My personal and professional adventure into Science

The pursuit of happiness – a Theridion grallator genome crowdfunding project

The pursuit of happiness: The basis of color in the happy face spider (Theridion grallator)

My friend and collaborator Stefan Prost is trying something new, to me. Genome Crowdfunding… I can only encourage you to pitch in and donate to the project, every $$ counts !! 🙂
Please go to the crowdfunding website to read more and to donate!

About the project

The Hawaiian happy face spider, T. grallator, is known for its striking color polymorphisms (variations within species), which include variable configurations of red, black, and white superimposed on a yellow background. We will use genomic sequencing to identify the genes responsible for color and pattern variation. This is interesting not only because the polymorphism is maintained across several different islands, but because other arthropods display similar patterns in the Hawaiian forests.

What is the context of this research?

The happy-face spider is a classic example of polymorphism (showing a variety of patterns) in nature, but there have been few studies to examine this at the gene level in arthropods. In the happy face spider, we observe the repeated evolution of color and pattern, also known as convergent evolution. From previous work, we know that the same color and patterns have evolved on different islands, but through different genetic mechanisms. This demonstrates that nature has come up with the same solution in different ways. Additionally, we know that two-thirds of a happy face population are yellow individuals and one-third is patterned. Researchers have hypothesized that this ratio is driven by a predator search image, but we can learn more by looking at the genetic code!

What is the significance of this project?

Understanding how diversity arises in natural systems is a pressing question, but until recently we have lacked the genomic and genetic resources to understand underlying evolutionary patterns. Using a genetic approach in happy-face will provide insight into genes which underlie color variation in arthropods and how morphological changes reflect ecological adaptation, which can lead to diversification. The past work on happy face makes it an ideal system, because we know how genes are inherited on each island. It is important not only to conserve our present species, but to understand how the diversity we see today was produced. In systems such as happy face, we have a unique chance to follow along with evolution, which can provide answers into ensuring its future survival.

What are the goals of the project?

The goal of this project is to identify gene loci or genomic regions associated with color and pattern variation in the happy face spider. We will use the high-quality genome obtained through this work and previously collected data to identify regions associated with color variation. From this, we will be able to understand the underlying genetic mechanisms which produce different colors and patterns. Additionally, we can gain insight into how selective pressures contribute to maintaining the amazing variety of morphs in the happy face. We hope to use this iconic species to communicate how important genomics can be to understanding diversity and hope to provide a basis for other researchers to understand how color and morphology may function in other arthropod systems.

Please go to the crowdfunding website to read more and to donate!

DTU Bioinformatics Seminar – Monday 15 August 10.00 – Deciphering biodiversity in Amazonian highland fields

Dear all,

I have the pleasure of inviting you all to a research seminar on Monday 15 August at 10.00 in room 62, building 208.

My Brazilian collaborator, and very good friend, Guilherme Oliveira from Vale Institute of Technology, Belém, Brazil, will give a presentation of some of the cool science they do in the Amazon. Research that we are working closely together with him to integrate in the new DTU Bioinformatics department.

Guilherme will be in Denmark for the full week (15-21 August), and if you are interested in scheduling a meeting with him please let me know.

Deciphering biodiversity in Amazonian highland fields

Guilherme Oliveira, Vale Institute of Technology, Belém, Brazil

Guilherme Corrêa de OliveiraThe Amazon is composed mostly of a vast flood plain. However, there are some unique habitats, such as the high altitude Canga fields. The Amazonian Canga’s are high iron content ancient weathered plateaus. They contain specialized flora and are surrounded by ferruginous caves that also harbor troglohilic animal species. Due to the elevated iron content, these regions are also prime iron ore sources. In the province of Carajás a national forest was established encompassing most of the Canga regions. Therefore, enabling mining operations coupled to conservation is of primary importance. Yet, the inhabitants of the Cangas are still largely unknown. Our work unites conventional taxonomy and next generation genomic approaches to describe the region’s fauna and flora. A first volume of the Canga flora containing over 500 species was produced and combined with DNA barcoding efforts provides a unique view of the environment. Plant species that need further investigation and resolution undergo chloroplast or full nuclear genome sequencing. A parallel approach is being carried out for the cave invertebrate fauna. In addition, metagenome signatures of the entire environment provide additional clues to the description of the environment.

Google Scholar

ITV Vale

Link to Facebook Event

Registration is not necessary – please spread the word.

Looking forward to seeing you all !

Invitation to the 2nd Annual Danish Bioinformatics Conference, Aug 25-26, 2016

ELIXIR Denmark is sponsoring and organising the 2nd Annual Danish Bioinformatics Conference, to be held on August 25-26, 2016, in Odense, Denmark.

The two-day meeting provides attendees with opportunities to share and discuss their latest findings, and learn about the newest national and international developments within computational proteomics, machine learning in bioinformatics, network biology in disease, non-coding RNA bioinformatics, population genetics and evolution, and transcriptomics and transcriptional regulation.

The following speakers already confirmed their participation:

AnaĂŻs Baudot, CNRS, France
Anders Krogh, University of Copenhagen (UCPH), Denmark (DK)
Anton Petrov,  EMBL-EBI, United Kingdom
Bruce Shapiro, NIH/NCI, USA
Robert Young, University of Edinburgh, United Kingdom
JĂĽrgen Cox, Max Planck Society, Germany
Lennart Martens, University of Gent, Belgium
Martin Simonsen, QIAGEN, DK
Peter Løngreen, Technical University of Denmark (DTU), DK
Rute Fonseca,  UCPH, DK
Søren Brunak, DTU, UCPH, and RegionH, DK
Jon Ison, DTU, DK
Mikkel H. Schierup, Aarhus University, DK

Relevant information and key deadlines:

  • Details regarding registration and accommodation—and conference programme, still not final—may be accessed via the ELIXIR Denmark website (http://www.elixir-denmark.org/)
  • Students (incl. PhD studens), members of the programme comittee, invited key note speakers and ELIXIR Steering Group members may register free of charge, while for non-students the registration fee is 1,200.00 DKK (excl. VAT). The fee covers catering, dinner and social activities;
  • Please note that the registration fee is non-refundable;
  • Registration deadline: August 10, 2016;
  • You are invited to submit an abstract for the poster sessions. All abstract submissions must be received on or before August 10, 2016;
  • However, among the abstracts received on or before May 1, 2016, some will be selected for 15-minutes oral presentations;
  • The winner of the best poster will be announced during the meeting closure;
  • Poster board size: 95 x 240 cm;
  • To ensure that you have a hotel near the event, please register and book your accommodation via the registration site by 1 May 2016, as there is a limited number of pre-booked hotels: Hotel Ansgar, City Hotel Odense, Radisson Blue HC and Hotel Windsor.

For any questions about the event, please do not hesitate to contact:

Myhanh Nguyen (myng@bio.dtu.dk).

 

Kind regards,

ELIXIR Denmark Steering Group:

Anders Krogh, Professor, UCPH, DK
Bernt Guldbrandtsen, Aarhus University (AU), DK
Jan Gorodkin, Professor, UCPH, DK
Mikkel Heide Schierup, Professor, AU, DK
Ole Nørregaard Jensen, Professor, University of Southern Denmark (SDU), DK
Søren Brunak, Professor, Head of ELIXIR Denmark, DTU, UCPH, and RegionH, DK

Conference Programme Committee:
Bent Petersen, Associate professor, DTU, DK
Ida Moltke, Assistant professor, UCPH, DK
Kasper Munch Terkelsen, Assistant professor, AU, DK
Kirstine Belling, Associate professor, UCPH, DK
Robin Andersson, Assistant professor, UCPH, DK
Stefan Seemann, Assistant professor, UCPH, DK
Søren Besenbacher, Postdoc, AU, DK
Veit Schwämmle, Assistant professor, SDU, DK
Vivi Gregersen, Postdoc, AU, DK

 

Sponsored by:

The Avian Phylogenomics project I was involved in is nominated as Best Research Result 2015

Avian Phylogenomics Project

I just received an email today informing me that the bird project I was involved in, is nominated as Best Research Result 2015 in Denmark. This is the second time one of the project I am involved in has been nominated, the first project was the 700.000A flock of genomesyears old horse.

This year we want to win !

Fortunately there is a way to reach the goal, I just need you all to vote on the project. It will be much appreciated !
The voting process is easy, even though the website is in danish.

 

The project itself was huge, a Science paper with 40 companion papers, you can see them all here.

 

5 good reasons to take your MSc degree in China

For the last two years I have been member of a teaching team that went to Beijing, China to teach danish and Chinese students. From my side they were taught in Introduction to Bioinformatics and Next Generation Sequencing.

Now the school is looking for more brave students who wants to pull up their plugs, jump into something new and go to Beijing for their master. If you are interested please take a look at the post below and then I hope to see you in China 🙂

5 good reasons to take your MSc degree in China

  • Get a head start on your future career
  • Study at a top University in China
  • Researched based teaching
  • Professional service and guidance
  • An unique intercultural experience

Dear student,

In this mail you will find some information about SDC, the different programmes and also studying and living in China. If you have any further questions, please do not hesitate to contact us – there are only good questions! Contact information is below.

SDC (Sino-Danish Center for Education and Research) is a partnership between all eight Danish Universities and University of Chinese Academy of Science (UCAS) in Beijing. The overall aim of SDC is to promote and strengthen cooperation between Danish and Chinese learning environments, and increase the mobility of students and scholars between the two countries. SDC offers seven unique MSc programs in Beijing. All programs are 120 ECTS and when you finish you will obtain a double MSc degree – i.e. a MSc degree from the Danish University and an MSc degree from the Chinese University. All programmes qualify for the Danish state educational support (SU). To read more about the programmes Master Programmes.

All courses are taught in English by Danish and Chinese teachers/researchers. Your classmates will also be a mixture of Danish and Chinese students and in some cases also other nationalities. Professional help and service – SDC helps you both before and during your stay in Beijing with all practical matters. Before departure to Beijing we host an introduction seminar in Denmark and upon arrival in China you will have 2 whole introduction weeks before classes start. First you will have one week just with the other candidates from Denmark and then following that, a week also with all the Chinese students. We also have an office in Beijing with both Danish and Chinese staff that can help and guide you in terms of both academic and practical matters.

Living in Beijing – Beijing offers adventures of all kinds – so pack your bags and get an experience of a lifetime! Although prices in China are rising, it is still very cheap in relation to most countries in the EU. You can easily live and eat for your SU. SDC offers accommodation on campus at a very favorable price, but it is also possible to find a flat if you want. For more information on living in Beijing Living in Beijing.

If you have any questions (academic, practical or other) please send an e-mail to contact@sinodansihcenter.dk and we will make sure you get a quick response.

 

 

Computerome videos

Many people have asked me for a post with Computerome videos, and as we just had two more videos produced I think this is the time for a post with them all. I hope you will enjoy 🙂

Computerome – Supercomputer generating more knowledge at a lower cost in a high security data environment

Usercase: Researchers from Statens Serum Institut (SSI) explain that they chose to use Computerome for their research projects such as IPSYCH because of the extremely high security levels in data governance, strong authentication processes and very efficient and professional service delivered by the staff at Computerome.
Part of the advantage of using Computerome is the large volumes of big data already available in the Computerome secure cloud. The researchers use this advantage to mine for potentially interesting diseases with all generated data and reference data. Using the power of Computerome they augment their research by generating more knowledge at a lower cost.
The researchers at SSI plan to expand collaborations with Computerome not only for business, but also for research. SSI’s collaborators at Harvard University, USA also have the access to Computerome and claim the infrastructure at Computerome matches or perhaps tops their own platform.

 

Copenhagen Fur

Computerome – A game changer in research – DeiC Pilot Project User case: Copenhagen Fur.
Industrial PhD student Emma Hagberg at Copenhagen Fur has had her project accepted as a National e-Science Pilot Project on Computerome. Moving the data analysis to Computerome has been a game changer. It has freed up both computational power and time allowing the researcher to do additional research while Computerome works thereby advancing the amount of research in the project. The National eScience Pilot Projects are funded by DeiC. The projects use the einfrastructure build by DeiC and the Danish universities to increase the use of escience in Denmark. The projects are open to all fields that can benefit from the e-science infrastructure.

 

Computerome – A look back at 2014

Computerome – year 1 operations

 

Presentation of the DTU Supercomputer Computerome

Presentation of the DTU Supercomputer Computerome

 

Computerome – DeiC Seminar

The talk I gave in danish at the DeiC Conference 2015: Deic Konference 2015

 

Computerome 2015

Now using MailChimp as the mail application

This is the first time I am writing a post using the MailChimp app, so I apologize if it does not look like it is supposed to. I have created the email campaign as an RSS feed, so to be honest I have no idea how it will look like.

I apologize for the somewhat boring post…

 

 

 

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

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