Thomas Kent ID paper published

 

The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes http://www.nature.com/articles/srep41529

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Charlotte from Kenya – Part 2

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After the initial two days of  sampling, I carried on with the rest of my sampling plan for the next ten days.  It mostly went without a hitch.  However, naturally, there were some problems encountered. At first, I ended up taking more samples than I needed. I admit, that’s probably the opposite of a problem. In science, it’s always better to over-sample than to underrepresent whatever species, population or ecosystem you’re trying to investigate. It did mean, however, that we were quickly running out of ethanol which I was using to preserve my samples.  Thankfully, I’d brought a back-up plan. Silica beads are an excellent alternative, and I used them to dry out/preserve the faecal samples I’d taken from giraffe. Most people are familiar with them as the little packets of silica that come with new clothes and shoes, clad with huge warnings saying “DO NOT EAT!”

I collected around 100 samples in total, which I personally think is pretty good going for only 12 days! A week into my trip came the arrival of Dr. Jens Carlsson, the principal investigator for Area 52 and my thesis supervisor. He helped me ensure that I was doing everything correctly, and liaised with John Byrne about the rest of my sampling. The project could not have gone forward without them.

An exciting part of my trip was the memorandum of understanding agreed between UCD and Pwani University, Kenya.  It meant that myself and Dani Shannon (doing her MSc in World Heritage Management and Conservation) were the first students sent over from UCD to Kenya under this memorandum, and it also meant that we had the pleasure of meeting three undergraduate students from Pwani, who came on the trip too. Paul, Robert, and Terry wanted to learn all about eDNA, so helped me with my sampling. They held tubes, passed me pens, had to put up with me stressing about my sampling, but hopefully learned at least one or two things! They were an absolute delight and taught me a lot about Kenyan culture, as well as becoming new friends. Hopefully the students will get over to UCD at some point. Their lecturer, Dr Bernerd Fulanda, was also on camp and was helpful on game drives. He has kindly agreed to help oversee the shipping of my samples back to Ireland.

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An honourable mention also goes to my friends who were volunteering with Friends from Ireland (FFI – the charity which helped to organise my trip). A few of them were asked by me “could you just glove up and help me hold a couple of these tubes?” So cheers to Ann, Dani, and Conall, and also to Sian whose extensive knowledge of the conservancy helped me track down zebra and giraffe. I could probably write a huge list of those involved, but I’d be here all day! So many thanks to all involved, I know that my project couldn’t have gone forward without you. Shout out to Ann Marie for making sure I was alive/feeding me and acting basically as a surrogate parent the whole time I was in Kenya. The trip was overall very successful and I would love to go back as a volunteer for FFI sometime in the very near future.

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So where do I go from here? I am back in rainy Ireland and currently waiting on my samples being shipped from Kenya. I’ve been doing one or two things in the lab -trying more new extraction methods – and will write up my literature review/methodology until the samples arrive. Once they’ve arrived, the eDNA is extracted, ran through a PCR and an agarose gel, sent off for sequencing, and the results are compiled.  The experience has been fantastic and I look forward to getting the results from my samples. We will soon know the extent of DNA degradation in zebra and giraffe poo after it has been left in situ. That’s all from poo patrol for now.

 

Charlotte from Kenya

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I’ve been assigned a particularly special task for my MSc evolutionary biology thesis. Under the supervision of Dr Jens Carlsson, and John Byrne (conservancy director/wild explorer), my project will examine eDNA in Kenya.

Galana conservancy is a wildlife reserve situated on the boarder with Tsavo East national park, in Southern Kenya. It contains masses of African wildlife. For my thesis, I’ll be focusing on Plains Zebra (Equus quagga) and giraffe (Giraffa camelopardalis). I’ll be collecting their scat in order to extract DNA. DNA like this is classified as eDNA (environmental DNA). Environmental DNA has the ability to revolutionise genetics.
So, what is it? An animal sloughs off skin cells, saliva, faeces, mucus, blood etc which are left in the environment and which contain traces of DNA. This is eDNA. The DNA can then be extracted and analysed for use in population genetics, management, species barcoding, and species monitoring. Population genetics measures the genetic diversity, richness, and level of inbreeding in a population. It’s essential for the long-term management of an animal population. Environmental DNA using scat has had little study. Therefore, the aim for my study is to develop a technique using eDNA from giraffe and zebra scat. This data could hopefully be used at a later point for population genetics (there has been little pop gen on zebra and giraffe either).
So here in Galana, I am running a sampling programme for collecting giraffe/zebra scat over the next 10 days. I have already carried out 2 days of sampling, which went well (aside from tracking a herd of giraffe for a good 45 minutes without a hint of poo and then watching them disappear off into the distance).
The trip is quite amazing so far. As well as zebra and giraffe, I’ve seen Impala, oryx, baboon, hippos, a lionness, warthogs, water buffalo, secretary bird, gazelle, elephants, gerenuk, crocodiles, as well as the animals I’ve probably forgotten to mention here.
More updates on poo patrol later.

Ocean Explorers gather at Marine Institute, Oranmore

 

Speakers at the Research Vessel Users Conference included (L-R) Mr Aodhan Fitzgerald, Manager, Research Vessels Operations, Marine Institute; Rosemarie Butler, Research Vessel Operations, Marine Institute; Kevin Sheehan, Advanced Mapping Services, Marine Institute; Dr Florian Le Pape, Dublin Institute for Advanced Studies; Dr Jens Carlsson, UCD and Mekayla Dale, Advanced Mapping Services / Ulster University.The Marine Institute held the second bi-annual research vessel users conference today (28th April) at its headquarters in Oranmore, Galway  to discuss the vast range of capabilities of both the RV Celtic Explorer and RV Celtic Voyager after their 2015 refits, as well as the use of the remotely operated vehicle, ROV Holland 1.

Director Mick Gillooly of Ocean Science and Information Services, Marine Institute, welcomed the attendance of over 70 marine scientists and researchers who will go to sea on the national research vessels this year. He said:  “The demand for survey time on the national research vessels and the quality marine research being carried out across the country shows that Ireland’s scientists are answering the call to better understand our oceans.”

“At a time when we can all see the impacts of climate change, it’s more important than ever to carry out research at sea, including oceanography, fisheries, and environmental monitoring.”

The conference provided information about using high resolution multi-beam mapping, the capabilities of the ROV Holland 1 on surveys as well as key speaker’s experiences using the equipment.

Dr Florian Le Pape of the Dublin Institute for Advanced Studies (DIAS) spoke about the deployment of an Ocean Bottom Seismometer (OBS) network off the Irish shelf as far as the Rockall Trough. Dr Le Pape recently deployed 10 Broad Band OBSs from the RV Celtic Explorer as part of an innovative research program between DIAS, the Helmholtz Centre GFZ Potsdam, Germany and instruments provided by the Alfred Wegener Institute, Germany, which uses the noise from ocean waves to generate seismic images of the earth’s crust.

Over 70 marine scientists attended the Research Vessel Users Conference at the Marine Institute.Deep sea mud volcanoes off the gulf of Cadiz and the high resolution multi-beam mapping of World War 1 shipwrecks in the Irish Sea highlighted the advanced capabilities of the research vessels for deep sea exploration.

The workshop was organised by the Marine Institute’s research vessel operations team also highlighted the value of ship time. Mr Aodhan Fitzgerald, Research Vessel Operations Manager, spoke about the future vessel availability, the ship-time competition for 2017, and how to prepare a strong research survey proposal.

The Marine Institute’s ship-time programme will provide €3 million funding in 2016 supporting 256 research days onboard the national research vessels, RV Celtic Explorer and RV Celtic Voyager. The programme gives researchers access to the national research vessels, as well as the remotely operated submarine ROV Holland I to carry out surveys that further our understanding of the ocean, support policy and development, as well as providing essential training to young researchers and undergraduates.

The programme is part of a busy schedule of research vessel programmes that includes statutory fish stock assessment, environmental monitoring, and seabed mapping surveys in Irish Waters and across the Atlantic basin to Newfoundland.

You can follow the surveys of the research vessels on the blog http://scientistsatsea.blogspot.ie where scientist on-board the national research vessels blog about their research at sea

More information is available at www.marine.ie

ENDS

Presentations

Dr. Florian Le Pape; DIAS “Deployment of an Ocean Bottom Seismometer (OBS) Network offshore Donegal”

Mekayla Dale; AMS intern/UU student “High resolution multibeam mapping experience: World War 1 shipwrecks in the Irish Sea”

Kevin Sheehan; MI Celtic Explorer’s deepwater multibeam: applications to date”

Robin Raine; NUIG “Chasing Dinophysis”

Hans Gerritsen; MI “New FEAS surveys: purpose & practice”

Paddy Kenny; POMS “Life at sea: The crew’s perspective”

Patrick O’Driscoll; POMS “ROV Holland 1 pilot advice: applications & planning”

Gordon Furey; POMS “Getting the most from the SCS”

Dr. Jens Carlsson; UCD “Deep-links, mud volcanoes in the Gulf of Cadiz”

Pauhla McGrane; GMIT “SMART: Training the next Generation of Ocean Scientists”

Barry Kavanagh; POMS “Safe marine scientific operations”

News Type:

Launch of UCD Science Showcase

Launch of UCD Science Showcase Vol 3 2Dec2015 (2)

Launch of UCD Science Showcase Volume 3, December 2nd 2015 

UCD O’Brien Centre for Science East

UCD Science was delighted to celebrate the launch of its latest Showcase with colleagues and friends. Professor Mark Rogers, UCD Registrar and Deputy President, did the honours and presented each academic featured with first copies of this publication.

 “I’m very pleased that this 3rd Showcase continues to highlight the diversity and depth of talent in the College of Science. It is also a wonderful means of letting the public understand the quality and impact of the College’s research and teaching.” says Prof Joe Cathy, Principal of the UCD College of Science.
An online copy of the showcase can be viewed here.

Memorandums of Understanding signed between UCD and Pwani University, Kenya

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December 10th 2015
Venue: Kenyan Embassy Dublin.

It is with great pleasure that we would like to announce that University College Dublin and Pwani University, Kenya have agreed upon Memorandums of Understanding to facilitate academic and student exchanges between our two countries.

The agreements follow an intense period of negotiation and consultation between University College Dublin and Pwani University in Kenya and were facilitated throughout by the NGOs Friends From Ireland, The Galana Wildlife Conservancy Kenya, the Watamu Marine Association Kenya and the Agricultural Development Corporation of Kenya. This initiative has the support of the Irish Ambassador to Kenya Dr. Vincent O Neill, the Cabinet Secretary for the Environment in Kenya, Professor Judi Wakhungu, and the M.D. of the Agricultural Development Corporation Kenya, Dr. Andrew Tuimur and has been kindly facilitated over recent months by the Kenyan Ambassador to Ireland Mr. Richard Opembe.

In addition to the announcement of the MOUs we are also announcing the following:

1. The creation of a Scientific Field Research Station at the Galana Wildlife Conservancy in Kenya, designed to promote knowledge and open up this critically endangered environment and its endangered wildlife to Kenyan and International students of the Sciences.

2. The commencement, by Friends From Ireland of the Galana Secondary School building project complex adjacent to the Primary and Infant School complexes constructed by FFI over the last three years.

3. The intention to support an application to have the Galana Wildlife Conservancy considered for inclusion as a World Heritage Site.
This is a new approach to community-conservation-education challenges in developing countries and has brought together voluntary National and International community and conservation groups, business groups, state agencies and those in relevant political offices, to ensure that promises are kept and goals are achieved.

This new model of multi-agency partnership, bringing volunteering and education together to tackle community and conservation challenges in Kenya will herald the beginning of a significant scientific study of this crucial eco-system and its endangered species, the development of the community which shares that environment and the development of educational facilities from infancy to third level education. It is a model that works through inclusion, the realistic consideration of community, cultural and conservation concerns, the management of realistic goals based on what can be achieved by listening to the issues on the ground and planning processes that start with real dialogue.

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I would like to thank The Kenyan Ambassador H.E. Mr. Richard Opembe for inviting us to make the announcement from the Embassy. I would also like to thank the representatives of University College Dublin, Friends From Ireland and the Minister, Mr. Damien English for supporting our endeavours. Indeed we wish him well on his visit to Kenya. For more information following this release please contact me at johnab@eircom.net or through the following websites

Information on upcoming community and conservation projects for 2016 will follow through these websites and related Facebook Pages

www.friendsfromireland.ie
www.galanaconservancy.com

Portraiture at sea

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As the expedition is coming to an end and the science part is over, on this stormy day heading back to Galway, I would like to present what has been secretly going on throughout this cruise, namely, portraiture at sea. I am the artist on board, a recent graduate from the Angel Academy of art, in Florence (Italy), a classical painting school, and I was here to do an experiment: portrait the crew and scientists on board. Portraiture has a long historical tradition, it has been done for centuries and it still holds incredible charm for me today. I am fascinated with faces and expressions and here I had great inspiration, also because I know the people in person, talk and interact with them, which makes a great difference. Trying to capture them in a drawing has been challenging for me, as my work is only at its start, and also a great honour because I think the people who represent the soul of this ship should be celebrated; and a portrait is the best way because it is not a photo, it has much more life and depth than a photo, and it connects people.

Above is a group photo during the “exhibition” that was held last night, (the venue was in the sitting room!) and it includes few of the subjects of the portraits. A big thanks to everyone and a special thanks to Raissa for her great support!

Blog by Alice Antoniacomi