CoCoHaCa Cruise Blog – Latest update


Monday’s 4am shift got off on the right note as myself and Siobhan decided to upgrade our midnight snack to midnight steak (sandwich) thanks to the delectable leftovers from Sundays’ dinner.

It has been really interesting being on the Granuaile, as an Irish Lights vessel she carries on the legacy of all the beautiful lighthouses around the Irish coast. Today Sarah from the crew let me have a look at the Portolan, a handwritten, draw and photographed book put together showing all the lighthouses around Ireland and all the knowledge about them and how to navigate to them. And I couldn’t make this up if I tried, it was compiled by Captain Hook (Captain Colin Myles-Hook).

With slightly shorter ROV survey lines we got a good few covered today. Lots of coral and Bogna and I were really excited to see a meter long shark (possibly bigger), an enormous monkfish and some really amazing sponges.


The morning dawned with a beautiful sunrise. Today was a massive success for the cruise, after finishing off the last of our video survey lives (and witnessing and absolutely spectacular sunset) we moved on to rock drilling.

With potential sites for the drilling identified in previous surveys of the area and also a few from our own video survey lines, the ROV team had a map and plan and a new drill to test. Yesterday was the first time a rock drill has been used on the Holland 1 ROV and the first time any ROV has drilled in Irish waters for science. This drill created for the Holland 1 is also unique as it allows us to drill rock exposures (vertical rock faces) instead of drilling down through the whole bank with a huge drill rig. It’s compact, powerful and gets right to the base of things. There have been some granites drilled on top of the bank a few years ago, but the two cores recovered on this survey are the first ever drilled from the base of the bank.

With cores taken from two different sites, our geology team are eager to get the samples back to Cork and begin deducing what kind of rock they’ve got their hands on. So far there’s been a lot of speculation (perhaps even a few bets) but no one is 100%.

We had hoped for one more chance at coring but the weather had other ideas and so as the winds reached gusts of up to 50km (gale force 9) and 3.5m swell we packed up our things and set course for home.



As the gale descended on us we quite literally battened down the hatches, with all our belongings in our cabins making a solid attempt at escaping right out the door. Last night there was great camaraderie in the dining room/living area as we attempted to rustle up snacks while not getting thrown across the room. The opposite to being scared, the mood onboard was positively jolly. Sleep was funny with all the motion, but we got some great videos of the waves at around 5am this morning.  After a bit of sleep, we’ve spent our rolling transit day (it will take a full 24h to be back in site of land) backing up our data, checking through our videos and just generally getting ready for the end of the cruise.

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CoCoHaCa Cruise Blog – Update


Finn Ni Fhaolain

With all our coring completed successfully earlier in the week it was high def video time. With 6 scientists on board we work in shifts of two and hang out in the ROV Shack with the ROV guys (singing “ROV Shack” to the tune of “Love Shack”), logging CTDs, taking video, snapping stills and logging the different species, substrates and sediments that we see. Since we’re generating so many hours of video footage it’s really important to note different interesting features and their time stamp and lat and long locations so it’s easier in the future for other scientists to work with. Last night we had a brief pause in work as a gale force 8 wind caught us in a 3 meter swell. But the bridge crew kindly angled the ship away from the worst of it.

The down time was spent drinking tea, eating chocolate and swapping sea going stories and hearing about the worst weather everyone has been out in. I’m currently writing, sitting on the floor of the conference room as we brought all the electronics down off the table in case they went flying when the ship would roll. There was a lot of laughing, so no time for cabin fever to set in. Being far too easily amused I thought it was great to see water flowing sideways out of the taps when the ship would roll. An absolute highlight of the trip so far was getting to see a pod of pilot whales off the stern just before sunset last night (we had been watching waves splash across the deck). The biologists among us we delighted to see our “first bit of blubber” on the trip.


Today we were mostly seeing non-reef areas on our video log but saw some interesting species like rabbit fish and some sharks. While it isn’t quite as exciting to watch areas of sand, it is important to record which areas have life coral, dead coral and just sand. By knowing where the coral is, isn’t and where it used to be (eroded coral framework with no live coral) it can help to build up an understanding of what environmental factors – e.g. slope, direction, current flow, sedimentation level, temperature etc – affect the “start up” and “shut down” of cold water coral mounds.


Absolutely fantastic day today, a real Sunday buzz going on. Very interesting coral mounds with massive cliff faces covered in live corals hosting a plethora of other species – octopuses, glass sponges, sharks, rabbit fish, sea pens, crinoids, tube worms.

After lunch we saw perhaps 4 pods and nearly 50 pilot whales including calves! Even the toughest among us were reduced to hollering “look at the baby whales” in delight on seeing the tiny tail flukes and little heads spyhopping. They stayed with the ship for quite some time and everyone came out for a gander.

To top off a great day Decco & Billy whipped up some amazing steaks (probably one of the best I’ve ever had) with all the trimmings and then the secret stash of chocolate was cracked out for the evening shift in the ROV shack. Needless to say moral is high!

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CoCoHaCa Cruise Blog Day 2


Finn Ni Fhaolain

After waking up for the 4am shift it was so exciting to see the first video recordings from the ROV. There was successful coring through the night and everyone was pleased to see that the brand new vibrocorer on the ROV worked well. The scientists have been trying to core this site for 3 years so this is new vibrocorer is a great success. The video allowed use to see all of the coring efforts as well as the coral habitats – some coral rubble, reef and cliff face. It was really exciting to see the different species on the reef – several different species of corals, crabs, urchins and even a deep sea shark!

Now its on to more coring, more video and a bit of CTD. On a foodie note we were all raving today about the amazing Thai green curry that the guys whipped up in the kitchen. As a dessert fiend I also went a bit mad for the rice pudding. Stomachs are full and spirits are high going into the evening shift.

Across the evening we cored the summits of two different mounds with successful cores from both areas. There was also a great array of wildlife with the different watches observing corals, urchins, crabs, tube worms, cushion starfish, lantern fish, ling, eels (potentially juvenile congers) and sharks. With the coring completed we are sailing off into the sunrise to our next location to start our video transects in earnest.

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CoCoHaCa Cruise Blog


Finn Ni Fhaolain

I was so excited to get the call from Andy (Wheeler) earlier in the year to join him and a great group of scientists from around the country for a research cruise to the Porcupine Bank Canyon Mounds. The mounds are about 300km due west of Dingle on the edge of the continental shelf. This area holds personal significant as it was my research area many moons ago for my thesis project in UCC with Andy as my supervisor.

For myself and most of the scientific crew this was our first time on the vessel the ILV Granuaile so day one was getting familiarised with where everything is and getting our safety tour. Add pics of survival suits. The Granuaile is owned by Irish Lights so her usual work is servicing and supplying the lighthouses around the country. She also looks after the weather buoys around the coast. I’m a big fan! As the charts generated from these buoys data are what surfers use for the surf forecast.

This cruise is all about getting high def imaging of the cold water coral mound habitats, with a bit of coring and some CTD profiling for good measure. The Holland 1 ROV has an amazing array of features, but for this mission we’re interested in its high definition video camera and the stills camera which will be used to recorded predefined lined running up the Porcupine Bank Canyon from the deep sea to the plateau at the top. This allows us to observe the change of habitat with depth (and other conditions) between, mud, rocky outcrops, coral rubble, coral mounds and areas of live coral reef. While we get most excited seeing coral and fish, its important to get a look at all the habitats so we can better understand the mechanisms of the entire canyon system. The CTD (conductivity, temperature and depth sensor) will be used to profile the water column of the canyon and allow us to observe the different water masses.

Onboard we have the crew of the Granuaile who’ve been so welcoming and I’ve already found a fellow surfer, next the ROV (remotely operated vehicle) team from the Marine Institute who look after the Holland 1 ROV and finally there is the scientists a mash up of UCC, GMIT and me!

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Plant Science London Field Trip – Part 3

BEES Plant Scientists at Tozer Seeds – part of the PS3020 London Field trip (Image: Tozer Seeds)

by Michael Rochards (APB3)

One of the world’s largest agrochemical, seed, and biotechnological companies, Syngenta, is a diverse active site with cross functionality. After tea and biscuits, we were introduced to the company by the biologist Jim Morton, who after a brief presentation, acted as our affable host around the greenhouses and the laboratories. The greenhouse tour took in work with Double Haploid breeding programmes between maize and winter wheat which allow for a plant to achieve homozygosity. Taking 7-8 years to achieve, every ear of corn checked every day for signs of pollination. Other greenhouses showed spraying systems (including a rain-station to replicate constant downpour, which would assess the efficiency of products in the field). Low tech met high tech as plants men were seen with plastic buckets, plants being sprayed by test solutions and the results assessed visually; biologists and chemists meet regularly to discuss results.

Students at Syngenta (Image: Eoin Lettice)

Then into the smarter laboratories; ‘mother’ plates holding novel chemical compounds and plants (here Arabidopsis) were allowed to grow (or rather not grow!) and then analysed with a high throughout phenotyping platform. 3-5,000 possible configurations being assessed which may eventually lead to one product; their ‘library’ a repository of tens of thousands of chemical signatures. An £8 million pound robotic system, probably the world’s most expensive cocktail shaker, takes samples, photographs (and lots of other things besides) and allows for assessments to be made of developmental solutions.

Demonstration of double haploid breeding at Syngenta (Image: Eoin Lettice)

After kindly providing lunch of sandwiches, crisps, and chocolate, an ecotoxicology presentation by Heidi Cunningham showed Syngenta’s work with environmental assessment models, which fitted well with our AE3010 module; altogether a welcoming and interesting experience, showing insight into Syngenta’s work.


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Plant Science London Field Course – Part 2

At the Millennium Seed Bank vault (image: Eoin Lettice)

Day Two by Bianca Govi (APB3)

Today we took a trip to Sussex to complete our tour of Kew by visiting Wakehurst Place. The site is unique in that it houses in-situ and ex-situ conservation efforts, and boasts the highest living plant biodiversity in the world. This latter claim concerns the Millennium Seed Bank, an active seed library of non-crop species, providing an insurance policy against extinction as well as education and research opportunities. The facility, which was inaugurated in 2000 and currently holds 82000 separate collections, has the goal of storing 25% of the world’s floral biodiversity by 2020.

the goal of storing 25% of the world’s floral biodiversity by 2020

Although the seeds preserved in the vault are not directly economic crops, human benefit is one of the strategic priority of the project. A significant example of how this can be achieved is through the storage and study of the genetic diversity of crops’ wild relatives, for future introgression breeding. At the moment, research in this area is focusing on wild rice species Oryza nivara, O. officinalis and O. longistaminata, and wild bananas Musa accuminata and M. balbisiana. Other target priorities in the selection of the new entries include criteria of endangerment and endemism.

UK Seed Hub entrance (image: Bianca Govi)

Seed material -ideally with accompanying herbarium samples- arrives to Kew from 170 partner institutions from 80 different countries, under the convention of Biological Diversity. Once in Wakehurst, seed parcels are stored in a dry room (at 15% relative humidity and 15°C) under a constant, controlled airflow for up to 6 months, to decrease moisture content. We were shown how samples are then taken to a cleaning laboratory, where material is cleaned and sorted manually, through sieves, aspirators and scanned in a medical X-ray machine. For this last step, a subset of 50 seeds is analysed, and the internal integrity of the contents used to estimate germination potential for the whole collection. After the cleaning, seeds are taken into the vault basement where they undergo further drying, are packed, and finally stored in one of the 4 cold rooms (-20°C). Although there is a high degree of variability between species, it had been estimated that the average seed’s lifespan can be increased by 50% for every 1% reduction in ambient relative moisture and 5°C drop in temperature. In general, conditions of low temperature and low humidity slow down seed aging by dampening the release and activity of reactive oxygen species within the tissues. This is unfortunately not true for “recalcitrant” seeds, which do not tolerate drying and storage.

Millennium Seed Bank glasshouse (image: Eoin Lettice)

Commonly, they are large-sized seeds (acorns, chestnuts, giant coconuts), but also some very small ones such as orchid micro-seeds can suffer from substantial drops in germination rates after desiccation. In contrast, some seeds have been observed to maintain their viability even under non-optimal condition. In the succulents’ glasshouse we had the chance to see a 10-year old potted Leucospermum, an African flowering shrub, with an adventurous life history. It was brought to Kew as a seed from the National Archives, where it had been sitting inside the leather-bound notebook of a Dutch merchant who had collected it around the Cape of Good Hope some 200 years previous.

After the tour of the building, we stepped outside, past the parterres representing natural habitats in a gradient from shore shingles, to grasslands, to heath, to bog land, and into the UK Native Seed Hub propagation field. This initiative initiative was launched to address the issue of habitat fragmentation and impoverishment and its goal is to provide the starting stock of seed material for native habitat restoration projects. Special attention is given to rare and difficult to propagate species, which are not widely available from commercial providers. At the moment the field is being used to propagate calcareous soil wildflowers, a particularly niche and threatened community. The area, which is open to the public during the summer, is decorated with willow and wire sculptures.

Millennium Seed Bank (image: Bianca Govi)

Finally we had a brief tour of the Wakehurst Gardens: developed by Gerald Loder, were donated by the following owner to the National Trust and are now managed by Kew. The plant collection features rare exotic entries such as the extinct-in-the-wild Franklin tree and the endangered Wollemia pine, which seems to do particularly well on the local soil. Native woodland protected areas are also part of the estate, making Wakehurst the first botanic garden to also incorporate in-situ conservation operations.

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Plant Science London Field Course

Palm House at Kew (Image: Eoin Lettice)

Day One by Calum Sweeney (APB3)

The day started with a tour of the Royal Botanical Gardens at Kew (RBG Kew)and their herbarium. The herbarium contains 7 million specimens of approximately 140,000 plant species. Jurriaan de Vos guided us through the various labyrinth like system of purpose built herbaria. Jurriaan had recently been on a research and sample collecting mission to Peru where he and his colleagues identified two new species as well as recorded first occurrences of plants in Peru.

The first room we entered was purpose built as a herbarium in the 1800s, now it is considered outdated as the temperature is variable and the cupboard doors can let insect pests in. The building has landmark status and so refurbishment cannot take place. The next herbarium had a lower ceiling as it was built after the invention of electric lighting and so tall windows were not required for natural light. The next room we were shown was the ‘post’ room where samples were prepared for sending to other institutions or were treated by freezing (72hr at -40oC) when returned from them. There has been a decline in material being sent out of Kew over recent decades due to the scanning of samples and genetic identification of plants. The last room was a contemporary herbarium, built to ideal specifications with a constant temperature of 15oC and a monitored relative humidity. This room was used to store plant samples such as from the legume family which are preferentially targeted by pests.

Students in the herbarium at Kew (Image: Eoin Lettice)

The fungarium boasts 1.3 million fungal specimens accounting for 60% of all known fungal diversity. The store is separated into UK fungi and the rest of the world. Fungal specimens from the UK are stored separately as they their care takes priority in the case of disasters such as fire. In addition amateur UK mycologists spend a lot of time with the UK specimens. The taxonomy of the fungarium is however 20 years out of date owing to recent advanced in genetic classification.

Fungi can happily reproduce asexually resulting in the same species of fungi being identified as two separate species, this confusion has been recently readjusted thanks to genetic analysis.  There are the equivalent of 27’000 “sexes” with regards to fungi, compatibility is assessed at contact between mychorrhizae which is followed by either successful reproduction or “war”. Fungi are in fact closer to animals than plants with their cell walls comprising of chitin rather than cellulose. Investigation into commercial fungal products has yielded fungal leather substitute and a milk made by a fungus which has the gene for milk protein inserted into it.

The fungarium at Kew (Image: Eoin Lettice)

Melanie Jayne Howes presented a lecture on the use of plant natural products and plant chemicals in the treatment of Alzheimer’s. Alzheimer’s is a degenerative neurological disease caused by a deficiency in the production of acetylcholine. One option of treatment would be to find a similar compound to acetylcholine in plant products and apply these to medicine. This was done and the chemical Anecoline was effective at treatment but caused severe side effects such as convulsion and extreme nausea. Alternatively Physostigma venesquosum (Calabar bean) was used to stop the breakdown of acetylcholine as it contains toxic alkaloids which produce this effect. The problem was P. venesquosum also caused severe adverse effects in patients. The solution was found in Narcissus sp. and Galanthus sp. Which produce a drug now known as Galantamine which shows high levels of efficacy in the treatment of Alzheimer’s. Two of the four drugs currently on the market for the treatment of Alzheimer’s are plant derived.  Plants also noted for their neurologically strengthening effects include Ginko biloba (250 year old specimen in Kew), rosemary, lemon balm, Lemon verbena and sage as well as Withania somnifera.

Bootstrap DNA by Charles Jencks at Kew (Image: Eoin Lettice)

Orchid conservation is conducted at Kew with a large focus on four species of orchid. One of these orchids is Cypripedium calceolus which can only be germinated if done so in conjunction with the particular fungal species. The seed coat is removed and fungal hyphae allowed to colonise the seed resulting in high and unprecedented rates of orchid germination in vitro. Orchid seeds are very small and germination is easier when they are fresh, chemical and physical germination inhibitors thwart germination attempts in mature seed.

At the end of the day I enjoyed resting my legs under the cherry blossom in the Japanese garden.  I also enjoyed the tropical humidity in the Palm house which contained ten metre high banana plants, shrubs with blue cheese smelling green flowers as well as the oldest potted plant in the world a cycad at 250 year old!

Palm House Interior (Image: Eoin Lettice)

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MSc Marine Biology Fieldcourse to Millport, Cumbrae, West of Scotland

by Mary Kate Bolger

As part of our course we went on a 5 day fieldtrip to Millport in the Isle of Cumbrae, Scotland.  We were apprehensive before we set out as warnings about storm Doris increased.  Sure enough when we landed in Edinburgh it was freezing.  As we continued on, the amount of snow on the ground increased, but luckily it had mostly subsided by the time we got to the seaside town of Largs.

After a short ferry ride to the Isle of Cumbrae, we settled into the Marine Station, and not long after that, we set out on our first mission – to count barnacles on the Butterlump shore.  For this task we broke up into 3 teams.  In each team, different people counted the different barnacle species.  One person counted Semibalanus balanoides, another counted Chthamalus montagui, and another counted, the rather exotic, Austrominius modestus.  We also counted the dog whelks.  After that we decided to have an early night… and then ten minutes later decided that a few “diet cokes” were needed down in the pub.

The next morning, we braved the not so rough seas.  It was rather cold, but after considerable warning about the weather prior to the trip, we were prepared.  We were all highly excited to see the countless worm species in our grab samples… but that all went out the window as soon as a Common Dolphin appeared.  According to the crew aboard the RV Actinia the dolphin was affectionately known as Kylie.  We were briefly distracted but then got down to business.  We took 18 grab samples in total. For each sample, we took a granulometry sample and then sieved all the sediment away so that we could identify the biota.  Finally, we did a beam trawl.  We then headed back to the lab and spent the afternoon and evening identifying different species.

On Saturday, we spent the morning identifying the rest of the species from the grab samples.  In the afternoon, a group headed out to continue with the barnacle counting, while the other group stayed in the lab to analyse the data from the boat trip.  For the next few days we alternated between report writing, data analysis, barnacle counting, and barnacle dissecting to see if there were any parasites.

On our last day, we went to the highest point in the island, and we all agreed it was one of the most beautiful places we had ever been.  We then drove down and ate our lunches by the waterfront and watched the seals frolic in the high tide.  After we finished our report, we headed down for one last “diet coke”, and a game of Charades, where driving was misinterpreted as milking (when I saw we’re a cultured bunch, I really mean we’re culchies) and Rob was highly unimpressed at our inability to impersonate William Shatner.  We had an absolutely fantastic time and would like to thank Rob, Ruth, and Mary Catherine for all their help and encouragement during the entire trip.


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Millport Fieldtrip ZY4020

By Ciara Sexton (Zoology 4)


The Temperate Marine Biology Fieldtrip to Millport was an excellent course. The variety of marine biology that we were able to study in such close proximity was great.

We were taken out on a research vessel to observe techniques used to gather and examine subtidal organisms. Studied rocky shores in a different way than before and carried out a thorough and interesting sandy shore practical.

m2The facilities at our disposal were great and all of the practical work was well organised. We benefitted from having hands on experience of study techniques and species identification. The balance of practical and theoretical work was very well done. We learned valuable skills for working on various aspects of marine biology and gained experience in designing and carrying out our own projects.

The week wasn’t a case of all work and no play either! We all learned a lot over an enjoyable week and got a taste of what life would be like if we lived on an island! Overall it was an experience that I would strongly recommend to anybody with an interest in zoology and marine biology.






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TY2016: A week at UCC School of BEES from a TY perspective

labWEBCora Twomey, Davis College.

This week I attended a week work experience programme for TY’s at UCC’s School of BEES. In my opinion it was a great opportunity not just being college and main campus and attending lectures, but by getting to see what it would be like for me in the future when I hopefully get to go to university and college.

Firstly I applied to go to the work experience programme by filling out entry forms as there was only limited places on the course, then when I had heard that I got accepted onto the week work experience I was delighted and couldn’t wait to go.

During the week at the School of BEES, we got to do a whole lot of different things that were all new experiences which I liked very much. We also got an insight into what attending the university would be like and if we did do a course there we would be told what would we be studying and doing during the course, and what our future job aspects could be.

We attended lectures and carried out practical work on each aspect in the School of BEES, like environmental science, ecology and environmental biology, zoology, earth science, geography and the study of birds, and marine biology. We also got to meet and talk with postgrads and current students and got to ask them about any questions we had or about anything we wanted to know about UCC and university in general.

Some of the practical work that we carried out included an aquatic ecology practical in which we observed and identified insects in both clean and polluted river water samples. Also we did a practical on identifying mammals by their hair and got look at samples under the microscope. We got to do an experiment with sea urchins and the way they hide and protect themselves by covering and hiding themselves under seaweed. Firstly we had 18 tanks with one sea urchin in each and a square of seaweed and a square of carpet. We then covered 9 tanks with a black plastic bag and left them for a period of time, we then came back and removed the bag and noted the changes in the covered and uncovered urchins. We also got to ring birds and hold them and do cool tricks with them which was also very entertaining and interesting.

The practical work was my favourite and the highlight of the week. I also really enjoyed the tours of the campus and School of BEES and the main library tour on campus which was very interesting and we also got to see books that aged back as far as the 12th century. We also got a tour of the ERI building which was interesting too. The tours was also a good point of the week.

Overall my favourite part of the TY work experience programme was carrying out practical work and attending tours of different parts of UCC. Also I enjoyed the friendly atmosphere at the School of BEES UCC as we were made feel at home from word go in the School of BEES, and made new friends during the week.

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