot of work waiting 🙂 In the meantime I found a hotel at an old castle, Ulfsunda Slott. Very nice and beautiful inside, they have really done an effort to preserve the old style and details. Very cool.

Elixir Denmark – First Danish Bioinformatics Conference in Odense on August 27-28, 2015

I have just signed up for the First Danish Bioinformatics Conference, which will be kicking off in Odense, Denmark on August 27-28, 2015, and I can only urge you to do the same. The conference is organized by ELIXIR Denmark Denmark.

Who should join?
Well, everyone interested in bioinformatics as the conference is relevant to all bioinformaticians who wants to be updated on the latest developments within the fields of Protein-, RNA-, and DNA- Bioinformatics, Medical Genomics, Population Genetics, and Systems Biology.

When is the deadline for registering?
The deadline for joining is 10 August, but if you register before 15 July, the registration fee is a bit lower (DKK 1250 | approx. EUR 167) compared to after 15 July (DKK 1687 | approx. EUR 226). Students (Including PhD students) are free of charge !

If you want to present a poster the deadline is June 28. All the details, including program, can be found here: DKBiC-2015-leaflet4.pdf

So go to the website to register and then I’ll see you there 🙂

 

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