BIYSC project category: Life Sciences

Can today’s agriculture and food systems feed a world population that is projected to reach more than 9 billion by 2050? This is the 21st century challenge for agriculture: to produce more and better food to feed a growing population with a smaller arable land. To achieve this goal, we will need to increase food production by 70% by 2050 in a sustainable manner.

For thousands of years, farmers have selected crops based on their visible characteristics -the phenotype-. A slow process known as conventional breeding was approached to convert plants that compete well in the wild into plants that perform well in agriculture, producing an important decrease in genetic diversity.

How can 21^st century plant scientists help breeders and farmers to obtain more productive crops that, at the same time, are adapted to a changing environment? How can we solve the genetic bottleneck? The answer is in genomics research. In this project you will study the DNA of horticultural species in depth, using molecular biology, genomics and bioinformatics techniques, as well as cutting-edge technologies for genome editing such as CRISPR-Cas.

You will face the challenge of identifying the melon genes underlying different phenotypes, mainly variations in the ripening process and the carotenoid content. You will need to use genetic maps and molecular markers (SSR, SNPs), extract DNA and perform PCR reactions to uncover the genetic variability behind the studied traits. You will also apply bioinformatics tools to pinpoint the unknown genes. Finally, you will design a strategy, based on genome editing, to produce a melon with the desired phenotypic qualities.

With this challenge, you will learn about genomics and you will be able to propose solutions to a real agricultural challenge -the post-harvest loss due to early ripening-, and to produce vegetables with healthier nutrients –carotenoids–.

Join this project and be part of a real agriculture case investigation!

Learning objectives

• To discover the latest molecular biology and genomics tools, used in plant breeding research as well as in other disciplines that make an extensive use of the molecular biology.
• To learn about the cutting-edge biotechnology that is behind the food we eat.
• To think as a researcher. In particular, at the end of the project you should be able to predict a phenotype using molecular markers and to identify candidate genes for important agronomic traits.

Matching profiles

Biotechnology, genetics, biology, agriculture

Required materials

Labtop, labcoat

This project will bring you to the most fundamental and challenging questions in cancer: what caused a tumor and how to fix it?

By using state-of-the-art genomics and epigenomics methodologies you, together with your team and top researchers in the Josep Carreras Leukaemia Research Institute, will process and analyze real samples to peer into its genomic and methylome alterations, two of the strongest driving forces of malignant transformation.

In the first part of the project, you will join our T-cell Acute Lymphoblastic Leukemia researchers to know more about the disease and start processing a set of real samples for sequencing, using standard molecular biology procedures. In the second part, you will join our researchers from the Cancer Epigenetics Lab and understand what epigenetics is all about and why its alteration may turn cellular identity upside down. You will further process the samples to get its full methylome and complement the information given by the genomics approach.

At the Genomics Core Facility of the Josep Carreras Institute, you will help our technical staff in the final processing of your samples and understand how to extract all those information from them. With their help, you will analyze the results and discuss on the potential origin of the disease and possible personalized therapeutical strategies.

Learning objectives

• Learn the basics of translational cancer research and the huge potential of molecular information for diagnosis and therapy selection
• Get basic skills in standard molecular biology protocols of DNA extraction and high throughput sequencing.
• Understand and get familiar with the research environment through direct contact with actual researchers and scientific discussion.

Matching profiles

Students with a strong interest in biomedicine and life sciences research will get the most of the course. Also, students interested in medicine and bioethics will have the opportunity to participate in debates on privacy and the limits of genetic information in the clinic.

Required materials

Laptop and lab coat.

Planarians show an unlimited capacity to regenerate, and they have fascinated naturalists for more than 200 years. In the 19th century, they were described by Dalyell as “immortal under the edge of the knife”. But it has been in the last 40 years when the genetic tools have allowed the understanding of the mechanism underlying this plasticity. In fact, it was a professor in our Department, Dr. Jaume Baguñà, who first had the idea to study the genetics of planarians, and we are now the heirs of these pioneer studies.

We know now that planarians have this amazing plasticity because they show a huge population of pluripotent adult stem cells, which are distributed all along the planarian body and can give rise to any planarian cell type. However, not only stem cells are required, but they also need to communicate with each other to instruct their cell fate; to know if they have to proliferate, to die, or to become a neuron.

The impressive thing is that all the genetic and molecular mechanisms that are known to be important for planarian regeneration are conserved in all animals, since the way of communicating between cells is evolutionary conserved. Thus, by understanding planarians’ regeneration we can also go further in understanding why humans cannot do it.

During this project, we will cut planarians in pieces and we will observe and analyze their process of regeneration. We will collect data about the growth of the new tissue, the recovery of the nervous and the visual system, the activation of the proliferation…. And not only that, but we will also study the same parameters in planarians in which a ‘mysterious’ genetic manipulation has been previously done. During the last days of the course, you will have to integrate all the data and analyze it, in order to explain the process of planarian regeneration in detail and to make a hypothesis about the role of the ‘mysterious’ genes that were manipulated.

The different sessions will consist of 1) Theoretical learning of the basics of planarian regeneration and the tools to be used, as gene inhibition by RNAi, which is the main tool in planarians to understand gene function; 2) Learning to manipulate and image planarians in a stereomicroscope; 3) Cutting planarians and follow the process during several days; 4) Performing immunostainings to analyze internal organs during regeneration and learning  the basics of immunofluoresecence; 5) Analysis of the visual function through observing planarian behavior in a chamber with a localized source of light; 6) Collect and analyze all the data to make conclusions about the process of regeneration in normal animals and in the ones in which the ‘mysterious’ genes have been inhibited, 7) Make a hypothesis about the function of the ‘mysterious’ genes; 8) Final discussion.

All the data collected will be analyzed and statistical analysis will be applied in order to draw conclusions and acquire new critical thinking and problem-solving skills. The data will be contrasted to the current literature. Students will formulate a hypothesis and think about strategies to apply the knowledge gained in planarians to improve human health.

Learning objectives

• To handle planarians and to work with them as a model organism to study stem cells and regeneration.
• To learn the scientific method.

Matching profiles

• Biology
• Genetics

Required materials

Labcoat and laptop

From the whole population, almost 70% of adults will suffer a highly stressful experience at least once in their lives. Stress and trauma are everywhere around us affecting our body, our brain, and our emotions. Despite being considered something negative, stress is an important reaction of our body that allows us to face real-life challenges and threats in order to keep us alive. Researchers and doctors are very interested in studying the mechanisms that regulate the stress response because their dysfunction results in damaging consequences for our health may trigger the appearance of mental disorders. One example is Post-traumatic stress disorder (PTSD), a very common mental disorder that may appear in some vulnerable individuals after experiencing a highly stressful event. People living with this disorder have disabling symptoms related to a deficient detection and management of threats in the environment, they also have strong and recurrent memories about their traumatic experience and some of them present considerable changes in their behavior that keep them hyper-alert and ready to avoid any cue related to their trauma. Importantly, these disorders are much more common in women compared to men and scientists still don’t understand why this is happening. Our research group is interested in knowing which neurobiological factors are making women and females more vulnerable to the effects of trauma and this time we are inviting you to join us in this journey.

In this project, students will work hand in hand with neuroscientists that use animal models to understand how stress affects behavior and brain function. They will acquire competencies to observe and analyze different kinds of behavioral tests that evaluate the levels of anxiety, exploration, memory, and social interaction, among others. They will explore how sex hormones interact with stress and try to rescue these negative alterations of behavior by using different pharmacological approaches shortly after trauma. Additionally, they will be able to evaluate the expression of crucial biomarkers of stress using biomolecular techniques. Using immunodetection assays, brain structures will be explored at a neuronal level, trying to identify which areas are the ones affected by stress. 

During this project, students will learn about the impact of stress on the brain and gain the ability to make their own future hypotheses. They will use state-of-the-art techniques widely used in Neuroscience and collaborate with scientists in their day-to-day. Also, they will acquire data processing and analysis skills which are crucial for any modern scientist. We expect students to be highly motivated to learn about brain function and how it processes stressors. With their work, they will contribute to the understanding of brain function and stress processing, specifically in females.

Learning objectives

• To study brain’s responses to an acute stressor
• To learn about several laboratory techniques, such as molecular biology and histology
• To analyze behavioral data 
• To interpret the results

Matching profiles

• Motivated by science and research
• Highly enthusiastic and collaborative
• Basic background in biology is recommended

Required materials

• Lab coat
• Personal laptop

This course aims to immerse students in the fascinating world of synthetic biology, uncovering the secrets of CRISPR/Cas9 technology and the art of crafting genetic devices that push the boundaries of what living cells can achieve. These groundbreaking devices empower us to modify the behavior of living cells, enabling them to carry out functions beyond their natural capabilities. In essence, students will explore the exciting field of cell reprogramming, gaining hands-on knowledge of shaping living organisms for innovative purposes.

Block 1: Introduction to Synthetic Biology.

1. Basis of Synthetic biology.
2. Introduction to genetic device design.
3. Computational simulation of designed devices.
4. Introduction to basic safety standards in the laboratory.
5. Introduction to experimental DNA modification techniques:

1. CRISPR/Cas9 technology.
2. DNA cloning and bacterial transformation.
3. Cell culture.
4. Electrophoresis.
5. Scientific communication:

1. Scientific journals and bibliography search.
2. Scientific presentations and posters.

Block 2: Crafting a Cellular Biosensor System.

The objective is to engineer a cellular device capable of synthesizing a fluorescent protein in response to external signals. To accomplish this, students will need to:

1. Design the proposed genetic system.
2. Experimental construction and characterization in Escherichia coli

Block 3: Precision Gene Disruption with CRISPR/Cas9 Technology.

The objective is to acquire an understanding of how CRISPR technology facilitates modifications within the targeted DNA region, specifically in this case, by disrupting the coding sequence of specific genes. To accomplish this, students will need to:

1. Engineer each CRISPR/Cas9 component
2. Experimental construction and characterization in the selected cell type.

Practical work

Small workgroups will be organized for hands-on experimental work in the laboratory. Optionally, each group may choose to prepare a scientific poster showcasing their results, which will be presented to the rest of the students. The findings will be further discussed in a round table format, encouraging collaborative analysis and insights.

An integral component of the course entails continuous monitoring of students to evaluate their progress consistently throughout all sessions.

Learning objectives

General Learning Objectives:

• Enhance teamwork skills.
• Cultivate effective communication and dissemination capabilities.
• Acquire proficiency in working within a multidisciplinary field that merges engineering, mathematics, computer science, and biology.
• Foster patience and perseverance in the workplace.

Specific Learning Objectives:

• Adhere to basic laboratory safety standards.
• Develop competence in handling fundamental laboratory materials.
• Master the design of genetic devices.
• Understand the use of CRIPSR/Cas9 technology to achieve DNA modifications.
• Utilize computational simulation methods for experimental design.
• Acquire proficiency in genetic manipulation techniques.
• Gain expertise in the preparation of posters and delivery of scientific presentations.

Matching profiles

This project is designed for students who possess:

• Elevated curiosity and a capacity to engage in multidisciplinary projects.
• Strong teamwork skills.
• Foundational knowledge in computer sciences, mathematics, and biology.
• Demonstrated creativity.
• High motivation in both scientific and engineering pursuits.

Required materials

• Laptop
• Lab coat (provded)

During this project, we aim to mimic the long process that starts with basic research all the way to the clinical application of the knowledge gained. We can divide the project into three main steps. First, we will learn about many different genetic tools researchers can use to study the putative genes involved in tumor formation. Second, we will hypothesize, based on the published literature, on the genes and processes implicated in tumorigenesis. Finally, we will propose a working model and search for a way to revert the phenotypes of this disease.

Our starting point will be to learn about the history of the fruit fly in research and understand the particularities of its biology. Nonetheless, this will be a full hands-on experience so we will also explain how to handle the flies, and which are the most important and interesting genetic tools that can be used to manipulate the genome of this model organism.

Students will also be taught how to search for information about cancer, the genes that are involved in this disease, and the main pathways responsible for the tumorigenesis process. From this, they will discover which databases they should use to find the best scientific publications and also repositories that store information about Drosophila melanogaster.

We will also take advantage of established Drosophila melanogaster transgenic flies that express disease-related genes. Using a well-established genetic tool, we will be able to express these genes in specific populations in order to study their effects. To examine the phenotypes shown by the diseased flies and to compare them with that of healthy flies, we will use various techniques such as immunostaining. In order to visualize our immunostainings, we will also go over the basics of confocal microscopy and we will use cutting-edge confocal microscopes. As the last step, students will analyze all the data obtained and perform statistical analysis in order to draw conclusions and acquire new critical thinking and problem-solving skills. They will formulate hypothesizes and think about strategies to decrease or abolish disease related phenotypes, as they do so, they will learn how to perform rescue experiments in order to test their proposed questions. The conclusions obtained from this kind of basic research studies are the first stone of the common ground for later application to humans, to the ultimate benefit of society.

Learning objectives

• Stimulate critical and structured thinking and problem solving abilities
• Learn how to plan experiments and generate hypothesis
• Learn how to work with a model organism (Drosophila flies) to address different issues in biology: classical genetics, generation and use of mutant and transgenic flies
• Understand the processes that lead to tumorigenesis
• Extrapolate the obtain results in a model organism to what happens in a human context
• Be in contact with real techniques performed in labs nowadays (dissections in vivo, immunostainings, advanced microscopy, image processing, statistics, mutant CRISPR generation, genomic PCR and sequencing…)
• Undestand the work behind research: idealization of the project, posing questions and hypothesis, analysis of data and crafting a presentation (storytelling)
• Learn how to work in a group

Required materials

Labcoat and laptop