An LC-MS, samples etc.

November 8, 2011 2 comments

In previous posts I have mentioned numerous times my Mass Spec woes. Unfortunately the LC-MS at DCU seems to have died completely and so I took matters in my own hands and have organised access to another instrument at GMIT (Galway-Mayo Institute of Technology). Today was my first visit to their labs, and I am really excited about the coming weeks when I can go to GMIT to finalise my Mass Spec method. I met with the lecturer in charge and the technician in charge and the technician, patiently explained how things worked and we managed to set up a method.

I will now hopefully visit the labs again next week for a couple of days, so that I would be able to keep working with developing and then validating the method. I am truly grateful to the people at GMIT who have made me feel really welcome and took time out to help me out. The instrument at GMIT is only in use 1 day a week it seems, which is truly a godsend for me, but nevertheless a shame. This is especially so when considering that people at my university have to share the LC-MS between them and it was always in high demand. At least I will make good use of this instrument now I hope.

Today I also received my second set of samples, which I started processing after coming back from Galway so that I could immediately proceed with SPE tomorrow morning. Though it was a busy day, I am truly happy today, because this is what I started a PhD for: hard work and possibilities.

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Categories: Research

An update

October 26, 2011 Leave a comment

It has been quite some time since I updated this blog I have noticed. Research wise I have not progressed that much, but I feel that my project is getting a bit more shape, albeit not in the original direction I had been hoping for. Since the ATWARM summer school which was a great success, I have been to a conference in Crete on Instrumental Methods of Analysis (IMA 2011) in September. It was truly a new experience for me, as it was my first large conference. I really enjoyed that most of the speakers were not students but heads of research groups and people from industry, so I got to hear about a wide range of projects in each presentation rather than a detailed explanation of one project. The hospitality in Crete was also second to none.

I have also attended a networking event organised by the ISPE Ireland affiliate (An association of pharmaceutical engineers) held in Dublin earlier in the month. It was a good way to meet individuals from industry and I enjoyed the discussions. A high point for me was that I won the ‘Postgraduate student award’ for my poster presentation. I really appreciate what that meant.

On a personal note I have become secretary of the Biological Research Society and I look forward to a successful year of events. I think we are a good team of hard workers who just want to get the things done, so it should be a positive experience.

Hopefully more posts will be forthcoming in the next weeks.

Categories: Conferences, Lab Work, Research

ATWARM Summer School

The first ATWARM summer school has come. It is being held at the University of Duisburg-Essen, from the 19th-22nd July. This is where the last ATWARM/QUESTOR meeting was held in May. This summer school is entitled ‘Enhanced technologies for water and wastewater treatment’. Till now the first 2 days are therefore nearly over, and it is proving to be a really interesting couple of days. When all of us ATWARM fellows meet up it is always a great time, and I am really impressed with the quality of the summer school. When it comes to activities like this I am really feeling honoured I am having the opportunity to participate.

The first day was mainly a theoretical day, where we were based on the Essen campus and started the dat by a lecture by Prof. Dr. Jorg Dettmar from the TU Darmstadt. The presentation was entitled ‘Novel cultural landscapes in the Ruhr metropolis’. We all agreed that it started off the day to a very high standard. For me it was not only interesting to see what he had to say about how the area developed and how culture determines very much what comes out of a place, but also to see the way he presented his ideas and how he used his academic knowledge to help develop the area.

Following this introductory lecture, a lecture was given by Prof Dr Jens Martin about ‘Water and Culture’. He linked how poetry by poets based in London in years gone by (mainly Johnathan Swift) were shaped by the current culture, and how they wrote poetry indicating water issues. This served as a starting point for presentations by all of the fellows about the relation between water and culture in their different countries of origin. We went from China to Romania, to Poland, Iran, Russia, Italy and Spain. Unfortunately some people took longer than the allotted time, so Malta, France and Ireland are yet to come.

In the evening the session was entitled ‘Basics in water and wastewater treatment’. First up were 2 introductory lectures. Dr Ralph Hobby (UDE) on ‘Overview of technologies for drinking water treatment’, followed by Dr Jochen Turk (IUTA) on ‘Micropollutants in the water cycle: occurrence, analysis and advanced technologies’. I especially liked the latter lecture as it was quite related to what I am doing, including some ideas about LC-MS/MS which is currently the bane of my life. Following this introduction different fellows from ATWARM gave short presentations on different technologies which are currently used. This was very useful as we are all coming from different areas, and therefore this allowed us to get up to scratch on the different technologies.

The day then ended by a key note lecture by Prof Dr Ing Andre Niemann (UDE) about ‘Integrate water management: issues, aims and problems’. he is an ‘ex-academic’ who went into consultancy and now back to academia. Therefore he really managed to show his expertise in the area resulting in a really interesting talk.

In the evening a guided tour around the Zeche Zollverein and old coal mine, which has now been turned into a sort of industrial park and has found numerous uses. It was truly an experience, not just to see how the miners worked, but also to witness how previously ‘dilapidated’ buildings could be restored and a wide area given back for use by the community whilst maintaining its previous heritage. Therefore the mines are still there, and the ‘industrial buildings’ were restored rather than just flattened out and a park built…they have enough of them in Germany as  e had heard a lot about these efforts by Prof Dettmar in the morning and it was an experience to witness the efforts first hand. I wish Malta does take aboard more such activities. After this tour was a relaxing evening dinner together, which was a perfect end to the day.

PhD status

July 4, 2011 1 comment

It has been quite a while since I last posted here. A lot has happened and I do not even know how I feel. I am no longer disappointed, but just have no feelings I guess, plodding on.

First for some good news: I have managed to validate my HPLC method using distilled water, have had my literature review paper submitted to a journal (though that is only the start of the publication process), selected the SPE cartridges I will be using and got accepted to a conference in Crete next September.

But then for the bad news. The Mass Spec is still not working (and no end in sight for it starting to work…what is most frustrating is that I have been waiting to get access to a mass spec since March i.e. for 4 months now. Whenever I ask my supervisors about getting access to another mass spec at another university they tell me things like…we have around 15 mass specs at our university…there is no reason for you to go to another university. But it is getting really frustrating, as I have reached a status of not having anything to do and not knowing what to do to progress. I need the mass spec to soldier on, but it seems like there is no end in sight to the mass spec’s problems.

A second issue that has cropped up is that my supervisor at Queen’s, who is the only person in the supervisory team who has knowledge of the isotopic side of my project will be leaving Ireland to go back to Canada. I don’t know how things will work out, but he said he is still interested in that project, so I will hope for the best and see how it goes. We should hopefully have a meeting with him soon (but one of my supervisors here at DCU who should be organising that meeting does not seem to be all that ‘hard-working’ in getting this meeting done…was told that they’ll email the guy in Queen’s after they get some things out of the way…cos they are a bit busy now…so they said in about 3 week’s time they will contact him…which in my opinion is taking things a bit slow.

Sorry for the rant, but I rally feel as if I am here in Dublin, ready to work and work hard, but cannot. I have done all I could think of without the mass spec, and have also done things which I need to repeat again with the mass spec, such as validating the method, which would not have been necessarily have had to be done twice (one for the HPLC and one for the mass spec) if I had a working mass spec. But I do not know how else to proceed. My supervisors always tell me I am ahead where I should be at this point and have done lots of work, but at this stage, I feel as if I cannot do much more. The added blow of my supervisor in QUB leaving (he was the one guy who actually understand environmental sampling and so on in my opinion and is the main driving force behind the project in terms of expertise) has left me without any feeling. I am no longer angry at not having a PhD, I just feel as if my feeling are of ‘whatever will be will be’, which is definitely not me. I need something to do, cos this is frustrating.

I hope things look up somewhat in the coming days/weeks, and will keep you updated.

Categories: Research

A Validation Week

Sometimes I think that having a holiday is what you need to guilt you back into working. Last weekend I went home (together with 3 friends from Ireland) for an extended weekend. I really enjoyed showing them the sights of Malta, and also meeting my sister who came over too. However once I got back into the lab I knew that I needed to get down to business. Since the Mass Spec is still not working (still waiting for the parts to arrive), I decided to make use of the HPLC part of the LC-MS instrument. Usually you are not allowed to make use of this front end portion of the instrument on its own. However since the MS part was not working I got permission to use it. Therefore this gave me time to work on my method’s transferability to the actual instrument I will be (hopefully) using.

Before my trip I had ascertained that the method transfers quite well, and I was pleased with the preliminary results. However I knew that as with any method this needs to be validated. Therefore on my return I started working on this section of the process. I have now finished the validation of the HPLC method and I am quite pleased with the overall results. I did have to remove an analyte from the 11 I had started with, since it did not validate in any test. But I am not too concerned about that. After all that is why I started with 11. My supervisors had initially told me not to go for more than 5 analytes, but I had argued that it is better to start with more, and then eliminate later on, depending on the results.

I certainly hope that the parts arrive soon, and that the instrument is fixed very soon. In the meantime, I have figured out what I could do to ‘fill the time’. The parts have been said to be delivered either yesterday (so no) or early next week. I desperately hope that these parts are the actual ones required and that once it is fixed it keeps working. Another girl who is finishing her PhD will probably get onto the instrument first. But as long as it is working there is hope.

DCU and Sustainability

This week seems to have been a big week for DCU and sustainability. One of my supervisors was part of this initiative and so people from our lab got roped in to attending a couple of meeting organised. Yesterday was a lunchtime talk organised by the Biological Research Society at DCU and the Institute of Biology in Ireland. The talk was given by Professor Roland Clift and it was on ‘Bioenergy – and why biofuels for transport are a nonsense’. Professor Clift is at the top of the pyramid in the area of environmental science and sustainability. I really enjoyed listening to him and getting an idea of how things work, especially in relation to policy making.

It was especially enlightening to see the openness with which he gave the presentation, and particularly relieved to see that even in the higher echelons of science and even more so in policy making, pragmatism is one of the main considerations. You do not necessarily do what is the best out there (and very often you would not even know what is the best), but you take a decision based on practical factors, some of which are not wholly ‘scientifically’ based. For example, why a particular year was chosen by himself and the rest of the team preparing a policy document in relation to a particular target, where one of the reasons was that it is not too close that people in government say it is not possible and therefore not do anything about it, yet not too far away that people can afford to sweep it under the carpet.

I could link his train of thought very well with some decisions I have had to make as part of my PhD, where sometimes selection was based on practical rather than a wholly ‘scientific’ basis, such as the selection of analytes for my project…it would have been nice to be able to analyse for everything (this could run into the hundreds), but it is simply not possible, and the analytes finally selected were based on a number of criteria, which include financial considerations and time considerations rather than simply ‘scientific’ considerations.

Then today, a one day forum was held on Sustainability at DCU. I could not attend the whole day, since I was getting some other training related to my PhD, but I really enjoyed the parts I could attend. I missed out most of the morning session, where different members of the panel presented what is currently being done at DCU in achieving a green campus and future initiatives to reducing the University’s environment impact and making the campus more sustainable. I was present for part of the presentation by Dr Yvonne Ryan from An Taisce, regarding the Green Campus initiative. I had previously attended a seminar by An Taisce, when I had just moved to Ireland, where I had seen their enthusiasm in the area of environmental awareness and initiatives. This was followed by a presentation by Maggie Fagan, a student at Colaiste Dhulaig, who was part of the ‘green committee’ at the college for further education for the past 3 years, during which time they have maintained their green campus status. Maggie talked about the initiatives they have taken and the particular considerations of importance.

After these talks, a DCU campus environmental audit was carried out. However I had to be back in training, and therefore missed out on that, though I was back for the reporting back by the different groups. One of the suggestions which was of great interest to me was the introduction of a Dublin Bike stand at DCU for students to use. This would be really handy, and I would definitely use it to go to the city centre or so, if it becomes available. I have been toying with the idea of buying a bike, and this would be a good alternative.

In the afternoon session, principal investigators from the different DCU schools (including my supervisor) gave a short presentation on the research in the environmental and sustainability sector being carried out within their groups, giving a better idea of what is happening on campus. I had known what some of the other groups are doing, particularly from the Chemistry and Biotechnology schools. However I had no clue about the research being carried out in the school of engineering.

Overall, successful meetings, and I look forward to seeing what comes of these couple of days.

Mass Spec Woes

May 20, 2011 3 comments

As part of my research I need to get access to an LC-MS. I have carried out most (all?) of the work I could do on the HPLC part and have been waiting to get onto the Mass Spec. Unfortunately this instrument is quite old and does not work well it seems. I have been hearing tales of horror about it from previous researchers using it, and it seems that the cycle repeats. It had been down since the beginning of March and they just got it to work again this week. I was supposed to get trained on it next week, but today I received an email saying that something else came up and it will be out for another ‘couple of weeks’.

I find this to be extremely frustrating, as I cannot progress in my research without this piece of equipment. I will hopefully go talk to my supervisors next Monday or so, and see how to proceed. One of the suggestions might be to go to another University and get access to their Mass Spectrometer. But generally these instruments are quite in demand, so to get access to one might not be that easy. I will see how this goes. Without it, I am not too hopeful about the future of my PhD.

Well, as you can see, I am not in the greatest of moods. I have been waiting to get access to the Mass Spectrometer for a couple of months now, and if only it worked, I would have progressed quite a bit I would hope.

Wish me luck!