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STREAMLINE Bioinformatics Workshop “RNA-seq data analysis”

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

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

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

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

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

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.

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UM trainings 2023

Dear Colleagues,

 

We are pleased to invite you to take part in on-line two-day training sessions organized within STREAMLINE project by our partners from the University of Maastricht, The Netherlands

The trainings will cover following topics:

7th and 9th of November 2023
„Data Protection and Data Sharing in Biomedical Research: Judicial
Guidelines and Legal Practices” which is
dedicated to data protection and data sharing in biomedical research.

 

17th of November and 8th of December 2023

8th  of December 2023 and 12th of January 2024

„Preparing and managing EC-funded projects/ project applications”
is aimed to enhance management skills of
both administrative staff and researchers.

You can find enclosed detail agendas of events.

All interested participants should register on link

https://forms.gle/ebyoK65eF5C8SPjq8

Please, feel free to share this information with your colleagues.

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STREAMLINE for students in October

In October, Dr. Andrijana Lazić presented the STREAMLINE project to students through an interesting lecture “Induced pluripotent stem cells as a model system for the study of neurodevelopmental diseases”.

Choosing the right professional path is one of the biggest challenges that students have in career counseling. Therefore, on October 17, as part of the “Find out first-hand” program, the Center for Career Development and Student Counseling of the University of Belgrade and the Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, organized a visit for final-year students from different faculties of natural sciences of the University of Belgrade. The students had the opportunity to become more familiar with IMGGE projects and career planning possibilities. Dr. Andrijana Lazić described to students challenging and thrilling work with human induced pluripotent stem cells technology, an exciting new era in the field of stem cell biology and regenerative medicine, as well as disease modeling and drug discovery.

A week later, on October 26, master’s and doctoral students of the Faculty of Science, University of Niš, from the Department of Biology and Ecology visited IMGGE. That was great opportunity for students from Niš to visit IMGGE laboratories and facilities, as well as to familiarize themselves with the STREAMLINE project and hear all about the possibilities of induced pluripotent stem cells in modern medicine.

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CERTH trainings 2023

Dear Colleagues,

We are pleased to invite you to participate in on-line trainings organized under the umbrella of the STREAMLINE project by our partners from the Centre for Research & Technology Hellas (CERTH), Greece

The trainings will cover following topics:

 

13th of November 2023
Proposal preparation for EU calls

Participants will have opportunity to hear about requirements for EU funding programmes and get practical advices regarding research projects planning and proposal preparation.

15th of November 2023
Managing a research project

During this training participants will get guidelines and recommendations regarding the management of EU-funded research projects including implementation, monitoring of project progress, risk management and reporting.

20th of November 2023
Improving soft/professional skills of ESRs

This training is dedicated to early stage researchers (ESRs) to help them write good quality research papers, to teach them how to present research at conferences, give them guidelines for CV preparation and etc.

You can find enclosed detail agendas of events.

All interested participants should register on link:

https://forms.gle/9pbXQHeUEMkph25r6

Please, feel free to share this information with your colleagues.

With best regards,

STREAMLINE team