EMBRACING THE CHALLENGE OF DIGITAL HUMANITIES
The world is becoming digital and the situation is similar for the arts and humanities. Federica Bressan is one of many researchers working in the area of digital humanities. She talks to us about her journey from her Marie Skłodowska-Curie actions (MSCA) project to her career as a Producer and Host at Technoculture podcast.
Federica in her own words
I am an Italian-Slovenian researcher and podcaster, with a background in music and technology. I received my training in Italy. In 2016, I relocated to Belgium thanks to a Marie Curie individual fellowship. This experience boosted my career in ways I didn’t even think possible. Among other things, it allowed me to engage with science communication, and to start my first podcast (Technoculture) which you could say is a spinoff of my Marie Curie project.
DEFINING THE DIGITAL HUMANITIES
Imagine how many disciplines have been impacted by digital transformation technology. The list is long and still growing. And it includes the humanities. Digital humanities is a term used to describe a broad field that covers the use of digital methods by arts and humanities researchers. According to the University of Cambridge, a pioneer in the development of humanities computing, an increasingly important element of the Digital Humanities is discussion of the way in which the digital landscape has changed our view of the humanities and, conversely, the insights that the humanities offer on such central issues of the digital age.
For Federica, the Digital Humanities is an umbrella term, above all: it’s not a discipline per se, but it connects many disciplines. “Much research that is now labelled under this term has existed for a long time, so there is a strong continuity with the past,” she says. The Digital Humanities can, therefore, be defined as a phenomenon that evolves with society. “You will get a different definition of Digital Humanities depending on who you ask,” she adds.
Federica works in a ‘niche’ area of the Digital Humanities. Her MSCA project DaphNet was launched with the following problem: most multimedia artwork produced since the 1990s is lost due to the lack of adequate preservation strategies.
To tackle this issue, Federica worked on a multidisciplinary approach to preservation. The DaphNet project aimed to reach a definition of a framework for the preservation of interactive artworks, as well as to ensure their future re-use and flexible access.
Our Alumna had to overcome numerous challenges to achieve her project in January 2019. “I stepped outside my field of expertise, moving from audio to multimedia. I think I initially underestimated some implications of this transition, but I am proud of the skillset I possess now as a result of the process,” she says.
THE EUROPEANA JOURNEY
Working now as a producer and host at Technoculture podcast, Federica has had the opportunity to become familiarised with Europeana, a European collection which provides access to 50 million digitised items.
“Europeana is the largest digital repository of cultural data in the world,” explains Federica. “It aggregates digitised books, paintings, photographs, recordings and films, and it offers a variety of services to dedicated communities: teachers, journalists, scholars and others.”
Intrigued by this collection, she recently interviewed Harry Verwayen (executive director of the Europeana Foundation) at the annual Europeana Conference in November 2019, which took place in Lisbon. Verwayen defined Europeana as a “co-creation space, where the user community helps to improve and build new narratives through the data.”
What’s more, in this interview, Verwayen quotes the co-founder of the Museum for the United Nations and keynote speaker at the conference, Michael Edson: “In the next 10-20 years, nobody will remember the product. They will remember the network that came up with new solutions for the challenges we’re facing today.”
Europeana faced numerous challenges, including climate change. “Harry Verwayen talks about the commitment of Europeana to decrease the carbon footprint of its digital infrastructure, by working with service providers that only work with renewable energy, setting a great example for every other cultural organisation in Europe and in the world,” says Federica.
SHARING IS CARING
Federica stresses the importance of the research community in tackling challenges related to digital humanities. “Nobody works in isolation today, so it is important to be aware that we share data and tools just like we share our history and identity, and most of all it is important to belong to a community,” she concludes.
Listen to the podcast “Creating value from cultural data in the age of digital transformation”
MANNA: NUTRITION AND IMMUNITY: MOLECULAR APPROACHES
Discover Project 2 of the MANNA network. You will find out that nutrition does have an impact on immunity.
The European Joint Doctorate in Molecular Animal Nutrition (MANNA) is an EU network whose mission is to provide a Double Doctorate level training programme, valid throughout all Europe, on innovative technologies applied to animal science and nutrition. The MANNA Joint Doctoral project is a Marie-Skłodowska Curie Innovative Training Network funded by the European Commission under the Horizon 2020 Programme. This is the third of a series of articles on the MANNA doctorate, through which we will discover in detail its projects and the related Early Stage Researchers (ESRs).
WHO I AM
My name is Gabriela Ávila and I come from Costa Rica, a wonderful place in Central America filled with nature, and most importantly with kind and hardworking people. I did my bachelor’s in Biotechnology at the Technological Institute of Costa Rica (TEC), and then I moved to Barcelona to do my Master in Biochemistry, Molecular Biology and Biomedicine at the Autonomous University of Barcelona (UAB). Spending a whole year abroad represented for me a very valuable experience as it allowed me to grow both professionally and personally. It gave me not only the opportunity to know different educational and research environments, but also new cultures and persons that I now have the pleasure to call friends. After finishing my master, I realized that I wanted to continue with my academic career and to deepen my knowledge and expertise in the OMICs field, so, I decided to apply for a position in the MANNA programme which fits perfectly with these interests. Now, I am the ESR of the Project 2: “Nutrition and immunity: molecular approaches,” under the supervision of Fabrizio Ceciliani (University of Milan), Armand Sánchez (Autonomous University of Barcelona) and Muriel Bonet (INRA - National Institute of Agricultural Research, France).
The host immune system is composed by a group of cells and molecules specialized to identify and destroy potentially dangerous microorganisms, toxins, cancer, and dead cells. The intestinal immune system is the largest immune organ in mammalian and avian species and constitutes the primary site of interaction between the host immune system, microbiota1, and nutrients.
Nutrition has shown to play a pivotal role in the modulation of intestinal immunity indirectly by changing the composition and abundance of microbiota and/or by exerting a direct effect in immune cell populations and their functions.
For such reason, diet supplementation with a wide range of nutrition molecules has been a common and widely used approach by farmers and animal production companies to achieve an improvement in animal performance, health, and welfare. Fatty acids like conjugated linoleic acid (CLA), polyunsaturated fatty acids (PUFAs) like the docosahexaenoic acid (DHA) and the eicosapentaenoic acid (EPA), dietary fibres like citrus pectin, and exosomes have all demonstrated to have immunomodulatory properties both in humans and animals.
Therefore, we aim to mimic what truly happens within the intestinal immune system of the animals when their diets are supplemented with those molecules. Thus, we will work with the most predominant subsets of immune cells there found, namely peripheral mononuclear cells (PBMCs). Moreover, to have more realistic and accurate information of which effects these molecules have on the animals’ immunity, at a cellular and molecular level, we also aim to include proteomic2 and transcriptomic3 analyses. The inclusion of these last approaches into our study are highly valuable and constitute the novelty of the work, as none of the studies carried out on these molecules so far had focused on the OMICs4 level.
Finally, we predict that through this integral assessment, using both in vitro and system biology5 approaches, we can have access to more transcendental and binding information on the impact of nutrition in the immune system of the animals, and consequently choose the best dietary supplements to assure their improvement in health and performance.
MY PROJECT SO FAR
During my first year at the University of Milan, I have set up protocols for the isolation and purification of different immune cells from cows’ and chickens’ whole blood. I have also studied the in vitro effects of fatty acids like the CLA and dietary fibres such as citrus pectin on bovine and chicken immune response, respectively. Specifically, I have tested how these molecules impact several immune functions (e.g. apoptosis, viability, chemotaxis, phagocytosis, killing capability…) of bovine and chicken mononuclear cells (lymphocytes and monocytes). In the next months, I will also perform the purification of exosomes from sows’ milk to test the in vitro effects of these and PUFAs (DHA and EPA) on porcine immune cells. I have also started the collection of samples to perform transcriptomic analyses during my second year at the Autonomous University of Barcelona (UAB), and proteomic analyses on my third year at the INRA in France.
HOW DOES BEING PART OF AN MSCA ITN IMPACT ME?
Being part of the European Joint Doctorate on Molecular Animal Nutrition (MANNA), a MSCA ITN, has been of great value for my professional and personal growth. It has not only given me the opportunity to acquire new technical skills on cellular and molecular biology, by working in high quality scientific laboratories all around Europe. But it has also given me the opportunity to get to know a great group of scientists and persons who work towards the same objective.
The creation of collaborations, bonds, and exchanges of knowledge between each other is one of the most rewarding things for me in all of this process. Moreover, the acquisition of soft skills for a more efficient communication of my research and teaching opportunities has also been possible. Indisputably, the experience of living abroad, discovering new cultures, languages and people has made me grown as a person.
Finally, being part of a prestigious and respected funding programme such as the Marie-Skłodowska Curie Innovative Training Network has provided me with great recognition within the scientific community.
1 Microbiota is formed by ecological communities of commensal, symbiotic and pathogenic microorganisms [found in and on all multicellular organisms studied to date from plants to animals].
2 Proteomics is the large-scale study of proteomes—set of proteins produced in an organism, system, or biological context.
3 Transcriptomics is the study of the transcriptome—the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell.
4 OMICs refers to the collective technologies used to explore the roles, relationships, and actions of the various types of molecules that make up the cells of an organism.
5 System biology is the study of the interactions of the components of various biological entities (including molecules, cells, organs, and organisms).
GABRIELA ÁVILA MORALES
EARLY STAGE RESEARCHER OF THE MANNA PROJECT 2
MANNA: WHAT HAPPENS WHEN YOU SUPPLEMENT THE DIET OF BROILER CHICKENS WITH EXTRACTS OF CUCUMBER AND CITRUS?
Discover the Project 3 of the MANNA network. You will find out that novel plant extracts could be an alternative to the use of antibiotics.
The European Joint Doctorate in Molecular Animal Nutrition (MANNA) is an EU network whose mission is to provide a double doctorate-level training programme, valid throughout Europe, on innovative technologies applied to animal science and nutrition. The MANNA Joint Doctoral project is a Marie Skłodowska-Curie Innovative Training Network funded by the European Commission under the Horizon 2020 Programme. This is the fourth of a series of articles on the MANNA doctorate, through which we will discover in detail its projects and introducing the related Early Stage Researchers (ESRs).
WHO I AM
I’m Francesca Riva and I was born in Italy, where in 2015 I graduated in Veterinary Biotechnology at the University of Milan after a fellowship period in the laboratory of parasitology. Continuing my studies, I obtained an MSc in Veterinary Biotechnology Sciences at the same university, where I discovered my greatest passion in Omics technologies. In 2016, I was selected for an Erasmus+ international exchange programme and I had the opportunity to acquire seven months of practical experience at the Department of Veterinary Molecular Genetics of the Autonomous University of Barcelona (Spain), where I developed my final dissertation project. In 2017, I attended a master course in “clinical research” at the Mario Negri Institute for Pharmacological Research in order to deepen my knowledge on different aspects related to the planning of a clinical trial. When I discovered the MANNA project, I was particularly keen to join it as its research field is an excellent match for my academic background and my passion for Omics.
I am the ESR of Project 3 of the MANNA network, and I am working under the supervision of Maureen Bain (University of Glasgow), Vladimir Mrljak (University of Zagreb) and Geert Bruggerman (Nutrition Science, Belgium) on the project titled “Effect of novel plant extracts on gut microbiota, metabolome and immune system of broiler chickens pre and post E.coli LPS challenge.”
The poultry industry has grown significantly over the last few decades due to genetic improvements and intensive production methods, and it is predicted it will continue to increase. Nowadays, the primary aim is to maximize production; however, chickens are raised in intensive farming conditions with a high risk of epidemic outbreaks. Prevention and control of poultry diseases have led during the last decades to a substantial increase in the prophylactic use of antibiotics. When antibiotics are not properly used, they may lead to antibiotic resistance. For this reason, antibiotics were outlawed in poultry and pig diets around the world, beginning in Sweden from 1986.
From that moment, many researches have been carried out to look for natural agents with similar beneficial effects to antimicrobial growth promoters and antimicrobial substances. Probiotics, prebiotics, enzymes, medium-chain fatty acids, essential oils and vitamins are already used as alternatives but, during the last few years, plant extracts have attracted the attention of the research community for their promising properties. However, the active compounds of plant extracts and their mechanism of action is not well known, so, the identification and standardisation of their beneficial chemical and/or biological molecules is one of the major challenge for animal industries. Among the variety of novel plant extracts, citrus and cucumber extracts have been chosen to be tested in my MSCA PhD project thanks to their availability, cost, active molecules (i.e. pectin, flavonoids, limonene, carotenoids, polyphenols, dietary fibres, essential oils) and the existing evidence of beneficial effects in poultry. Having a full picture of how these novel dietary ingredients interact with the bird’s microbiota1, metabolism and immune system could develop new dietary plans that would enhance bird growth, maximise feed efficiency and protect the birds from diseases.
Therefore, the main aim of my study is to test the hypothesis that supplementing the feed of broiler chickens with citrus or cucumber extracts can improve gut health through the modulatory effects of the microbiota, metabolome2, and immune system under standard and E. coli lipopolysaccharide (LPS) challenge conditions; LPS being an endotoxin able to stimulate the innate immune response. To investigate the aims, two in vivo trials have been carried out at Cochno farm, in Glasgow, to explore if each dietary supplement influences:
• the growth performance of healthy chickens (zootechnical data);
• the intestinal microbiota of healthy chickens;
• the gut morphology of healthy chickens (histology-morphometric measurements);
• the immune system of challenged chickens (acute-phase proteins investigation);
• the metabolome of challenged chickens (metabolomics study).
MY PROJECT SO FAR
During my first year at the University of Glasgow, I ran two in vivo trials on broiler chickens. The basal diet used in the trials was formulated and prepared at the Nuscience company in Belgium, while the experimental extracts (citrus and cucumber) were blended with the control diet directly at Cochno farm. During the trials, various biological samples (e.g. tissue and blood) and zootechnical data were collected to evaluate the growth performance of chickens depending on different dietary regiments (control, citrus or cucumber).
Samples collected from healthy chickens were used to study the microbiota and evaluate the microbial population at gut level of healthy chickens during a period of 28 days. The connection between the status of intestinal villi and the microbiota, as influenced by the diet, was also evaluated through a histology study based on the assessment of morphometric measurements at the gut level.
Samples collected from chickens challenged with E. coli LPS were used to study the acute phase response (APR), evaluating some biomarkers of toxicity (acute phase proteins, APP, in plasma) to understand the effects of LPS on the immune system of chicken fed with different diets. Novel APPs will also be explored and assessed in collaboration with Life Diagnostics, USA, a company partner of my PhD project.
Next year, my study will mainly focus on metabolomics at the University of Zagreb, where the unexplored metabolome of challenged chickens will be used to identify metabolites that could be used as biomarkers of health.
HOW DOES BEING PART OF AN MSCA ITN IMPACT ME?
Having a chance to participate in an MSCA ITN such as the MANNA programme is one of the greatest professional experiences an Early Stage Researcher could have and will remain a milestone of my career’s development. MANNA is giving me the opportunity to link Animal Sciences to OMIC technologies, expanding my scientific prospects as a researcher.
I had the opportunity to run in vivo trials on chickens, increasing my knowledge on nutritional and management requirements to conduct a good experiment on the animals. I also had the opportunity to carry out experimental feed planning and production on my company’s secondment in Belgium (Nuscience), which allowed me to integrate academic and commercial interests.
MANNA is providing me with the opportunity to participate in trainings and conferences that boost my knowledge in Animal Sciences in association with OMIC technologies while also improving my communication and scientific skills.
Next years, I will travel to my second university (University of Zagreb) and one of my industrial partners (Life Diagnostics) to carry out part of my PhD work. So I will have the opportunity to work in different laboratories and environments. Through these collaborations, MANNA will offer me a real-world experience, which is very useful in building my future as a researcher.
1 Microbiota is formed by ecological communities of commensal, symbiotic and pathogenic microorganisms found in and on all multicellular organisms studied to date, from plants to animals.
2 Metabolome refers to the complete set of small-molecule chemicals found within a biological sample (blood, urine, faeces).
EARLY STAGE RESEARCHER OF THE MANNA PROJECT 3
PARTNERING WITH THE NON-ACADEMICS: IS IT AS EASY AS ON PAPER?
PhD training in neglected tropical diseases (NTDs) – The necessary and challenging collaboration between academic and non-academic institutions.
EuroLeish1, an MSCA ITN focusing on the control of parasitic disease leishmaniasis, organised a thought- provoking session during the 12th European Congress of Tropical Medicine and International Health (ECTMIH) in Liverpool, UK in September 2019. Although there are good reasons behind the recent shift towards collaboration between academic and non-academic partners, the experience and lessons learned rarely get the spotlight. The aim of this session was to have a frank discussion about this topic, based on the fellows’ experiences. This was relevant, as at least 4 out of the 15 PhD projects within the EuroLeish network (2015-2018) were designed with partnership in mind. These non-academic partners range from private pharmaceutical companies, small-to-medium enterprises (SME) and non-governmental organisations (NGO). They were involved since the beginning of the network and played an active role, including training and secondment of the fellows for a period of maximum 11 months (remember that mobility clause?).
EuroLeish was ambitious, with its slogan “control of leishmaniasis, from bench to bedside to community," incorporating basic, translational and implementation research projects. The project drew from different scientific disciplines (i.e. molecular biology and epidemiology, drug discovery, vector control and immunology) but focused on a common goal, leishmaniasis control. As of end-2019, 10 PhDs were successfully completed.
In the session in Liverpool, Aya Hefnawy and Joana Pissarra, who worked respectively on drug resistance and developing a new vaccine, presented their experience about collaborating with pharmaceutical companies. Aya worked with GSK, using one of their compounds to explore the utility of including drug resistance studies early on in the R&D pipeline for a new anti-leishmanial drug. She described how the company’s policy also applied to her: results must be scrutinised and greenlighted, often much earlier than public presentation is made or a paper is out. Her thesis is still under embargo for that very reason. Joana was supposed to visit the company’s facility but due to mishaps in coordination this could not take place.
As experienced by Bruno Hinckel, whose PhD was mostly based at an SME, the pros include well-equipped laboratories and infrastructure fitting to the corporate culture. However, the ‘academic’-driven evaluation – e.g. in terms of a rigid publications target – seems to neglect transferable skills obtained in a different cocoon. Temmy Sunyoto, whose PhD focused on access to leishmaniasis care in Africa, reported positive synergy with Médecins Sans Frontières’ advocacy wing, the MSF Access Campaign, especially in regard to being able to interact with the users of her research results. Secondment proved useful in sharpening her advocacy and science communication skills.
What stood out as the common good of being in a mixed academic and non-academic collaborative set-up was the breaking out from the silos, the possibility of glimpsing a different atmosphere, work ethos and situations besides an academic context. The incorporation of trainees’ mobility into the network, together with the commitment, strong affiliations and technology transfer between the participants, provided a highly synergistic framework for success. The pitfalls were many, but fellows coped by adopting a “what can't kill us only makes us stronger” attitude.
All the speakers noted that it is paramount that everything is well-defined from the beginning, avoiding administrative hassles. Secondment at these partners also involved meticulous planning related to clearances, and, if in another country logistical and administrative arrangements. The continuous engagements, in terms of annual meetings and retreats, proved to be useful also in solving communication issues. Furthermore, the experience gained in the non-academic partner was considered an advantage instead of a barrier, becoming an added value to their non-conventional PhDs. The fellows are now more ready than ever to take on new challenges!
1 The EuroLeish (http://www.euroleish.net/) project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie International Training Network grant agreement No 642609.
SYNTHETIC BIOLOGY AND BIO-ANALYTICS FOR THE FUTURE: RNACT
Developing a green economy is a top European priority. This creates an urgent need to train European researchers in the fields of synthetic biology and bio-analytics, focusing particularly on the ability to solve complex challenges in the design of relevant proteins. The Marie SkłodowskaCurie Innovative Training Network “RNAct - Enabling proteins with RNA recognition motifs for synthetic biology and bio-analytics” addresses this need by creating a comprehensive and crossdisciplinary consortium of 10 Early Stage Researchers (ESRs) at the forefront of their research. The RNAct project’s main goal is to post-transcriptionally regulate gene expression and to detect specific RNAs by designing and characterising proteins containing RNA Recognition Motifs (RRM), which are regions that recognise these biomolecules.
RNAct brings together seven beneficiary institutions from five different European countries. Four academic organizations (VUB, CNRS, CSIC, and HMGU) and three companies (Giotto Biotech, Dynamic Biosensors and Ridgeview Instruments AB) join forces with the support of six partner universities (University of Liège, Lorraine University, Technical University of Munich, University of Florence, Polytechnic University of Valencia and Uppsala University) to build up a highly interdisciplinary network to tackle the ambitious goals of the project.
THE COMPUTATIONAL/ EXPERIMENTAL BINOMIAL
The project promotes and integrates interactions between the computational and experimental fields as well as academic and industrial settings. ESRs 1-5 are developing computational methods whereas ESRs 6-10 are working on in vitro and in-cell experiments. All the data and results obtained from both sides are integrated in a central database, favouring the cross- fertilisation of wet and dry disciplines. On one hand, computational and experimental ESRs will be paired with each other to gain interdisciplinary insights through buddy visits; on the other hand, secondments will allow the fellows to be exposed to innovation both in academy and industry.
THE WORK PACKAGES
The RNAct research is organised in three connected scientific work packages to accomplish the main goals of the project:
Work package 1 aims to design and characterise RRMs. The ESRs will work with proteins containing one RRM and proteins containing several of these domains.
Work package 2 aims to represent and design dynamic proteins. Since dynamic regions of proteins adopt different conformations, obtaining accurate in silico structural models from experimental data is a difficult challenge. Here the ESRs will integrate experimental data in computational approaches at the protein sequence, structure and interaction levels, and will study how these data can be actively used for protein design.
Work package 3 is focused on the bio-analytics and synthetic biology fields. The ESRs will test the designed RRMs in cells and will incorporate them in biosensors to detect specific RNAs. All the results generated in this part will be useful to keep improving the RRM design cycle.
THE DESIGN CYCLE IN A NUTSHELL
The three work packages are connected in a yearly design cycle. This ‘RRM design cycle’ starts with computational approaches at the sequence and structure levels of proteins and RNA. In this way, we identify positions and mutations along the proteins and check how they might affect the RNA binding. After an experimental validation with high-throughput methods, the best performing RRMs will be further investigated at the atomic level with structural biology approaches and will be applied in (i) synthetic biology (e.g., incorporate an RRM in bacteria to enable post-translational regulation) and in (ii) bio-analytics (e.g., incorporate the selected RRMs in disruptive technologies such as switchSENSE® and LigandTrace® to detect specific RNAs in vitro and in vivo, respectively). RNAct introduces new elements in existing computational approaches to enable the incorporation of protein dynamics and RNA interactions in protein design, and connects this new computational methodology via a tight feedback loop with experimental approaches at the molecular and cell levels.
All the ESRs have started working on their respective projects and InteR3M, the first version of the database, is already up and running. It includes all the available information about RRM and RNA binding, and all the ESRs will provide new data from their computational or experimental assays to keep improving it.
The RNAct ESRs are now reaching their scientific cruising speed and are ready for the challenges ahead by collaboratively looking for the best solutions and innovations in both the synthetic biology and bio-analytics fields.
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ANNA PÉREZ-RÀFOLS (Giotto Biotech, firstname.lastname@example.org)
JOEL ROCA-MARTÍNEZ (VUB, email@example.com)