Category Archives: About Remediate

Summer School in Raadvad

Neha Mehta gives us her thoughts on the second REMEDIATE Summer School, which was held at Lyngby Vandrerhejm. Thanks to Lisbeth Axelsen and Kristian Brandt for their hard work in organising a great week!

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Thanks, Web of Science!

This is how every one of us feels after finding a paper that describes a statistical approach to the experiments we are doing. Nanoseconds of utmost joy, a colossal amount of gratitude towards the author, the publisher, and Web of Science for sharing the knowledge. And what if the same concept is shared by someone to us through a talk? This knowledge sharing while giving appropriate examples from different  studies was done by the tutors at Summer School 2.
This summer school promised to hone our skills in statistical applications and paper writing. This was actually an understatement. The truth is that we were immersed in a captivating series of lectures, rewarding discussions, and individual study time to apply newly learned concepts to our own projects. Summer School gave us the chance to learn things like:

The importance of microbiology in risk assessment
Remediation of contaminated sites is a complex, lengthy, and costly procedure. To decide the remediation goals, it thus becomes imperative to understand the risks to human health and environment due to contaminants. Most of the environmental risk assessment framework used for decision making at present only accounts for chemical analysis. It seems equally important to understand the health of soil in terms of the microorganisms; the effect of metal content on the growth and development of microorganism colonies, as much as knowing the total metal concentration and their bioavailability. To further elaborate our understanding on the subject we visited the Collstrop site to see how different contaminants may cause risk to environment.

Environmental risk assessment methods should try to reveal the soil health in terms of ecology, toxicity, and chemical analysis as defined in the TRIAD approach.

SS collstrop

Paper writing skills
Correcting one report, modifying the next; hopping from one experiment to another; meandering from one university to a different university for a secondment; presenting a poster, giving an oral presentation; preparing a to-do list to glancing at a done list; scheduling ICP-MS time to learning SEM; running a code on R to installing MATLAB: life is always a roller-coaster. Amidst all this, one thought that keeps on popping into our brains: AM I GOOD AT WRITING?
The problem was solved by the session on paper writing that told us that every researcher should first identify themselves as a writer. How a simple thing like saving the bibliography in a separate folder for the article we are working on right now, can save a lot of time. The introduction should always follow a funnel approach and we should first start working on the body of the article were some of the tips shared to make writing easier.

Like all things that are worthwhile, it takes time to publish; it also gets easier with practice. So don’t wait any longer. Start writing that paper now.

SS paper writing

Presentation Skills
This time we had a project meeting just before the summer school. Every presentation was recorded on a video camera. Supervisors were given a form to comment on the presentation skills of the ESRs.
Ohhh no… I did not rehearse… you did not tell us… this is not fair, we just came yesterday night and did not get a proper sleep. Yes, this is how we all reacted to the idea of Julie-Anne and Nick. But we had a sigh of relief, when these forms and videos were shown to us again in groups and we had chance to discuss among ourselves on how we can improve. There was no mentor, no supervisor telling us we were right or wrong. We were all friends set on a mission to improve ourselves, to help each other, looking at videos, eating the evening snacks and telling each other.

We may have discovered a simple procedure to help in the remediation of brownfield sites, now we should get out there and tell everyone.

Discipline
Preparing for next set of experiments in lab at night to submitting a report in wee hours of morning. We all have control of our schedules. One of the biggest benefit of being a PhD student is that we have all the freedom to plan our day according to the workload. In such a scenario, we often fall out of daily routine.
So here came lessons on discipline. Summer School was organised at away from the hub-bub of Copenhagen. So if we woke up late and missed the breakfast, there was no 7Eleven nearby. Lunch timings and dinner timings were fixed. Finishing dinner till 7:00 pm led to a situation when some of us were running in night, starving and looking in each other’s room for food. This is how we were all given a chance to live a healthy life. Waking up early to attend lectures, going for long walks to see deers and stroll on the beach in the evening, getting to sleep on time kept us motivated and energetic throughout. It was also important for inculcating self discipline.

Self discipline is when your conscience tells you to do something and you don’t talk back.
W.K. Hope

SS dinner

Statistical methods and application of R
Hovering a cursor from MS Word to MS Excel; writing an email, to using Mendeley for managing my bibliography; plotting maps on QGIS, to using SURFER for interpolating the data: we forget to pay heed to R, or to any statistcial software for that matter.
Somehow, everything that we forget or do not pay attention to, was included in the program of Summer School. The session on application of R taught us about writing code and data analysis using linear regression method, Principal Component Analysis and clustering approaches.

Statistical methods provide us with the conceptual foundations in quantitative reasoning to extract information from the sea of data.

Team Building
Missing a call from one of our fellow researchers, replying late on WhatsApp; looking at our Facebook feed, finding out about our friend’s achievement through Researchgate: there are multiple occasions when we find ourselves guilty of not remaining in touch with our friends. When an interdisciplinary project has students in five different countries, this is something that is bound to happen. To make the bonds of friendship stronger, no stones were left unturned by the organisers. We spent one of our evenings at Dyrehavsbakken Amusement Park. It is the world’s oldest amusement park. Pedaling cycles to the park, holding each other’s hands on a horror ride, shouting together in another ride gave a joyful refreshment to our friendship.

Away from the city, in a lush green location, learning from people who know their subject down to the minutest detail. Lessons not just on science, but on every aspect of being a successful researcher, was definitely a wonderful experience.

SS fairground

Life after a PhD

Stacie Tardif brings us some lessons from those who have walked the path before us

The Danish Academy of Sciences and Papers recently hosted an event for PhD researchers in Denmark and their transition into post-doctoratal positions. Several guest speakers from very different backgrounds were invited to speak about their journey into their career, and to provide some insight and advice to us youngsters. With looming statistics

Taylor, Martin et al. (2010) [1]

Taylor, Martin et al. (2010) [1]

claiming that only a small percentage (0.45% in the UK [1]) of individuals will make it to full professorship, it is inherently clear that we must start thinking early on about exploring different career options. We received all sorts of advice, from detailed information regarding grant application opportunities in Denmark, to more personal anecdotal stories and reflections on what these individuals wished they knew before starting off their careers.  Several themes recurred throughout the day:

  • Be a risk taker and take part of high risk/high return projects
  • Is academia really for you? Have a plan B
  • Go abroad and move away from your PhD supervisor
  • Find a mentor
  • Build a personal brand and generalist profile
  • Don’t wait, apply for your own grants

The chairman of The Carlsberg Foundation, Professor Flemming Besenbacher, started off the day with an inspiring talk, appealing to our generation to embrace scientific social responsibility. He stated that the 21st centuries’ current global issues such as food production, water resources, and climate change can only be tackled with breakthrough innovations, and therefore as young individuals in society, he urged us to be risk takers:

World Economic Forum (2015) [2]

21st Century skills
World Economic Forum (2015) [2]

take part in innovative and interesting research which may ultimately result in fewer publications but will be much more substantial in impact. He also maintained that we should start considering other options than academia. As PhD researchers, we are currently developing numerous transferable skills which have been outlined in a recent report by the World Economic Forum [2] to be critically important in order to prosper in today’s society. As such, it is important to reflect on our personal competencies which may or may not be appropriate for the pace and space of academia. Professor Besenbacher counseled us to keep the following in mind when thinking of our future careers:

6 key elements for career planning:

  1. Understand yourself
  2. Develop your strengths
  3. Work with the best
  4. Share your success
  5. Innovate, don’t imitate
  6. Always work efficiently

Step 1 & 2- Know yourself and research your options

  • What skills/competences do you want to use?
  • What motivates you?
  • What values are important to you?
  • What kind of career do you want?
  • What type of work environment do you enjoy working in?
  • How should your workday be structured?
  • What do you want from your career?

Step 3 & 4-Set goals and make a plan

  • Make an informed decision about what is right for you and maybe have an idea for plan B
  • Prepare to jump: network your CV and cover letter and practice your elevator pitch!

Regardless of our future in academia or not, the skills required to write an excellent grant application are highly transferable to writing up successful job applications. Throughout the day we received lots of good advice on the ins and outs of grant applications. Before starting the process of writing a grant or applying for a job position, strong emphasis is placed on reading the call, paying particularly close attention to the small subsections that describe the assessment criteria. It sounds silly to highlight, however, it seems to be one of the main reasons why applications are rejected. No matter how qualified the person or brilliant the idea, with a pile of imminent applications ahead of them, members of the panel are likely to be running on little to no sleep, and looking for reasons to shrink their pile.

Grant applications are all about you, your network and your great idea! But what is a great idea, you may ask?

  • Original and inventive
  • Well motivated in terms of impact
  • Grounded in and relevant to research fields

The panel, which in many cases is comprised of 5% of researchers from your specific field vs. 95% from other related but different disciplines, want to understand your great idea! As a result, it is imperative to keep it focused, simple and concise. Many applications have very strict page limits (do not put anything in the appendices, the panel is not allowed to read them) but it is important to keep in mind that other people have the same restrictions as yourself, and so it is doable. Do not repeat the same information in the application as this is a waste of space and time for members of the panel. To save space, make use of figures and charts (e.g. Gantt charts) which can incorporate a lot of information in a small amount of space. Applying for funding through industrial post-doctorate positions is another way to go. These are typically 1-3 year positions carried out by a recent PhD graduate (under 5 years after graduation in Denmark) that have an industrial focus. It involves teaming up with a mentor in a public sector institution (academia) as well as a mentor within a company. You are extremely cheap labor and therefore it is inherently benefitial to the company (and yourself of course) to have you there so don’t be intimidated to approach companies with your great idea. In addition, several databases and professional matchmaking clusters are available to graduates seeking these types of opportunities. Most importantly, industrial post-doctorate grant applications in Denmark resulted in a 50% success rate in 2016 and a predicted 45% success rate in 2017. This is significantly higher than grants awarded for post-doctorate grants in the public sector. These positions can also serve as a foot in the door and a stepping stone to a more permanent position within the company.

Here are some grants to apply for in Denmark (similar one’s can be found in most countries); keep in mind that most of the time, these grants are not tied with citizenship:

Other speakers throughout the day highlighted the importance of moving away from your supervisor and going abroad. This, at least in Denmark, seems to give you an edge over other candidates as you are not only developing your skills as a researcher and broadening your perspectives/ideas and visions, but also developing an international network which makes you very competitive. Debate was underway regarding the ease of movement once established with a family, however with proper preparation, one speaker even moved her entire family including children to another continent.

Image by Angelo Su via Image Source

Image by Angelo Su via Image Source

The importance of finding good mentors along the way was empahised on several occasions. These mentors can advise you on scientific matter, introduce your to relevant networks and people and help you understand the mechanisms and unwritten roles of funder organizations such as the public, private and research councils. Finding several different mentors along the way is also a good idea as they can advise you and teach you different approaches, skills and techniques. You will, of course, benefit in different ways depending on the mentor but finding at least one mentor that has the same interests/visions as you will be extremely valuable in the long run. Lastly, it is absolutely crucial that trust and honesty is built between you and your mentor. It is imperative that your mentor is able to tell you some hard truths along the way, if required.

Image by NASA Goddard Space Flight Center via Image Source

Image by NASA Goddard Space Flight Center via Image Source

 

It is important to understand that positions in academia are exceedingly competitive and there is some value in building a generalist profile, which can be adapted to several positions in different institutions. Instead of specializing very narrowly in a certain area, it may benefit you in the long run to have a profile and track record that is flexible.

 

“Uncertainty is the new normal: complexity is increasing and therefore this calls for a paradigm shift in science” 
Professor Basenbacher

As such, adaptability is crucial. It is also important to build a personal brand and work on your 30 second elevator speech. People want to know what you do but will quickly lose interest if you go into too much detail. If you are able to boil it down to several simple keywords/buzzwords, people will be able to categorize you, put you in a box and ultimately, shuffle you from one box to another depending on their needs. As academics, branding may seem like something that belongs in the business world, but try to think of it as being a recognizable expert or specialist in “blank” discipline. As your “brand” grows, this may open up new opportunities in the form of interviews, publications, podcasts, invited speaker talks and even local TV gigs and most importantly, new collaborations.

The most important advice we received that day was to be passionate about our work and to love what we do. Without this, success, whether that is through the academic route or otherwise, will be fleeting and somewhat anti-climactic. Needless to say, I walked out of the room feeling inspired and with a sense of urgency to get to work, be innovative, take risks and enjoy the ride!

For more detailed information about the day’s proceedings and individual speaker’s presentations use the following link: http://www.youngacademy.dk/da/Aktiviteter/Phd%20seminar.aspx

References

1.            Taylor, M., B. Martin, and J. Wilsdon, The scientific century: securing our future prosperity. 2010: The Royal Society.

2.            Forum, W.E. New vision for education: Unlocking the potential of technology. 2015. World Economic Forum, Geneva, Switzerland.

 

Celebrating Science History

By Ricardo Costeira

In 1917, while working with bacterial isolates from wounded World War soldiers in France, Félix d’Herelle published what he called the discovery of “an invisible, antagonistic microbe of the dysentery bacillus”. d’Herelle had  discovered bacteriophages, viruses that infect bacteria. One hundred years later, phage research is intrinsically linked to other major scientific events: from the identification of DNA as the genetic material, all the way to the discovery of CRISPR-Cas systems.

This year, it was with excitement that I I flew to Paris to attend the 100th anniversary celebration of bacteriophage research at Institut Pasteur, the “cradle” of bacteriophages and, arguably, the most important microbiology research institute in the world.

Over the course of 3 days, I was honoured to listen to world-class scientists sharing major breakthroughs in phage research and, as a REMEDIATE scientist working on environmental virology myself, I received the honour of sharing my own findings with the rest of the phage scientific community in what was a very special event.

From studies on global ocean viromes and biogeochemical cycling, to studies on phage therapies as solutions for antibiotic resistance, these 3 days in Paris showed that phage research is booming all around the world and that it is as important as ever before. One can only wonder what the next 100 years of phage research will bring!

group photo

 

Meet the Researchers – Panos Kirmizakis

QUB has recruited a new ESR, Panagiotis Kirmizakis (or Panos to people who know him). Here’s more about him in his own words:
Panos blog photo

Born and raised in Greece. I graduated in Environmental and Natural Resources Engineering in Technological Educational Institute of Crete, in Greece, 2014. After that, I embarked on a MSc programme at the same Institute, graduating in October 2016 with a Master in Geoenvironmental Resources and Risks and a written thesis in Laboratory scale application of Spectral Induced Polarization (SIP) method for environmental monitoring.

After my studies in Greece, I moved to Belfast for the REMEDIATE project. My role in Queen’s University focuses in geophysical approaches in site assessments. I will try through fully controlled laboratory experiments and larger scale applicationσ in contaminated sites the utility of geophysics in environmental monitoring.

I will carry out most of my work at Queen’s University Belfast which is ranked in the top 200 universities in the world according to the 2015-2016 QS World University Rankings. Queen’s is much more than just a place for work as it is located in Northern Ireland; a place is not probably the first destination that someone will think about vacation, but it is worthy to visit. The earth of joyful “ginger-heads”, good drink and the beautiful nature. And if you do not believe me just take a walk along the river, where the eye cannot find the end and the soul rejoices seeing seagulls flying above your heads.

A done list

A beautiful illustration from Yi, based at the University of Copenhagen, of the frustrations and joys of being a PhD student:
As-chip primer
1 Dilute the 99 arrived As-primers;
2 Use Primer-Blast to check the specificity of 99 As-primers;
3 Use AlleleID to check the parameters of 99 As-primers;
4 ARGs HT-qPCR of the CCA samples;
5 ARGs HT-qPCR of the Tellus archived soil samples;
6 Order the oligo of 99 targeted fragment;
7 Regular PCR with 99 As-primers;
8 Sequencing of PCR-product of 99 As-primers;
9 Pig manure manuscript.

That’s a recent to-do list. I like to start every day with writing and checking my list, because it’s one way for me to clear the fog so I don’t miss anything important and can quickly move into “working” status.

However, there was a lot on my plate: faced with this long list of tasks, even imagining how I should manage my time to shorten it to a more refined list made me feel tired. “One by one, one by one, just pick one and focus on it first”, I told myself, and dragged my body into the lab with my tired “soul”.

Chip system

Days passed. One day I found, not for the first time, that I couldn’t fall asleep, and I was staring at my to-do list. I suddenly realized the to-do list is not only helping during work time but also “helping” me after work! I couldn’t help wonder if there is a so-called work and life balance, especially for a fallen leaf who is far away from its root.

By talking to friends and colleagues, I realised I am not the only one who has this problem, and I found a solution. “There are always more things waiting for you to do, you should think about what you have done instead of what you haven’t done.” That day, I made a done list after I finished work:

1 Ordered the primers;
2 Centrifuged and diluted the primers;
3 Parameter check;
4 ARG HT-qPCR of CCA samples (1/2);
5 Conference registration;
6 Targeted fragment collection.

After this, I had a very good sleep…

Chip system2

To-do lists and done lists are like yin and yang. A to-do list can direct you to focus on the tasks, and a done list can motivate you in a happier and more positive way, and can be used to review the day and give you a chance to celebrate accomplishments. PhD life can be fulfilling and challenging. Balanced self-management provides comfort for fallen leaves waving and dancing in the wind. From that day on, every time I feel overwhelmed, I ask myself before I finish work, “What is on your done list?”

One step at a time

Our ESR at the University of Turin, Neha Mehta, has written a post about the responsibilities and opportunities we have as scientists. We hope you enjoy it!

While mapping locations of samples on my computer, I found myself sitting and pondering the last sampling trip. I have been on many trips in the last year, for collecting mining waste dotted over mountains, for working with soil near the waste, and to collect water samples (to find out if the water was using perseverance and hard work to slowly dissolve the metals around it and carry them large distances, or if the metals were loyal enough to remain attached to the rocks and not fall in love with ions in the water).

Sampling feels different in different seasons, and this was first time I had done it in the autumn. I went with Giorgio and we were joined by Scolari (an employee from Comune di Gorno, Lombardy). We were there to sample water springs and water from mining tunnels that would reflect the level of metals in the background and in contaminated water.

When I got out of our car, I could see colours in the mountains that were not evident when I had come earlier in the year. Apparently it was views like this that made the author Jim Bishop write “Autumn carries more gold in its pocket than all the other seasons.”

travel

How meticulously nature paints itself. When I was taking pictures of the sample site, I could not stop myself taking photographs of mountains and the paths decorated by leaves.

The ecstatic feeling soon disappeared when I started walking in the mountains to collect samples. The leaves and water made some of the locations slippery and so scary that we were all walking like tortoises even with proper shoes. Leaves that hide holes beneath them; leaves on plants and around that hide the water source itself. I kept on repeating to myself “Slow and steady wins the race, slow and steady wins the race” as if it was only this hymn that was saving us and our instruments from falling down; and we kept on walking.

sites

The area had a plethora of flora and fauna: we came across cats, dogs, horses, big and small mushrooms, a donkey, salamanders, goats, and cows grazing on surrounding fields, appearing here and there and sometimes walking with us until either of us changed path, as if they were keeping us company in our work that could lead to the betterment of not just human life but also the local environment, perhaps thinking ‘How weird these human beings are, they do not know how to walk properly even with shoes!’ or maybe just looking at us and getting busy in their chores again.

fauna

At this point someone reading this might wonder if I was collecting samples or taking photographs. Where are the samples? Where are photos of sampling locations? In case you failed to notice, look again at the pictures. The team walked to long narrow tunnels used for underground mining of zinc and lead.

The tunnels have their own stories on how men used to drill along the tunnels and cut the rocks, and women used to segregate the rocks with minerals from other rocks. Tunnels that silently roar ‘Oh you! You are also one of those who want to have everything, but do you really stop for a moment and try to imagine the effects of mining on workers, the backbreaking work and the precision through which it passed; the chemicals that were used to wash those rocks?’ How neophiliac and shortsighted we really are: we look at something, buy it, use it, and forget it. It cannot go on.

mine

Someone like me must come and show the pictures, trigger the cognitive process again, shout if we are not paying heed. No matter how much we try to overlook our footprints and try to remain caged inside our own comfort zones there will be something which will come in different forms in front of us. Therefore, we need to find answers for our own benefit, for ourselves to have peaceful sleep in night. We cannot leave all kind of marks on earth and go on Mars or the moon to live happily ever after! I was experiencing centuries in a few minutes and using knowledge of every discipline I have come across. History, chemistry, geography, geology and environmental engineering were all in my head.

Then I suddenly remembered words of wisdom from my mentor Professor Domenico De Luca: “Neha, passo dopo passo [step by step]! When you get emotional while you are doing research, remember just one mantra. Take a deep breath and move forward with just one step. Do not think too much and keep on taking every small step you can.”

After all the conversations inside me stopped, I took the smallest step I could take at that moment, and continued measuring electrical conductivity, the temperature and other physiochemical qualities of water.

Here are some bonus pictures from the sampling trip. Do not forget the lesson… ONE SMALL STEP !!!

one small step

Meet the Researchers – Suman Kharel

Suman blog resize

“If you can’t be in awe of Mother Nature, there’s something wrong with you.” – Alex Trebek

I was born in a peaceful country: Nepal, as often said, a utopia of natural beauty. I grew up in the foothills of the Himalayas, an area of marvellous scenic exquisiteness. Nevertheless, our natural surroundings are under threat from serious environmental challenges. There’s a necessity and urgency for cognizant use of natural resources, protecting the environment from degradation and elimination of pollutants present in the environment. Our biological nature demands clean air, water, soil and energy, and biodiversity for our good health and well-being. This is why I joined the REMEDIATE project as a Marie Curie Early Stage Researcher in TE Laboratories Ltd and Dublin City University. My research objective focuses on the development of innovative methods to monitor organic contaminants in soil and water. I am currently working in the R&D department of TE Laboratories, surrounded by very friendly and supportive colleagues.

I completed my undergrad in Microbiology and Chemistry from the Tribhuvan University, the oldest and most renowned University in Nepal. After my degree, I moved to Germany to pursue my Masters in Water Science in the University of Duisburg Essen. My Master thesis was based on the development of an analytical method to assess Triclosan (a biocide) and its methylated products in soil and earthworms from biosolid amended agricultural sites and the German Environmental Specimen Bank.

I am a globetrotter and inverse paranoid. I love listening to music, reading books, doing sports and having get-togethers with friends whenever I have spare time. Finally, I would like to say that the opportunity to work within the elite research group of REMEDIATE, juxtaposing with an emphasis on networking & training, plus independent & extensive research in a specialized area, has been a special privilege to me.