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Short overview on CU trainings in January 2024.

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Under the umbrella of the STREAMLINE project, our partners from Cardiff University, United Kingdom held virtual training “Importance and best practice for Data Integrity”. The training was dedicated to participants from Western Balkan region. Topics covered during this training were what is data integrity, why is it important and how to incorporate the data from various resources and how to build a database. We use the opportunity to thank Prof. Adrian Harwood and Dr. Janet Harwood for organizing and sharing their experience.

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A special award for Dr. Danijela Drakulić and Dr. Nataša Kovačević Grujičić

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Since Yamanaka and Takahashi generated first human induced pluripotent stem cells (hiPSCs) from adult somatic cells in 2007, iPSCs have become a major tool in many areas of research, such as disease modeling, drug testing and development, and regenerative medicine. One of the most important advantages of iPSCs is that they maintain the genetic background of the host donor. iPSCs derived from patients with specific disorders, such as neurodevelopmental disorders, provide a unique in vitro model system for studying molecular mechanisms underlying their pathophysiology.

Our colleagues Dr. Danijela Drakulić and Dr. Nataša Kovačević Grujičić received a special award from IMGGE for introducing the methodology and the generation of first patient-specific iPSC cells in IMGGE and Serbia. We congratulate them on this award and hope that we will soon read a publication about their results related to iPSC cells derived from patients with 22q11.2 Deletion Syndrome.

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Short overview on UM trainings

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Thanks to the STREAMLINE project and our partners from the University of Maastricht (UM), participants from Western Balkan region had a great opportunity to participate in virtual training „Preparing and managing EC-funded projects/ project applications“. This training was organized in order to improve management and skills of both administrative staff and researchers. Like last year the training was divided into two Sessions – Session 1, hold on December 8th, 2023. and Session 2, hold on January 12th, 2024.

The first session was theoretical part of the training during which the participants had the opportunity to learn about funding alerts/tips and tricks as well as post-award management of EU grants. The second session was the practical part of the training. Through group practice, the participants presented how they would respond to different EU calls by implementing the knowledge they gained.

We would like to thank Prof David Linden, Marco Brandes, and Tom van den Crommenacker for the organization of these training and sharing valuable and practical information as well as tips and suggestions we received after the presentation of homework projects.

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STREAMLINE Bioinformatics Workshop “RNA-seq data analysis”

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December 11. – 15. 2023.

Over four decades ago, Frederick Sanger and his colleagues developed a method to decode the genetic information stored in DNA. The first human chromosome to be sequenced was chromosome 22 in 1999, and the first human genome was mapped in 2001 as part of the Human Genome Project. Over the past two decades, technologies for DNA sequencing have progressed rapidly. Nowadays, next-generation sequencing technologies allow rapid sequencing of millions of DNA fragments simultaneously, providing information about the structure of genomes, gene expression profiles, genetic variations, and epigenetic modifications. These technologies enable the development of targeted therapies and precision medicine approaches and facilitate studies on genetic diseases, cancer genomics, and microbiome composition. Consequently, there is a growing demand for bioinformatics approaches to analyze the big data obtained by next-generation sequencing technologies.

Thanks to the STREAMLINE project and our partner from the Maastricht University, over 50 participants from the Institute of Molecular Genetics and Genetic Engineering, University of Belgrade (IMGGE) had great opportunity to learn about new bioinformatics tools for RNA-seq data analysis. On December 11 to 15, 2023, Maastricht University and IMGGE organized online STREAMLINE Bioinformatics Workshop “RNA-seq data analysis” that included interesting topics and hands-on training. The lecturers were Dr. Friederike Ehrhart, Dr. Florian Caiment, Dr. Marcha Verheijen, Dr. Tooba Abbassi-Daloii, Dr. Martina Summer-Kutmon, and Dr. Susan Steinbusch-Coort (Maastricht University), and instructors for hands-on training were Dr. Friederike Ehrhart and Aishwarya Iyer from the Maastricht University, and Dr. Danijela Drakulic, Dr. Natasa Kovacevic Grujicic, and Stefan Lazic from the IMGGE. Academician Milena Stevanovic, STREAMLINE project PI, gave a warm welcome to participants, introducing them to the importance of the STREAMLINE project, and Prof. David Linden gave an overview of the workshop at the end of the training.

Topics covered during this workshop were: how to obtain raw counts from FASTQ files, how to obtain a list of differentially expressed genes from raw counts, and which tools to use for functional analysis and visualization of the results (WGCNA, WikiPathways, Pathvisio, and Cytoscape).

Thanks to all for joining us in the first kind of this workshop in Serbia.

Successfully completed STREAMLINE „RNA-seq data analysis“

On Wednesday, January 24th, we awarded the certificates to the participants of the STREAMLINE Bioinformatics Workshop „RNA-seq data analysis“ held from December 11 – 15 2023. We also announced STREAMLINE Bioinformatics Summer School that will be held in Thessaloniki in June 2024.
Once again, we want to thank everyone who participated in the workshop.

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Overview of the staff exchanges at Maastricht University

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Welcome back Dr. Danijela Drakulić, Dr. Nataša Kovačević Grujičić and Stefan Lazić! After almost two and a half months, members of the STREAMLINE team returned to Belgrade from their staff exchange at the Maastricht University, Netherlands. Their staff exchanges were dedicated to mastering the RNA-sequencing and bioinformatics data analysis and digitalized repository formation. They learned how to adequately isolate RNA for RNA-seq, perform library preparation and sequencing and how to check the quality of samples for RNA-seq. Staff exchange dedicated to bioinformatics data analysis covered the following topics: how to obtain „raw counts“ from FASTQ files and identify differentially expressed genes, how to perform gene set enrichment/overexpression analysis, Weighted gene coexpression analysis, data visualisation in pathways, and how to create pathway models with PathVisio, and network analysis using Cytoscape. They came back full of impressions and ready to implement acquired knowledge in our institute.

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Short overview on CERTH trainings held in November 2023

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Within STREAMLINE project researchers from Western Balkan region attended the trainings that were organized by our partners from Centre for Research & Technology Hellas (CERTH), Greece.
First training, “Proposal preparation for EU calls”, was devoted to the overall structure of the EU programme followed by descriptions of project proposal preparation, call documents, evaluation criteria, and then project management. Second CERTH training held in November, “Managing a research project”, gave insight and guidelines concerning management of EU-funded research projects and monitoring of its progress. The last training organized by our partners from Greese, “Improving soft/professional skills of ESRs” has been devoted to early stage researchers (ESRs) in helping them writing good quality research papers, with presentation of research at conferences, CV preparation. We would like to thank Dr. Spyros Petrakis, Ms Athina Karachaliou and Mr. Dimitrios Kaboukos for the organization of these events and sharing valuable and practical information with participants.

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22q Awareness Day

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November 22nd is the International 22q11 Day, with an initiative to increase awareness about 22q11.2 deletion syndrome (22q11.2DS)  by wearing a red wardrobe and lighting several buildings in red around Europe.

22q11.2DS is a genetic disorder caused by a heterozygous microdeletion of region q11.2 of chromosome 22. It is the most common microdeletion syndrome in humans with an estimated incidence of approximately 1/4000 per live births. After Down syndrome, 22q11.2 deletion syndrome is the second most common cause of developmental delay and congenital heart disease. There is a wide spectrum of clinical manifestations in patients with this syndrome, even within the same family. Approximately, 25% of patients with 22q11.2DS develop schizophrenia. Intellectual disability is detected in approximately 45% of patients with 22q11.2DS, while Autism Spectrum Disorder is seen in 14-50% of cases. It accounts for approximately 2.4% of people with developmental disabilities and approximately 10% to 15% of people with Tetralogy of Fallot (a type of heart defect). Males and females of all ethnic backgrounds are affected in equal numbers.

A diagnosis is quite challenging for 22q11 individuals due to their extremely diverse range of symptoms. Actually, 50% of people with 22q11 never receive a diagnosis. However, early treatment of the symptoms can lessen their severity, thus a person with 22q11 can have a far better life if diagnosed early. Additionally, early diagnosis helps educators better adjusting the learning environment, health experts better modify their treatments, and parents better preparing for the arrival of their kids. Increasing public knowledge will thus lead to earlier illness diagnosis and better treatment.

JOIN STREAMLINE team members in spreading the word about 22q11.2 deletion syndrome by wearing something red today.

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STREAMLINE PROJECT ACTIVITIES AT CARDIFF UNIVERSITY

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Two members of the STREAMLINE team, Mina Perić, PhD and Vanda Balint are currently on the staff exchange at the Neuroscience and Mental Health Innovation Institute in Cardiff, UK. They are learning how to make brain organoids from induced pluripotent stem cells (iPSCs). Our team members are also studying how to analyze neuronal electrical activity recorded on a Multielectrode array (MEA).

Uncovering the underlying cellular and molecular mechanisms of brain function will help us understand the biological basis behind human psychology. The nervous system is composed of two basic cell types: glial cells (also known as glia) and neurons. While glial cells provide mechanical, trophic, and metabolic support to neurons, the communication between neurons is fundamental to all of the functions associated with the nervous system. Neuronal communication is an electrochemical event. The Multielectrode array (MEA)-systems record, amplify, and analyze signals from biological samples in vitro. Cells are grown in specially designed sterile cell culture plates (containing embedded electrodes) and placed in the MEA instrument for analysis. Cellular functionality can be determined by capturing spontaneous electrical activity as presented in the movie below:

A cerebral organoid, or brain organoid can be described as an artificially grown, in vitro-generated cellular system or a miniature organ resembling the brain. Using human pluripotent stem cells to create in vitro brain organoids allows researchers to understand the developmental mechanisms and maturation of the nervous system. Brain organoids derived from patients’ induced pluripotent stem cells (iPSCs) can be used to investigate disease pathogenesis in the nervous system.

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Highlights from Data Protection and Data Sharing in Biomedical Research Training

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The STREAMLINE partners from the University of Maastricht (UM) held a two-day training devoted to researchers from the Western Balkans. Like last year, the training was consisting of lectures given by experts from UM and self-study prepared by the participants based on material provided by the training organizers. Throughout group practice, the participants presented their own work following the training guidelines. We use the opportunity to thank Dorothee Horstkötter, Helena Bossini Castillo, and Birgit Wouters for organizing the event and sharing their experience.