S3++ 2015

Požega, July 25th - August 4th

Projects Workshops Lectures


Testing of Developmental Neurotoxicity by in vitro methods

The exposure to industrial chemicals, pesticides (like glufosinat ammonium) and drugs during the early childhood cause the increasing incidence of neurodevelopmental disorders worldwide. However, due to the lack of studies, only several industrial chemicals have been identified as developmental neurotoxicants so far. Hence, our assignment will be to prove possible developmental neurotoxicity of glufosinate ammonium which is one of the ingredients in the nonselective herbicides with suggested in vitro and ex vivo neurotoxic effects (like the cytoskeleton pesticides-induced deterioration) on the brain during the early childhood.

The experimental approach will be related to in vitro aspects (cell culture) of our neurotoxicologic studies, allowing us to analyze post-translational impairments and their consequences at the cellular level of the tumor cell culture obtained from a rat C6 glioma. In order to evaluate cellular proliferation, migration and viability of C6 cells exposed to different concentration of pesticides and their metabolites, MTT test will be performed. In addition, SDS-PAGE and Western blot analysis will be performed on proteins like GAPDH and MAP2 to inspect effects of pesticides on these proteins.

Iva Salamon
University of Zagreb/ Faculty of Science and University of Orleans, France

Iva is a student of molecular biology, enrolled in the Bioindustrial Techniques (Techniques Bio-Industrielles) Programme jointly implemented by both the Faculty of Science in Zagreb, Croatia and the University of Orléans, France. Currently, she is working on her Master thesis in the field of neuroscience/neurotoxicology. Her dominant research interest targets the understanding of genetic, cellular and molecular basis and mechanisms that have an important role in normal neurodevelopment, neurodegenerative impairment and disease progression. In her free time, Iva likes to cook, watch movies, and just chill out with her friends.

Life of a web request. How the Internet works?

The Internet is becoming one of the most important tools people use to read, do and share research, messages and ideas. Many people use it as a tool, but not everyone really understands how the Internet and the networks work, evolve and keep spreading their influence. The Internet is by itself a very vivid subject of research related to the domain of distributed systems with very active and open research, mixing industry and academy. Making computers talk to each other seems obvious today, but network protocols, enabling us to do so are the results of a long process involving engineering and scientific research.

The goal of this project would be to study, understand and recreate all protocols that make the Internet the way it is. We will study the Internet’s structure and protocols through experiments and dissection of network activity. We will use and write programs to explore what happens at the networking level as you surf the Web, use a search engine, send emails and more. All these protocols would be tested and in the end, students would be able to craft a little Internet system working within their own network.

Rémy Léone
Telecom Paris Tech, France

Remy is a PhD student working at Telecom Paris Tech in the field of Wireless Sensors Networks. His research interests are passive monitoring of networks, active estimation of energy reserve and lifetime expectancy of a network. Remy was a student of S3++ in 2007 and a member of Paris Montagne Association since 2006. This association is involved in the spreading of science popularization among the youngsters by giving a flavor of scientific research.

Percolation - An insight into random systems

For the majority of us brewing coffee or tea by pouring hot water over the filter containing coffee or tea is an everyday activity. Underlying the filtering part is the process of percolation, which refers to fluid flow through porous materials. Lets imagine a block of such a material. If we pour some liquid on it, will it be able to move from hole to hole until it reaches the bottom? A mathematical model known as the percolation theory gives the answer to this question. Due to its simplicity and robustness this model also found an application in a wide variety of other problems ranging from the conductivity of materials, biological evolution, epidemiology, all the way to the formation of galaxies.

To begin the project we will design a toy model in 2D, which will help us in understanding the basic properties of percolation. The project will be realized both experimentally and through a computer simulation in the C programming language. Simultaneously, we will get acquainted with the basics of statistical physics and other relevant theoretical aspects. The gathered knowledge from the first part will be important in understanding the phenomenon in a more complex system, which will ultimately present the second part of our project. We will design an experiment to observe a percolative phase transition in a 3D material and determine the critical exponents predicted by the renormalization theory.

Toni Marković
University of Zagreb, Croatia

Toni is a 4th year physics student at the University of Zagreb, Faculty of Science. He was a Summer School participant three times (S3 2009, S3++ 2010, 2011) and a swapshop leader (S3 2012). Although he spent his last summer working in the field of biophysics, his interests have shifted to a solid-state physics. Playing basketball and video games preoccupies a good amount of Toni’s free time. He also enjoys learning tricks, solving puzzles, reading fictional books and cycle. Not at the same time, though. That would be dangerous.

Automating Biology - An End to End Approach

The inability to reproduce the majority of results in the biological research has long been the “elephant in the room”. With the cost of research and development skyrocketing, it is critical that we address the issue of reproducibility. Presently, there are many interesting approaches being used to tackle the problem; such as ‘reducing inconsistencies’ by defining standard formats to share the resulting data of biological research, ‘minimizing human-error’ by automating the biological experiments and removing the person-to-person variability while carrying out experiments and finally ‘improving communication’ by making the scientific data more accessible to everyone.

In this project, the students will learn about the approaches used to minimize the ambiguity in biological research. There are different approaches being developed to automate biological experiments and we will learn something about the hardware platforms currently used (microfluidic devices and pipetting robots). We will attempt to address the above mentioned problems of reproducibility by drawing upon from different paradigms of computer science. In this regard, we will discuss a simple programming language that we are currently developing, capable of describing biological experiments and the subsequent automated execution on different platforms. The students will describe biological experiments in an easy-to-use programming language which will allow them to learn the different ways of conducting experiments in biology, as well as what transformations experimental protocol needs to go through in order to be automated.

Vishal Gupta
Technical University of Madrid, Spain

Vishal has a bachelor’s degree in biotechnology and a master’s degree in nanobiophysics. He is presently pursuing his PhD in a field of Artificial Intelligence at the University of Madrid. Scientifically, he likes a mix of biology, physics and engineering. When he is not working, he likes to read, dance, cook and travel.

Ismael Gomez Garcia
Technical University of Madrid, Spain

Ismael obtained his bachelor's degree in mathematics at the Universidad Autónoma de Madrid in 2011. In 2012, he also obtained his bachelor's degree in computer engineering, followed by a master’s degree in computer science at the same University. Now, he is doing his PhD on a directed evolution and microfluidics automation, with particular focus on topics related to bio-lab automation and modeling of evolutionary processes. When he is not working, he likes playing football, reading and listening to music.

Making of the Limbs: From Pinkies to Thumbs

Embryonic development is a very tightly controlled process. Many genes need to be expressed at the right time, right place and right amount in order for the proper formation of body parts. If we look at our hands, most of us are born with five fingers on each hand. The structure of our hands allows us to hold pipettes, type on computer and do many other things. Even though some people have long slender fingers and some have short stubby fingers, the size proportion between fingers and the organization of fingers are similar. Nonetheless, some people are born with hand abnormalities, such as fused, extra or missing fingers. Understanding the genetic mechanism behind the hand formation will not only provide possible clues to the cause of these hand abnormalities, but will also aid in the quest of comprehending the process of limb regeneration.

In this project, we will investigate the gene expression patterns in normal mouse limb development. First, we will use in situ hybridization techniques on tissue slides to map out and visualize the temporal and spatial expression domains of different genes involved in limb formation. The students will learn the basic concept of embryonic development with the focus on the limbs. They will also be introduced to in vitro RNA visualization methods. Next, we will explore the consequences of the certain genomic aberration on limb development by studying some human syndromes manifesting as limb abnormalities. The students will learn the concepts of long-range gene regulation by enhancers. They will learn how to validate the mutations by PCR and gel electrophoresis. Through these exercises, the students will gain insights into common lab techniques and thought process used in developmental biology.

Leslie Pan
EMBL Heidelberg, Germany

Leslie is doing her PhD at EMBL Heidelberg, studying chromosome dynamics of long-range enhancers and its target genes. She obtained her bachelor’s degree in Chemistry/Biochemistry from University of California, San Diego. She worked as a clinical trial coordinator before her studies at Karolinska Institutet. She can be found in restaurants trying out new food, or in her flat reading non-fiction books and watching cartoons in order to learn German. This will be the first time she is participating in the Summer School.

Crystal growth: An experimental approach

Even if we are not aware of it, crystals are everywhere in the nature. Minerals, snowflakes, even the table salt, they are all made of crystals! But they are not just pretty things made by nature. Crystals and especially crystal growth are essential for mankind. For example, most of our medicines are made by crystal growth. In order to have useful and harmless medicines, we need to perfectly master this process. Crystal growth is also used for jewelry, food development and even for military applications! Scientific fields which use crystals are quite abundant and diverse, ranging from the creation of medicines to the improvements in the food development, and will continue to grow in the future.

This project is formed out of two parts. First we will discover how a crystal is made, (mainly theoretical properties will be covered, such as construction of crystal structure). Then, we will investigate how crystal growth works by doing chemistry. In this part, we will grow several crystals from different components to see possible forms and colors and finally the completion of the crystal growth. We will study the importance of this process and particularly the role of possible modifications, which can be of special importance in the pharmaceutical industry. Finally, formed crystals will allow us to establish links between theoretical and experimental concepts in crystal growth.

Juliette Piquard
University of Grenoble, France

Juliette is currently doing a PhD in crystal growth at University of Grenoble. She is particularly interested in characterization of the matter of the crystal compartment. In her free time, Juliette likes to read books, watch movies and play games. Also, she draws a lot, especially comics. She is involved in a club that popularizes science, with special focus on chemistry. Juliette has already participated in the Summer School in 2007 when she was involved in an astronomy project.


Round table - Careers in Science


Kristian Vlahoviček

Kristian Vlahoviček studied molecular biology at the University of Zagreb, Croatia and obtained his PhD in Bioinformatics, working on a prediction of physicochemical properties of DNA. He spent 10 years as a research fellow at the International Center for Genetic Engineering and Biotechnology in Trieste, Italy. He established a computational biology group at the Zagreb University in 2002, where he moved permanently in 2006 with the EMBO Young Investigators Programme installation grant. He teaches computational biology and bioinformatics at the Division of Biology, and is also an adjunct associate professor at the University of Oslo, Norway. His bioinformatics group develops computational tools and uses machine learning techniques to tackle open questions in developmental genomics and metagenomics.

Research swapshop

Lab troubles -The protocol isn't good enough? Let's change it!

Nowadays every major biology study demands molecular research. One of the basic methods in molecular biology is the isolation and analysis of DNA. The protocol of DNA isolation might seem terrifying since the isolation protocol consists of many long named chemicals. However, the application of biochemistry allows us to understand the different mechanisms of chemicals affecting a cell. Once we understand these mechanisms, we can change the protocol to serve our needs.

Swapshop leader: Lara Vrbanec, University of Zagreb

Frozen: Cryogenics and temperature control

Cryogenics is the physics of phenomena associated with matter at very low temperatures (below -150°C). Whether the goal is to study effects in materials, cryopreserve cells or entire organisms, research superconductivity or perform cryosurgery; it is of vital importance to learn how to keep and handle liquefied gasses. This workshop aims to provide explanation and understanding of a set of experiments with liquid nitrogen, including making your own ice-cream.

Swapshop leader: Nives Bonačić, University of Zagreb

Mad Scientist On A Budget: Rule The (Virtual) World!

Programming is an invaluable skill in all fields of today's scientific research. And it is the most useful tool a mad scientist on a budget has! It allows for cheap and efficient model based experimenting and tackling complexity by clever visualization and automated pattern matching. Join me on this workshop and learn how to install the Python programming language, along with the most popular scientific library SciPy, and then take your first steps into programming based experiments with a viral spread simulation. We will model a real viral infection and see (really, with a video!) how long it takes to infect the entire population and then introduce vaccinations and use the computer to calculate the herd immunity threshold and see how it changes based on the properties of the vaccine and the virus.

Swapshop leader: Marko Ivanković, Google Zurich

Treasure hunt

Metal detectors are electronic devices that enable the detection of hidden metallic objects. As such, they are used for various purposes such as archaeology, airport security, civil engineering and, most importantly, to detect lost coins or jewelry on a beach. Most metal detectors are electronic oscillators, which is why we will first go over the necessary theory of complex impedance and resonant circuits, and afterwards the students will construct their own metal detector and try their luck on one of Požega's lawns.

Swapshop leader: Marija Došlić, University of Zagreb

Bird field research and wildlife conservation

Birds are amazing! They fly, they are colourful, they sing and they migrate. Due to the various patterns of their behaviour, lifestyle s and distribution plethora of methods for bird research exists. It does not matter if you interested in their migration patterns, partners choice, breeding dispersion, food preferences or in everything mentioned, you will find a method to find what you are interested in, or at least find an expert who will help you. We will go through various birds field research methods, some of which are quite basic and old and some of which are relatively new and offer great potential for further development. We will connect the method with wildlife conservation science so you could see the direct application of methods in the real life.

Swapshop leader: Vedran Lucić, BIOM


Lecture schedule

July 26th 2015
Sara Martínez de Lizarrondo (University of Caen Lower Normandy, France): How Microparticles derived from cells patch brain hemorrhage?

July 27th 2015
Ross King (Manchester Institute of Biotechnology, UK): Can a Robot do Science?

July 28th 2015
Milena Estorniolo (École des Hautes Études en Sciences Sociales, France): Anthropologist view on lifestyle of Baniwa people

July 29th 2015
Domagoj Vucic (Genentech, USA): Targeting inflammation in tumors and tissue damage diseases: from caterpillars to bed side

July 31st 2015
Wolfgang Huber (EMBL Heidelberg, Germany): Data driven! Adventures in computational biology, genomics and personalized medicine

August 2nd 2015
Thomas Fleischer (Oslo University Hospital, Norway): Epigenomics in breast cancer: Tumor development and clinical application

About the lecturers

Sara Martinez de Lizarrondo, PhD
University of Caen Lower Normandy, France

Sara Martinez de Lizarrondo, a biochemist/biologist native of Spain, obtained the European-PhD in Cellular and Molecular Biology in the Atherosclerosis and Inflammation laboratory of the Center for Applied Medical Research, at the University of Navarra. Her thesis was focused on the role of MMP-10 (a member of a protease family responsible for extracellular matrix degradation) as a link between inflammation and thrombosis. Sara is currently working as a postdoctoral fellow in Pr. Denis Vivien’s Laboratory (UMR-S INSERM U919 Unit) at Caen, France, a group leader in the stroke field. One of its main objectives is the development of original tools for both diagnosis and therapy of stroke. Sara’s work aims to use Microparticles, also called MPs, as haemostatic patches to stop bleeding in patients suffering from a brain haemorrhage. She recently received one of the 2014 L’Oréal-Unesco French Postdoctoral Fellowships for this project. Her main achievements are related to the field of cell-derived MPs, in particular regarding their roles in thrombosis and haemostasis.

Prof. Ross King, PhD
University of Manchester, UK

Ross D. King is Professor of Machine Intelligence at the University of Manchester, UK. His research interests are in the interface between computer science and biology/chemistry. The research achievement he is most proud of is originating the idea of a “Robot Scientist”. His work on this subject has been published in top scientific journals, and has received wide publicity. He spends his weekends walking along the Welsh coast.

Milena Estorniolo, PhD
École des Hautes Études en Sciences Sociales, France

Milena Estorniolo did her graduate studies in Social Sciences and her Master in Social Anthropology, both at the University of São Paulo (USP), Brazil. Currently, she is a PhD student in Social Anthropology and Ethnology at the École des Hautes Études en Sciences Sociales (EHESS) in Paris, France. Member of the Amerindian Studies Center of the University of São Paulo (CEstA - USP) since 2008 and of the Laboratoire d’Anthropologie Sociale (LAS – EHESS) since 2013, she has conducted research in the Amazon on the relationship between the Baniwa people and the fish breeding techniques in the context of the upper Rio Negro fish farming project and how indigenous people related to science. She is also interested in food practices as a way of understanding the relation between the Baniwa people and non-human beings.

Domagoj Vučić, PhD
Genentech, Inc., USA

Domagoj Vucic, PhD, is a Principal Scientist at Genentech, Inc. in South San Francisco, USA. He obtained his B.S. from the University of Zagreb, Croatia, and his Ph.D. from the University of Georgia, USA. He completed his postdoctoral training in the laboratory of Dr. Vishva Dixit. Dr. Vucic’s laboratory investigates the biological role of modulators of signaling pathways (e.g. ubiquitination-mediated regulation of NF­kB pathways), and their involvement in cellular processes triggered by TNF family ligands and other pro­inflammatory stimuli. At Genentech, he is a Leader of a project that is developing compounds for blocking uncontrolled inflammatory responses and/or enhancement of the survival of damaged cells and tissues.

Wolfgang Huber, PhD
EMBL in Heidelberg, Germany & EMBL in Cambridge, UK

Wolfgang Huber leads a computational biology research group at the European Molecular Biology Laboratory (EMBL), with appointments at the Genome Biology Unit in Heidelberg and at the European Bioinformatics Institute (EMBL-EBI) in Cambridge. He is a co-founder of the Bioconductor project (www.bioconductor.org), one of the world's largest bioinformatics software projects. In his research, he develops bioinformatics and statistical methods for multi-omics. The research group aims to understand inter-individual differences by large-scale statistical modeling and integrating multiple levels of genomic and molecular information from individuals with their phenotypic variation in health and disease. Wolfgang obtained a PhD in theoretical physics from the University of Freiburg, before he went to work for IBM in the “Silicon Valley” (San Jose, CA) on cheminformatics. He moved into the field of bioinformatics in 2000 with a postdoc at the German Cancer Research Centre (DKFZ).

Thomas Fleischer, PhD
University Hospital Oslo, Norway

Thomas Fleischer is currently working as a post‐doc at the Norwegian Radium hospital in the group of Professor Vessela Kristensen, where he also obtained his PhD in association with the University of Oslo. His research interests lies in cancer epigenomics and genomics, with a focus on breast cancer. He has published articles that have contributed to the understanding of the role of epigenomics in development of cancer, as well as how DNA methylation markers may be used by clinicians for making treatment decisions.