Earlier this month, postgraduate students of the Zoology department compete in the fourth annual ‘School of Natural Sciences Lightning Talks’ alongside students and staff from Botany and Geology.
We all presented 120-second snapshots of our research and were judged by a panel. Judges included the Head of the School of Natural Sciences Professor Fraser Mitchell, Science Gallery’s Aine Flood and Trinity’s press officer for the Faculty of engineering, mathematics and science, Thomas Deane.
Zoology had two winners on the night, Darren O’Connell (@oconned5) for his presentation on ‘Character release in the absence of a congeneric competitor’ and myself, Rachel Byrne, on my research titled ‘Parasites of badgers in Ireland- an untold story.’
In 1872 Yellowstone National Park was established as the first National Park not only in the USA, but in the world. President Ulysses S. Grant signed into law the Yellowstone National Park Protection Act, and so the National Parks were born. Today 59 National Parks exist throughout the United States, covering approximately 51.9 million acres with the goal of maintaining in perpetuity both wildlife and their habitat. Since 1916 the National Park Service (NPS) has been entrusted with the care of these National Parks, and this year they celebrate their centenary.
The National Parks have been referred to as “America’s best idea”, an ideology that has spread across the globe promoting the conservation of what little natural habitat and resources remain. What began as a single National Park in 1872 has spread to over 100 nations and been built up to approximately 1,200 National Parks.
In the wake of Trump’s shock election win, researchers, scientists, conservationists and a significant proportion of the public are lamenting for our natural world.It is no secret that Donald Trump does not openly believe in climate change, refusing to accept the overwhelming scientific evidence. Not only this but he has also promised to dismantle the Paris Agreement which sought to limit the temperature rise associated with global warming to below 2°C in order to reduce the risks and impacts of climate change.
Today the NPS actively teaches about, and warns of, the dangers of climate change to both the National Parks and the natural world at large. However, it is feared that the NPS will be silenced under a Trump Administration. Under the second Bush Administration talk of climate change by the NPS was prohibited under a decree from the Secretary of the Interior. Similar circumstances are expected under a Trump Administration, with Sarah Palin expected to be made Secretary of the Interior. If this comes to fruition then Palin would oversee the extraction of natural resources on approximately 500 million acres of public land, including the iconic National Parks, such as the Grand Canyon and Yosemite. Palin’s stance on natural resources leaves little hope as she has actively campaigned for the drilling of oil within the Alaska National Wildlife Refuge, the nation’s largest Wildlife Refuge, at the expense of the wildlife within it: “If a caribou needs to be sacrificed for the sake of energy … I say, ‘Mr. Caribou, maybe you need to take one for the team.’” Continue reading “Trump and the future of “America’s best idea.””
When grading assessments as a demonstrator, I try really hard to give helpful, constructive feedback. It’s important for everyone to learn from their mistakes and develop both as scientific thinkers and as writers. However, there are a few mistakes that happen very often and really grind my gears. If you want to impress your grader and improve your marks, avoid the mistakes below like the plague.
Species notation. A species should be written this way: Genus species and abbreviated species. The italics are crucial.
Please, do not misuse commas. A great brief on this can be found here. As a side note, all of Mignon Fogarty’s tips can be helpful and her podcast is stellar.
Spell check. Your word processing software should run this automatically. In case it doesn’t, please run your assignment through one. There are even free ones on the internet.
Parenthetical phrases. It’s (sorta) annoying that this colloquial writing technique infiltrates your writing. Either say it, or don’t.
Vague statements. Avoid phrases like “understanding is good” or “pollution is bad”. Be descriptive. If it seems like filler, it probably is filler. You can write meaningful things, so please do.
Don’t go too far the other way. Saying that “Nothing of value has been done without X” is pretty hyperbolic and will definitely get my ire up.
Lists are generally not part of scientific writing and should be avoided. Don’t tell me everything you needed in a list. Don’t tell me what you did in a list. Write me a beautiful, descriptive, informative paragraph.
I love abbreviations as much as any millennial raised on internet speak, but it’s really important to let people know what the abbreviations you’re using mean. Write it out, then give the abbreviation immediately. Oh my goodness, OMG, is a great example here. Otherwise we’re in this situation:
The dreaded /. Please don’t do/try this at home. It’s so frustrating! Write out a conjunction. You can reference this for clarification:
It’s perfectly ok to start a sentence with the word “this”, but you must be incredibly crystal clear about what you’re referencing. There is ALWAYS another word you could use that would add clarity to your writing, and it’s almost always better to just use the word you mean.
That’s all. Avoid these issues and your grader might work through your assignments with a smile. Always remember to write CLEARLY and CONCISELY. Now, you’ve just got to nail down the actual science…
Most of us were glued to the hugely anticipated premier of Planet Earth 2 this Sunday. We watched lovesick sloths meander through the mangroves, giant dragons battle it out on Komodo, and penguins getting fecked off cliffs by monstrous waves.
But if there was one scene that got us talking more than any other it was the literal race for survival that took place between a newly hatched marine iguana and an ominous pack of southern black racer snakes. The baby iguana had us shouting at the telly and clutching our faces while we watched its mad dash to the freedom of the ocean’s edge, avoiding the snakes’ fangs.
While we hoped against hope that the hatchling would make it, David Attenborough reminded us that for the snakes this was also a matter of life and death. Snakes have to eat, and for them the iguana hatching season means their best chance all year for hunting food. Continue reading “Iguana vs Snakes | Planet Earth 2”
In 1993 Free Willy leapt onto cinema screens around the world. The story about a young boy who saves a killer whale from a run-down theme park was an instant hit for Warner Bros. However for Keiko, the whale who played Willy, the story did not have a Hollywood ending. While Willy jumped to freedom as the credits rolled, Keiko remained in captivity. What followed was a global effort to return Keiko to the wild at all costs, even to Keiko himself.
Keiko, a male killer whale (Orcinus orca), was born in the North Atlantic off Iceland, sometime between 1977 and 1978. His life took a strange turn when in 1979 he was captured and sent to the Icelandic aquarium in Hafnarfjörður. He was then sold to Marineland of Canada Inc. in 1982 and moved to Ontario, joining a small group of other killer whales. Finally, Keiko was sold to the amusement park Reino Aventura in Mexico City in 1985, for $350,000. While in Mexico Keiko lived alone in an approximately 500,000-gallon chlorinated tank, except for the occasional company of Bottlenose Dolphins. Having little animal companionship, Keiko developed strong bonds with his human carers.
Keiko’s life took an even more unusual twist when he was cast in the lead role of the 1993 Warner Bros. film, Free Willy. This surprise hit reached a global audience and was a huge economic success for the studio. Keiko depicted Willy, a killer whale saved from a run-down theme park and returned to the wild. However when filming ended, Keiko remained in captivity, languishing in Mexico. The irony of the situation did not go unnoticed by the press, and activists waged a public campaign to make Keiko the first captive killer whale to be returned to the wild.
With growing public support, the Free Willy-Keiko Foundation was established in 1995 with $4 million from Warner Bros. and $2 million from the cellphone billionaire Craig McCaw. Reino Aventura agreed to donate Keiko to the foundation and in 1996 he was moved to an extensive 2-million-gallon seawater rehabilitation facility which had been constructed at the Oregon Coast Aquarium, at a cost of $7.3 million. Keiko’s health drastically improved once arriving in Oregon and he gained several thousand pounds. In Oregon, the complex task began of teaching Keiko how to be a whale again. Keiko had to be taught basic skills such as how to hold his breath for long periods, swim greater distances, and to ultimately catch and eat live fish. These skills would be critical if Keiko was to ever be returned to the wild. Progress was made and in August 1997 Keiko did indeed catch and eat his first live fish. While in Oregon Keiko became a public sensation and between 1996 and 1998 more than 2 million visitors made the pilgrimage to the see the Hollywood celebrity at the Aquarium. However Oregon was not the end point of the project.
The staff of the Free Willy-Keiko Foundation set the goal of releasing Keiko into a sea pen in the North Atlantic by 1998. Negotiations with multiple governments led to Iceland being selected as the release site. Ireland was also heavily considered and significant government support was put forward, but the lack of frequent killer whale sightings around our coasts made this option unrealistic for Keiko’s long-term release. In 1998 it was determined that Keiko was exhibiting normal killer whale behaviours and was healthy enough to be released. Up to half of Keiko’s daily intake of food now comprised of live fish and on September 9th, Keiko was lifted from his tank and transported to Klettsvik Bay in Vestmannaeyjar, Iceland, 19 years after he had been captured.
No expense was spared in Iceland. The project had nearly 20 people, boats and even a helicopter to ensure Keiko’s reintroduction had every chance of success. Keiko’s team continued to feed him while in Iceland and once fitted with a tracking device, Keiko was finally taken out to sea on ‘sea-walks’. The success of the project relied on integrating Keiko into an existing pod of wild killer whales, preferably the pod from which he had been taken. However Keiko’s early interactions with wild killer whales were not as promising as had been hoped. When in the presence of wild killer whales, Keiko remained on the periphery, at distances of 100–300m, and he was not observed feeding when among the wild killer whales. Instead he remained motionless or swam slowly. Stomach samples taken after these interactions showed no evidence of any food remains, confirming that Keiko did not feed when with wild killer whales.
Over time progress was observed and on the 30th July 2002, a brief physical interaction was seen when Keiko dove among wild killer whales. However a tail splash from one of the wild Whales elicited a startle response from Keiko, who swam back to his tracking boat. This was the only time Keiko was seen diving among killer whales and the only physical interaction observed. The project took another hit in early 2002 when Craig McCaw lost millions in the Dotcom Crash and withdrew his support from the project. With annual operational costs of approximately $3.5 million the project was taken over by the animal protection organization, the Humane Society of the United States (HSUS), with a greatly reduced budget and a ‘tough love’ policy. This policy saw Keiko’s team downsized and interactions with Keiko by his care staff also significantly reduced when in the presence of wild whales. Yet hopes grew when it finally seemed as though the entire experiment had paid off.
In August 2002 Keiko left southern Iceland and began a 900-mile journey to Norway. It was hoped that Keiko had finally been accepted by wild killer whales and had chosen to leave humans. Unfortunately, when he showed up in the Halsa Community inside a Norwegian fjord he wasn’t following a pod of killer whales, he was seeking contact with humans and allowing children to ride on his back. He had been on his own for nearly 60 days, yet based on girth measurements he appeared in good health and it was presumed he had eaten during that period. Keiko became an instant hit and thousands of visitors came from across Europe to visit Keiko in Norway. His caretakers relocated to Norway and began feeding him once again. They continued to conduct ‘sea-walks’ with Keiko for the next 15 months. During his time in Norway Keiko did not interact with any wild killer whales and actively sought out and initiated human contact, frequently following boats. Keiko died on the 12th December 2003 in the Taknes fjord in Norway, alone at the estimated age of 27. The cause of death was presumed to be acute pneumonia, although no necropsy was carried out.
Keiko’s reintegration into the wild was a complete failure according to numerous scientists and professionals, such as Dr Naomi Rose of the HSUS. Although he had numerous experiences with wild killer whales and was physically free to leave, Keiko continually returned to his caretakers for both food and company, never integrating with other whales. In retrospect it has been agreed that Keiko was not a suitable candidate for release due to his long history in captivity, social isolation, young age at capture and strong bonds with humans. However, Keiko’s story hit an unusual chord with the public and the public’s drive to see Keiko returned to the wild was something of which animal rights groups unashamedly took advantage, according to Dr Rose.
Costing more than $20 million dollars, Keiko’s release has shown us that release of long-term captive killer whales is incredibly challenging, if not impossible. Although we might find it appealing as humans to release such animals, in reality this may severely impact the well-being of the animals concerned. The HSUS and other groups involved in Keiko’s release wanted Keiko released at any cost and Jeffrey Foster, a trainer who cared for Keiko in Oregon and Iceland, believes that “the cause got in the way of doing the right thing [for Keiko]”. Mark Simmons, the director of animal husbandry for the Keiko Project, has even gone on to speculate that Keiko’s release from captivity amounted to animal abuse. Mr. Simmons has noted that Keiko’s health was drastically impacted when he was reintroduced and had it not been for continued medical interventions, Keiko would have died shortly after release.
In reality Keiko was a confused animal who depended on people, and the fact that his return to the wild was not a Hollywood success has raised huge concerns over the ethics of trying to return other captive Whales and dolphins to the wild. There has been a recent surge in opinions asking for the release of all captive killer whales, however if Keiko has thought us anything, it is that this is potentially self-serving and could be dangerous to the individual animals concerned. Today approximately 56 killer whales live in human care, the majority of whom were born in captivity. If Keiko, an animal born in the wild and with every resource available to him, could not be returned to the wild successfully, then what can we expect of animals born in captivity? And who can we expect to pay for it, considering that the sheer cost of maintaining Keiko in a sea pen proved unsustainable.
Keiko lived for five years in Iceland and Norway, but he never came close to being a wild whale again. Removing Keiko from Mexico was undoubtedly the right thing to do, however the best thing for Keiko in the long-term may not have been his release. The fact that maintaining Keiko in Iceland was financially unsustainable, and that Keiko never reintegrated into the wild, suggests that the best thing for Keiko may have been to live out his life in Oregon. Residing at the Oregon Coast Aquarium would have provided long-term financial stability to the project, ensuring the best possible quality of life for Keiko and perhaps even extending his life. This would also have allowed Keiko to remain in the company of the humans he relied on so much, rather than being forced into a life that he maybe never truly understood.
“Parasites are not generally regarded as being loveable. When we refer to people as parasites we are not being complimentary, we are not praising them. We tend to think that a parasite is the sort of person who goes through a revolving door on somebody else’s push. This is unfair. It’s unfair to real parasites… It is time for parasites to get a little more respect!” – Professor William C. Campbell during his 2015 Nobel Prize acceptance speech.
In 2015, Prof. William C. Campbell, a Trinity Zoology graduate, won the Nobel Prize in Physiology or Medicine, for his discovery of ivermectin. The drug can be used to treat a wide range of parasites, but is most widely known for its effectiveness against river blindness. In 1987 the pharmaceutical company Merck enabled the free distribution of the drug to developing countries.
This Nobel Prize, which Prof. Campbell shared with his then colleague Prof. Satoshi Ōmura, is an important accomplishment not only for the Professors themselves as the cherry on top of their careers, but it is also important for the wider academic community.
This Nobel Prize is of importance to what Prof. Celia Holland described as ‘the international worm community’. This community has been struggling for many years to get recognition and funding. This prize therefore finally highlights the importance of parasitic worms. A lot of these parasites are often, despite their wide prevalence, classified as ‘neglected tropical diseases’. Neglected tropical diseases mainly affect the poor communities and are often forgotten in research and in the ‘public health agenda’. It remains to be seen whether some parasites will ever be able to shake their neglected status, but this Nobel Prize and associated international attention could be a great step in the right direction.
Hopefully, other pharmaceutical companies will take note of this prize. Giving away lifesaving medicine should be celebrated. We all know of the negative press pharmaceutical companies have gotten such as the recent price hikes in epi-pens. However, we tend to forget and ignore when pharmaceutical companies go to great lengths to help those in need. I see this prize also as a celebration of Merck for showing how it can be done differently. Because, really, what is the point of us producing any medical research if it doesn’t translate into affordable medicine?
During Prof. Campbell’s visit to TCD, the provost announced a new lectureship position in parasitology in honour of Prof. Campbell and the work he has done for the international worm community. Needless to say that this position would not have existed without Prof. Campbell’s Nobel Prize. Parasitology is a struggling field worldwide and every lectureship position is one to be valued and celebrated. This lectureship shows the commitment of the university to parasitology and will reinforce Trinity’s leading role in parasitological research within Ireland.
Additionally, this is an inspirational story for a lot of people. The story of ivermectin is a great motivation for parasitologists like myself. I work on a parasitic nematode called Ascaris, which infects 800 million people worldwide every year. Much like river blindness, it is also a neglected tropical disease, and as is often the case for these types of diseases, there isn’t much interest or funding going around. So it’s great at the start of my PhD to see that this type of research can also be honoured and valued.
I’ve read interviews of Prof. Campbell where he said that this prize meant the end of his retirement. I’m sorry to hear that his well-deserved retirement has been shaken up, but Prof. Campbell took one for the team and is promoting parasitic worm research to whoever wants to listen, just as he did before, only now he has a broader audience.
Author: Gwen Deslyper (seen charming Bill at 1:49 )
One of my favourite parts of working as a researcher during the summer (aside from quiet campuses with less students around) definitely has to be the “conference season”. Indeed, I don’t need to convince many people that conferences are one of the lively and exciting parts of doing science that rightly mix traveling, networking (and sometimes drinking) and learning about so many new things (and sometimes hangovers).
One of the problems though is that they can sometimes be overwhelming. It’s hard to find a balance between the right amount of networking (how many friends/collaborators do I want to meet and how many new ones do I want to make) and the right amount of learning (which talks do I want to attend and how much can I get from them). Although everyone has their own technique to deal with these questions, it seems to me that it boils down to the number of people attending the conference and the objectives of the conference organisers. One solution is to aim conferences towards a more manageable size with a clear emphasis on networking and learning.
One such conference is the annual BES Macro conference! As has became a happy ritual over the last 4 years, I was awaiting July with impatience for this year’s one organised in Oxford by Natalie Cooper and Rich Grenyer. As a disclaimer though, I do not consider myself as a macroecologist at all (most of my work is on macroevolution methods). So why do I go every year? I don’t even know what macroecology is! Well one of the first points is that this conference covers a vast array of topics, this year reaching far beyond the classic bird species richness heat maps with presentations on microbe populations in tree holes and sampling biases in the fossil record! The second point is because I think this conference contains all the ingredients that I think make a good conference:
First, mix different career levels:
For early career scientists like myself it can sometimes be a bit intimidating to mainly hear talks by “veteran” scientists. In fact I often think to myself just before giving a talk, how lame mine will be in comparison to the other people. Not that mixing different career levels makes my talk less lame (!), it has at least the benefit of making me feel better. It also has the undeniable benefit of making it easier to network with the big wigs if you spoke in the same session as them. At BES Macro 2016, each session was a good mix of every career level making it much more casual. Even the plenary speakers ranged from Professor Tim Blackburn to About-to-be-doctor Hannah White!
Second, make most of the talks short:
People have mixed feelings about lightning talks: from the speaker’s point of view, when you have exciting results it can be frustrating to convey your message in 5 minutes. Also these talks are sometimes more difficult to write than a classic 10-15 minutes one! However, from a listener’s point of view, think about how much more you absorb, on average, from these extra 5-10 minutes that make a classic talk? On a couple of talks: probably much more; on 2 days or more of conference: probably not that much! Besides, if 5 minutes was not enough and just peaked your curiosity, it makes an excellent opportunity to network (“Hi, I really enjoyed your talk. About that, [insert your burning question here]?”).
Third, add a nice dose of transferable skills:
Another point of conferences that can be negative is that you chain-listen to many many talks all day long. That has the benefit of giving a good overview of your field of research but can also make you slightly sleepy! One solution to break this continuous rhythm of talks is to do it with discussion sessions that can either be about transferable skills or about big questions in the field. For example, at BES Macro 2016 we had an excellent discussion session on reproducibility and another on the classic “What is Macroecology?” question.
And finally, don’t forget to add some rants:
What makes a good conference lies also in how much you feel part of the field of research covered by the conference. One way to convey that is to be part of or at least listen to the “hot” debates shaking the field. In this conference for example, we had two “official rants” by Shai Meiri and Adam Algar on what is going wrong in macroecology (but still how much cool work is done).
And of course, the main ingredient is the attitude of the people towards the conference. As Rich Grenyer put it in his welcoming introduction: “this conference is formally informal.”
So you’ve just finished your PhD and sent out a frantic flurry of post doc applications, amidst all of the excitement, you’re invited to interview; how should you proceed? Below are some of the things I learned from my first post doc interview recently:
A couple of weeks ago I embarked on a new first for me; my first interview! I grant you that it is unusual to be having one’s first interview at the age of 26; I had worked, but never interviewed in the formal sense, with a panel of strangers. There seem to be three broad classes of post doctoral jobs advertised; a) those advertised by a particular lab, usually with a particular person, where you are interviewed directly with the person you are hoping to work for. b) Grants like IRC or the Wellcome trust where you write a proposal and often, while a panel reviews this, you never have to actually interview in person. c) The kind I’ve just done; where a centre or department gets money and so you are interviewed by a panel from the department (and university in general sometimes), but not by the person you are applying to work with. With some trepidation I accepted the interview. I wasn’t sure at this stage that I actually wanted the position if offered but decided to take the opportunity to interview for experience alone at any rate. Here are some of the things that I learned and would advise (though remember, this is an n=1!):
Before the interview:
If the position is somewhere that you need to fly/travel to, arrive a day early if you can. This will relieve some of the stress of any travel delays and help get you in the zone
If the person you would be working with is not actually going to be on the panel try to arrange a meeting with them before the interview (day before if possible). This gives you the chance to meet if you haven’t done so before but also get their opinion as to the position. I got lots of great tips when I did this about what the panel may be looking for but also some valuable insights.
Tying in with the above, if you can visit the building it is going to be in beforehand, particularly a university, it really helps to get a feel of the place, the workspace and see whether this is somewhere you would enjoy spending your time.
Meet the other candidates! I know that this is perhaps a little controversial and may not work for everyone, but I ended up meeting some of the other candidates going for the job while I was there and found it really useful for a few reasons. Firstly, and mainly, it helps to remind you that these are people too, also nervous, which certainly made me feel more comfortable, knowing others were in the same boat. The other big reason is that it enables you to meet people at a similar stage and potentially with similar interests to you, which is always nice!
Try not to fret too much about whether you want the job until/if you’re offered it! This is something I really struggle with but the truth it, you owe it to them to give a good interview, particularly if they are paying for you to come over, but after that, then it is entirely up to you and you can pick and choose. It is you that you have to put first and if that means that after all you don’t want the job, that’s ok!
Do your research! It certainly helps if you already have a connection to the place but doing some research on both the department and the people in close proximity; who work on something similar or complimentary to what you are proposing. It helps for this to think outside the box too; I referenced a Prof in Physics even though this was a biology post.
Chat to the admin staff, it is usually they who have gone to the effort of timetabling the whole affair and booking rooms for you, so make sure to thank them and also ask what it’s like to work there. They have nothing to gain/lose in this so they will be very honest!
During the interview:
Be friendly! Whatever the outcome of the interview or your decision, these are potential future collaborators and leaving a good impression will mean a lot.
Take a moment to respond to questions. A moment considering your response can come across more confident than leaping into an answer before they have finished asking.
I was always taught that in a conference presentation, when asked a question, to answer the room rather than just the questioner. Certainly make them your primary contact but being sure to address the room as well. I think this works for interviews too, ensuring to engage the whole panel in your answers, I think this speaks to your communication skills and also just generally keeps everyone together.
Name drop to wazoo! Talk about the people in the department or School that you might work with or seek advice from, talk about other people already in your network that might not be in theirs and how you might get them to contribute for seminars etc.
Where will you be in 5 years? The dreaded question! Be honest here; in my case I had just submitted my PhD corrections the week before (a point one of the panel chuckled at during the interview…), so I did not have the grandiose expectation that I would be in a faculty position running my own lab in five years time, and I said as much. I think this can quickly be turned into a positive saying that this is an exciting time where you can see what you like and build up skills so that in five years you might have in mind the research themes that you want to develop for when you are going to look for a faculty post.
After the interviews there was what I described to myself as an “awkward mingle lunch”, where members of the faculty and candidates had the chance to mingle over muffins. At first I thought this was a terrible idea and was tempted to run away but actually it turned out to be really fun. Everybody was more relaxed and you could get a little insight into the social atmosphere of the place, see if you think you’d be a good fit.
Ps. I did get offered the post and decided to take it!
Title: How population density influences social mammal ecology: A case study of the European badger.
The local density of a population of social mammals can affect many aspects of its ecology including social structure, mating systems, dispersal behavior, territorial behavior and the dynamics of disease. Scientists and policy-makers need a comprehensive understanding of the local population density as this may dictate the most effective management strategy. The European badger provides a particularly good species to investigate the effects of population density on other density parameters because its density varies by orders of magnitude across its wide geographic range. Further, it acts as a wildlife reservoir for bovine tuberculosis in the UK and Ireland, where it is subject to control operations. Currently, a haphazard classification of local population densities hampers a clear understanding of the badger’s ecology, leading to inappropriate management systems. We have conducted a meta-analysis to investigate the relationships between social group size, territory size, and group density and population density in badgers. We demonstrate that population density fundamentally alters badger ecology, affecting the interactions both within and between social groups. We also propose a classification system for densities of the European badger which highlight important ecological differences between populations across the density spectrum. Our findings provide a more cohesive picture of the species’ ecology across its range, facilitating appropriate targeting of disease management and conservation regimes.
Title: Characterisation of endophytic microbes within Sphagnum magellanicum from Clara Bog, County Offaly, Ireland: Implications for enclosed environment hydroponic systems in Space.
This work investigates potential mutualistic relationships between endophytic microbes and species of native Sphagnum moss sampled from Clara Bog, County Offaly, Ireland. The application of the ion-exchange ability of Sphagnum moss to water remediation and recourse recovery within an enclosed hydroponic system has been investigated by the author at NASAs Space Life Science Laboratory, Kennedy Space Centre, Florida. While this research indicated that Sphagnum could be utilized in this manner, it resulted in yet more questions, specifically in relation to microbial interactions and growth mechanisms within the Sphagna:plant test bed.
It is postulated that endophytic microbes growing mutualistically within S. magellanicum may be responsible for (a) anti-algae and anti-microbe effects within the hydroponic system and (b) increased nutraceutical content within the associated salad crop. Microbial DNA isolated from 100ug samples of S. magellanicum, was extracted and used to identify microbial endophytes using standard barcoding primers. Genetic fingerprinting is being utilised to type the endophytes. Isolation and culturing protocols from Sphagnum plants have been developed and applied for the characterisation of microbial species during hydroponic systems using S. magellanicum as a growth medium. Further investigation of mutualism between identified endophytes and a cultivar of Lactuca sativa known as ‘Lollo Rosso’ is ongoing.
Supervisor: Anna Davies & Martin Sokol
Title: The effectiveness of renewable energy policies in encouraging renewable energy generation.
Over the last twenty years the EU and its individual countries have been engaged in implementing policies to increase the use of renewable energy (RE) as a generation source. Motivations for this support of RE generation include, but are not limited to, concerns over climate change and pollution, national security risks associated with fossil fuels, and a wish to increase the competitive position of RE in markets which have been traditionally dominated by carbon based power. The issue of climate change and renewable power’s role in addressing this complex challenge has, in particular, been brought into sharper focus following agreement on emissions pledges from all the EU countries, and a new target of keeping global warming below 1.5C in December 2015 in Paris at COP 21; targets which will require a material response by policy makers throughout the EU. An understanding of what policies have been most effective in increasing RE is therefore critically important in designing new schemes, a comprehensive analysis of which has not been completed to date. I am therefore conducting a comparative analysis of the effectiveness of RE policies in encouraging RE generation (solar and wind, which given their advantages in cost and deployment have been the dominate focus of policy) across the EU from 1995 to 2015, with a primary focus on four countries of contrasting contexts, Ireland, UK, Italy and Portugal. While several studies have attempted to determine the effectiveness of various policies in various countries, these have been limited in scope and have not attempted to account for the variety of policy design features or individual country, market and key actor characteristics that influence policy strength. Adopting an energy transitions theoretical framework, this research would constitute the first study undertaken to determine how policy has effected the growth of renewables across Europe.
Supervisor: John Parnell & Trevor Hodkinson
Title: Systematics of the genus Embelia Burm.f. (Primulaceae – Myrsinoideae)
Within the Primulaceae family, the Myrsinoideae form a highly variable tropical group, ranging from climbers and shrubs to trees, and characterised by the presence of dark dots on the leaves and fruits. This subfamily contains over 1300 species, divided into approximately 40 genera. Many of these genera are in need of taxonomic revision, as their limits are poorly defined and sometimes rely on ambiguous characters. Among these genera is Embelia, a genus of climbing shrubs distributed mostly in South and South-East Asia, tropical Africa and Madagascar. Embelia displays extensive morphological variation – especially regarding the position, shape, size and merosity of the inflorescences and flowers. It is distinguished from other Myrsinoideae only by the climbing habit, and the relationship with morphologically similar genera has not been critically evaluated yet. The last monograph of Embelia by Mez (1902), recognised eight subgenera and 92 species, but the total number of species is currently estimated at 150-200, and the subgenera used by Mez must be assessed and refined. My project aims to combine morphological and molecular data in order to test the monophyly of Embelia and to provide a taxonomic framework of the subgenera.
Eoin Mac Réamoinn
Supervisor:Cliona O’Farrelly & Paula Murphy
Title: Toll-Like Receptor Gene Expression During Early Murine Embryonic Development.
Toll-like receptors (TLRs) are renowned for their fundamental roles in immunological surveillance and response initiation. While TLR proteins in invertebrate species, such as Drosophila, carry out functions in the immune system and in “building” the body plan in the embryo, such non-immune functions have not been thoroughly investigated in mammals. Although TLR genes have duplicated independently in these lineages, and may therefore have diverged in aspects of their functionality, limited studies have recently reported the expression of TLRs in the developing mammalian embryo (Kaul et al., 2012). We report a systematic study of Tlr gene expression in early to mid-gestational murine embryos using whole-mount RNA in situ hybridization and 3D imaging (using Optical Project Tomography), the combination of which has allowed us to record the precise tissues and stages at which these genes become expressed. We have found that the expression of these receptors is particularly enriched within the central nervous system with many Tlrs displaying complementary expression patterns in developing neural tissues, as is the case with Tlrs -1, -5, -6, and -7 in the neural tube at embryonic day 10.5. These findings are in line with experimental data showing that Tlrs -2, -3, and -4 can influence neural progenitor cell proliferation and self-renewal (as reviewed in Barak et al., 2014). In addition to the expression data we have generated, whole-transciptome data is being mined to build a comprehensive picture of Tlr activity during embryogenesis and will aid in the building of specific hypotheses for functional testing.
Title: Do principals of cross congruence apply in a naturally disturbed habitat?
Cross congruence is a measure of the degree to which diversity (number or composition of species) of different taxa follow broadly similar patterns in response to environmental conditions. In situations where cross congruence is strong, measuring the diversity of a single taxon can provide information regarding overall diversity, and this has led to the development of indicator taxa. Indicator taxa may be used to indicate general patterns of biological diversity or environmental conditions, often with the inference that where the environmental conditions are favourable for one taxon, other target taxa will benefit. The use of indicator taxa has obvious economic appeal, but cross congruence has been shown to vary greatly in different studies. Habitat heterogeneity and environmental stress can reduce the correlation of diversity among different taxonomic groups.
Within the EU, states which have signed up to the Habitats Directive (Council Directive 92/43/EEC) monitor the condition of habitats of conservation concern (Annex I habitats) using standard methods and report their results to the European Commission. Indicator species are used as part of this habitat assessment. Dune slacks, an EU Annex I habitat, are temporary ponds in sand dunes which can persist for long periods, many having been formed as part of the initial dune-building phase. Despite being stable physical features, they experience both environmental stress (annual flooding and desiccation) and temporal habitat heterogeneity, and this raises questions: do principals of cross-congruence apply here, and are indicator species effective? This study compared patterns of diversity among three different taxonomic groups, to test whether cross congruence was observed. Communities of plants, snails and water beetles in twenty-four dune slacks in Ireland were compared using diversity indices and ordination techniques. Dune slacks were assessed on the basis of the indicator species used in reporting to the European Commission, and the biological assemblages of sites which passed and failed the assessment were compared. The results of this research will help to evaluate current monitoring techniques which are in use throughout the EU and guide monitoring approaches for dune slacks in Ireland.
Title: Stronger perturbations increase the complexity of ecological stability
The stability of ecosystems determines the sustainability of the biological resource and services that nature offers us, and an understanding of mechanisms and drivers of ecological stability has vast implications for the sustainability and management of natural resources as well as the protection and restoration of ecosystems. Much effort has been contributed to understanding the factor that determines the stability of biological communities. A challenging aspect of stability is its many components, including asymptotic stability, resilience, resistance, robustness, persistence, variability and so on, but most of the previous research failed to analyse ecological stability from an comprehensive angle and we know remarkably little about the mechanisms underpinning relationships among components of stability. Therefore, focus on single stability elements may cause an underestimate of the “real stability” of ecosystems. Here in our research, by simulating the dynamics of 13 four-species food webs following perturbations varying in strength, we show that stronger perturbations decouple the relationship between stability components, i.e. that the efficacy of the single stability element in representing the general character of ecological stability becomes lower under strong perturbations. It is therefore necessary to investigate ecosystem stability from multiple angles, especially under strong disturbance frequently shown in real nature. The decoupling effect of perturbations on the multidimensionality of ecological stability is universal across most of the 14 food-web motifs in our research, implying a similar pattern in more complex large ecological networks.
Title: Population dynamics of Pinus and Ulmus in Europe during the Holocene.
This work investigates and compares the population dynamics of Pinus and Ulmus in Europe, during the Holocene, at varying temporal and spatial scales, by using recently developed and novel modelling methods. The first component characterises the European-wide post glacial rise and mid-Holocene decline experienced by both genera. Pollen data was extracted from 330 sites on the European Pollen Database (EPD). The depth of rise and decline events for each genus in each site core was defined by applying a spline curve, to remove stochastic noise from the pollen data, and identifying the range of depths along which the pollen values increased or decreased.
The R package Bchron was used to calibrate radiocarbon dates and produce an age-depth model for each site, using stochastic linear interpolation and Monte Carlo methods. The age-depth model data was applied to the event depth range to produce a probability distribution of when the rise and decline events occurred.
The second component characterises Ulmus and Pinus when they were abundant on the European landscape. Depth and magnitude data of maximum pollen values for both genera were gathered from the EPD. The age-depth models were used to determine the age of the maximum pollen value depths.
These data were then plotted on maps and empirical Bayesian kriging was used to interpolate the spatial and temporal dynamics of these population events in the two tree genera. This work, therefore, presents novel techniques to quantifying tree population dynamics, and also provides insight into the specific dynamics of two major tree genera in Europe.
Supervisor: John Parnell & Trevor Hodkinson
Title: Phylogenetics of Camellia (Theaceae) in Indochinese Peninsula
Tea, camellias and oil camellias from the genus Camellia L. (Theaceae) are commercially highly important. About one third of all known Camellia species occur in the Indochinese Peninsula, of which half are endemic. Many new names of Camellia are still being described from this area, which may suggest that it was previously under-collected. Almost no work, however, has focused on the phylogenetics of Camellia in this area. This project aims to address these issues using morphological and molecular approaches. Morphological studies, consisting of a comparison and description of various macro-characters of specimens and palynological analyses, will be undertaken to clarify the boundaries of species in this notoriously variable genus. DNA markers derived from nuclear and chloroplast genomes will be selected to generate molecular sequence data, which will be used to reconstruct a robust phylogenetic tree. A new classification of this genus could then be proposed based on both morphological and molecular data. Species that have potential to supply new traits to the cultivars of tea, camellias and oil camellias could also be identified.
Title: Biodiversity in willow evapotranspiration systems for wastewater treatment
Constructed wetlands are increasingly seen in Ireland and abroad as a solution to the on-site treatment of wastewater from domestic and other sources in rural areas. They are likely permanent features in our landscape that will proliferate into the future. Willow evapotranspiration systems are a subtype suitable for application in areas with low permeability subsoils. These systems are often promoted as having a beneficial role with respect to biodiversity but this has not been rigorously evaluated. This project aims to assess the plant and invertebrate biodiversity of these systems and the contribution they make to the biodiversity of the wider landscape. The factors driving biodiversity in these systems are being investigated and thus this project will provide management recommendations to maximise this biodiversity. This project involves cross discipline collaboration, drawing on expertise from both the TCD School of Natural Sciences and the TCD School of Engineering.