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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birdring2WEBAndrea McSweeney St.Angela College Cork

I found this week very interesting, personally I didn’t know much about BEES or see myself in a BEES course in the future but this week showed me what one would be like. I really enjoyed the different lectures as I learned a lot about the different degrees. It was a very good way of getting young people to consider bees as a college course as now we have an insight into what it would be like and it’s at a time where we must consider our career options.

Personally I really enjoyed the Careers talk as that’s where I felt I learned the most about each particular degree and the requirements of each course. It was a very sociable week and I not only learned from the lecturers I also learned from other transition year students. We got a very good insight into college life here at UCC as we got campus tours and talks with current Bees students.

This week was very interactive as we got to work up close with the birds while doing the bird ringing. I liked the fact that we were shown what a life studying birds was like as a job. I was unaware of the places one could travel to with a job like that and how many people one would meet.

After finishing my week of BEES I don’t know if I have yet found the college course for me but it definitely showed me a whole different aspect of courses and I side to it     I wouldn’t even of considered before.


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TY2016: The BEES-t Week

b1Isabel Gallagher, Coláiste Muire, Ennis

This week I attended the BEES Transition Year Programme 2016. I thoroughly enjoyed this week and gained a lot of useful information about the Biological, Earth and Environmental Sciences course here at UCC.

I was incredibly nervous on the first day, as I am from Clare and did not know anybody who would be doing the course with me. I had concerns about who I would spend time with for the week, however this was not a problem as we were all in the same boat. On the first morning, the group met with the course co-ordinator Simona, who helped us all to feel at ease and organised the week very well. Within a few hours on the first day, everybody had made friends and we all began to bond as a group.

The week commenced with an introduction to the course. We then went on a tour of the BEES buildings so that we would be able to find our way around for the week. I found these very interesting, as I had never been to UCC before. Later in the day we completed our first practical, which was an observation of the insects found in both clean and polluted rivers.

We had the opportunity to carry out a wide range of practicals throughout the week, which I really enjoyed. One of my favourites was the sea urchin practical. We were each supplied with a sea urchin in a tank. Our task was to drop various rocks and shells into the tank to observe what the sea urchin would go for. Another practical I enjoyed was bird ringing. We all went outside and got to look at various types of birds and record different measurements such as their weight, fat and muscle.

On Wednesday, we had a Q&A session with a current fourth year student studying Geology. This was very helpful as he told us about being a BEES student and also just student life at UCC. Later in the day, we went on a tour of the main UCC campus and Boole Library. During our tour of the library, we visited the Special Collections department. I loved this as we got to see some very interesting and incredibly old books.

On Thursday I had made a lot of friends and felt very settled in the course. We had an interactive career talk that morning, and had to organise ourselves into groups to create a poster on a BEES subject of our choice. That afternoon we completed a Geology quiz, which I found very intriguing.

This week was an incredibly experience, and was well worth doing. I got to meet a lot of new people, and gain a huge amount of information related to the subjects I love. It has helped me to decide that I am very interested in this course, so I am very glad that I competed this valuable week.

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TY2016: Buzzing after my week at BEES


Aoife Dillane                                                                                Presentation Secondary School Tralee

This week I attended the BEES TY programme at the school of biological earth and environmental sciences in UCC. I really enjoyed my week here and would highly recommend it to anyone interested in the environmental side of science.

Being from Kerry, I was quite nervous at first to come as I thought everyone would know each other but this was not the case and everyone on the course was very friendly. I wasn’t sure what it would be like or if I would even be interested in what was going on but I found it to be a great experience of what college life is like and what type of courses I am interested in.

Over the course of the week we did had lectures on topics like geology, zoology, marine biology, plant science, environmental science and ecology, we also did a number of practical’s. My favourite lecture was the zoology lecture we had. We got a general overview of what studying zoology at UCC would be like and then we focused in on the aquatic side, doing a practical with sea urchins. I also enjoyed the marine biology lecture we got where we learned about life in the sea and how global warming is effecting certain species of animals.

On Tuesday we got a tour of the ERI where we learned about the work they do there and we were able to ask the scientist there questions about the type of work they were doing and what courses and subjects they did to get into the job they were in. One man was working on a way to use methane gas in a productive way.

We also got a tour of the main UCC campus and the library there. We learned about the history of the college and got to see the oldest book they had in their library.

On Thursday we got a talk on invasive plant species which I found very interesting. We were shown type of plant species that was brought into Ireland that had covered the bottom of Corrib Lake and had killed all its fish.

We also did bird ringing where we caught birds and were shown how they track them in the wild. They told us how each bird has a unique voice and how they can identify familiar bird’s voices.

Over all I loved my week at BEES and I can definitely see myself pursuing a career in one of these fields

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