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

 

An art project that makes sounds based on the monitoring data from the pollution in a river. Anyone interested in doing the same for one of their sites?
The Animas project
Something for our ESRs from the Poundplace blog as we enter a busy period for them all. Hat tip to Naturejobs.                                                                                                                                                                                   This image was republished from Pound Place; under a CC-BY-SA licence

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.