Live Cell Imaging Course 2024
2024-12-03 - 2024-12-05 | IMG
The course is very practically-oriented, theoretical lectures are followed by 6 hours of hands-on session every day in small groups. You will learn widefield, confocal, and advanced methods including super-resolution, photomanipulation, and FLIM. You will have a chance to work on high-end microscopes and compare wide variety of approaches and instrumentation.
For detailed program and overview of taught methods and microscopes please check course webpage: https://course.img.cas.cz/lci/
Looking forward to seeing you!
Jan Valečka and Helena Chmelová

Seminář Michaela Procházková, M.Sc.
2024-11-27 15:00 - 16:00 (Europe/Prague) | Posluchárna Milana Haška / Milan Hašek Auditorium
“CRL4COP1 ubiquitination complex as a balancer of early odontogenesis”
Cullin-RING ubiquitin ligase (CRL) complexes have been heavily studied in connection to cancer progression but there is limited evidence about their physiological roles. One of the exceptions is disruption of limb development by thalidomide induced by inhibition of CRL4 complex via regulation of Fgf8 (Ito et al., 2010). Notably, Fgf8 expressing population is essential also for development of tooth primordia and we found CRL4 genes to be specifically expressed within odontognic epithelium. We further identified COP1 as a substrate binding protein which can bind ETS transcription factors, downstream targets of Fgf pathway, and unveiled that conditional deletion of CRL4 genes severly affects size and morphology of molar primordia and future teeth.

IEM CAS Introduction to Programming for Image Processing 2024
2024-11-27 08:00 - 2024-11-29 17:00
Due to reaching capacity for in-person participation, registration is now only available for online attendance. Thank you for your understanding.
Basic information
The course is tailored to users already familiar with the basics of image processing. It will be focused on automatization, high throughput and basic scripting. Course participants will learn how to create and edit macros in ImageJ and how to write more sophisticated scripts for batch processing. Furthermore, they will learn the basics of image processing in Matlab and Cellpose.
Duration: 3 days
Language: English
Programme
Location: Turquoise Auditorium
Speakers: Barbora Hyklová, Štěpán Kortus, Iva Švecová, Jakub Zahumenský
Day 1 / Wednesday / 27. 11. 2024

Introduction, macro recording and editing in ImageJ
Writing a complex macro for batch processing – automatic data import, cell segmentation, measurements, export in organized format

Day 2 / Thursday / 28. 11. 2024

Script automation, ImageJ customization
Cell segmentation using Cellpose and integration of Cellpose into the workflow
Demonstration of a complex ImageJ/Cellpose workflow

Day 3 / Friday / 29.11. 2024

Optional: Discussion of individual projects and data analysis questions.

Requirements
Prior Experience with ImageJ: Participants should have a basic familiarity with ImageJ and its fundamental features. They should be comfortable with tasks like image import, basic processing (e.g., brightness/contrast adjustments), and measurements.
Own laptop: Participants are required to bring their own laptop for hands-on exercises. If you do not have access to a laptop, please inform us in advance, and we will provide you with one. Prior to the event, you will receive a list of required software programs to install for the course.

Registration
Registration here: free of charge

IEM CAS - BIOCEV Regeneration IV
2024-11-26 10:00 - 17:30
We are pleased to announce the annual mini-symposium BIOCEV Regeneration IV, which will be held on November 26th, 2024, in BIOCEV Centre, Vestec.
BIOCEV Regeneration is an annual open one-day mini-symposium that brings together researchers from different fields of biomedicine, from regenerative medicine and tissue engineering to cancer research, drug discovery, and cryobiology.
This year, the BIOCEV Regeneration IV will focus on the exciting field of cryobiology and cryobanking and highlight its important role in state-of-the-art biomedical research. The mini-symposium is endorsed by the international Society for Low Temperature Biology (SLTB) and will bring together keynote speakers and young researchers from different biomedical disciplines, employing low temperatures in their research and development. This year we will focus on two major directions of cryobiology: cryotechnologies in clinically-oriented research (ATMP production, cell and tissue banking for therapy and diagnostics) and biodiversity preservation and regeneration.
The mini-symposium will be held in the main conference hall and surrounding spaces of the BIOCEV and broadcast online.
Along with several lectures given by our invited speakers, we encourage early career researchers to contribute to our symposium and share achievements in stem cell research, tissue engineering, 3D culture, cancer research or cryobiology during the poster session.
The event is free of charge. More information can be found in the official invitation.
We look forward to seeing you.

Registration

18th BioCEV-Krč Methodological Seminar
2024-11-25 15:00 - 16:00

Seminář Matthias G. Fischer
2024-11-21 11:00 - 12:00 | Posluchárna Milana Haška / Milan Hašek Auditorium
Max Planck Institute for Medical Research, Heidelberg
“Viruses of unicellular eukaryotes: A tale of giants and hyperparasites”
Viruses of protists play important roles in ecology and evolution by influencing microbial population dynamics and shaping eukaryotic genomes by endogenization. Of particular interest are complex DNA viruses whose particle and genome sizes overlap with those of bacteria. In this talk, I will highlight some remarkable properties of these giant viruses and explore their relationship with smaller DNA viruses, called virophages, which can parasitize giant viruses and thus act as an antiviral defense system in certain protist species.

Seminář doc. Mgr. Lumír Krejčí, Ph.D. - ZRUŠENO
2024-11-20 15:00 - 16:00 | Posluchárna Milana Haška / Milan Hašek Auditorium
“Homologous Recombination – From Repair of DSBs to Processing Stalled Replication Forks and Human Diseases”
Our lab focuses on the mechanisms ensuring accurate DNA replication and the role of homologous recombination (HR) in preventing genome instability. We investigate how endogenous hard-to-replicate regions, G-quadruplexes (G4) and R-loops, impact replication and contribute to disease development. A key aspect involves studying the formation and regulation of RAD51 filaments during HR. We explore how positive regulators like BRCA2 and RAD51 paralogs promote filament assembly and its stability, while negative regulators like RECQ5 and RECQ4 helicase help balance replication stress and genome stability.

Den otevřených dveří
2024-11-19 09:00 - 14:00 | IMG
Prohlídka laboratoří, ukázky experimentů v oblasti molekulární genetiky, imunologie, buněčné biologie, virologie, prohlídka posterů a diskuse k vybraným tématům.

Lecture „The role of cornichons in the biogenesis and functioning of monovalent-cation transport systems“
2024-11-18 16:00 - 17:00

Seminář Aleš Neuwirth, Ph.D.
2024-11-13 15:00 - 16:00 | Posluchárna Milana Haška / Milan Hašek Auditorium
“Unravelling autoimmunity in Addison’s disease using a new mouse model”
Autoimmune Addison’s disease is a disorder targeting steroid-producing cells in the adrenal glands. Due to the lack of suitable animal models, the immune mechanisms underlying adrenal destruction remain largely unknown. To address this, we developed the first defined mouse model of experimental autoimmune adrenalitis by immunizing C57BL/6 mice with immunogenic peptides derived from CYP11A1, a rate-limiting enzyme in steroidogenesis. This model allows us to study the pathogenesis of Addison’s disease and provides a unique opportunity to investigate the fate decisions of self-reactive CD4+ T cells and their clonal lineages in a well-defined autoimmune setting.

Lecture „Tissue-specific sex-dependent difference in the metabolism of fatty acid esters of hydroxy fatty acids“
2024-11-11 15:00 - 16:00 | Kinosal, Vídeňská 1083, Praha

IEM CAS Institutional Seminar Series 11/2024
2024-11-07 14:00 - 15:00
Conserved mechanism of Xrn1 regulation by glycolytic flux and protein aggregation
Lecturer: Satyendra Mondal, MSc. / Department of Functional Organisation of Biomembranes
Annotation: The regulation of eukaryotic gene expression via mRNA degradation is an evolutionarily conserved process, with the 5′-3′ exoribonuclease 1 (Xrn1) playing a pivotal role. In yeast, following the depletion of fermentable carbon source, Xrn1 is sequestered at the plasma membrane-associated protein complex, the eisosome, where it becomes inactive. In this study, we show that the plasma membrane localisation of Xrn1 requires the core eisosome components and identify a putative eisosome-binding domain of Xrn1. Our findings demonstrate that the eisosome binding of Xrn1 is subject to the halting of ongoing glycolytic flux rather than the availability of fermentable carbon sources. Furthermore, we show that the localisation of the human orthologue of Xrn1 resembles that of its yeast counterpart when expressed in yeast. Our results advance our understanding of the plasma membrane-associated regulation of Xrn1 and indicate that the regulation principle may be evolutionarily conserved from yeast to humans.
The seminar will take place on 7. 11. 2024 from 2 p.m. in the Turquoise Auditorium of the IEM CAS.
We look forward to your participation.

Den otevřených dveří - FGÚ
2024-11-07 | Kinosal, Vídeňská 1083, Praha

3-day course on Single cell analysis - from qPCR to sequencing
2024-11-04 - 2024-11-07
This course will provide valuable insights and practical skills in the rapidly evolving field of single cell analyses and spatial transcriptomics. With a maximum of 10 participants, you’ll receive personalized attention and the opportunity to engage deeply with the subject.
If you’re interested in joining us, please respond via email to sindelka@ibt.cas.cz as soon as possible, as space is limited.
We look forward to an enriching experience together!

Seminář Martina Zíková, Ph.D. - ZRUŠENO
2024-10-30 15:00 - 16:00 | Posluchárna Milana Haška / Milan Hašek Auditorium
“Impact of Medulloblastoma-Derived Extracellular Vesicles on Neural Stem/Progenitor Cells”
Medulloblastoma is the most common malignant brain tumor in children. Recent advances in understanding its genetic and molecular heterogeneity have uncovered at least four distinct subgroups, each characterized by unique transcriptional profiles, DNA alterations and clinical outcomes. Extracellular vesicle secretion has emerged as a critical mediator of communication within the tumor microenvironment. In this presentation, we will discuss our progress in deciphering the effects of extracellular vesicles derived and purified from medulloblastoma cells on neural stem/progenitor cell gene expressions.

Seminář Prof. Dr. Daniel Sauter
2024-10-23 15:00 - 16:00 | Posluchárna Milana Haška / Milan Hašek Auditorium
“Viral Influencers: How endogenous retroviruses regulate innate immunity and senescence”
The human genome harbors a significant number of endogenous retroviral elements, remnants of ancient viral integration events. While often referred to as “genomic fossils“ and “dark matter of the genome” many of these elements function as promoters or enhancers for cellular genes. This presentation will show how a specific subset of endogenous retroviruses is activated during infection, orchestrating the expression of genes involved antiviral immunity and cell cycle regulation.

Představení kandidáta na předsedu AV ČR - prof. RNDr. Libor Grubhoffer, CSc., dr. h. c. mult.
2024-10-22 10:30 - 11:30 | Posluchárna Milana Haška / Milan Hašek Auditorium
Dne 24. 3. 2025 skončí druhé čtyřleté období ve funkci předsedkyně AV ČR prof. RNDr. Evě Zažímalové, CSc. Volba kandidátky/kandidáta na předsedu AV ČR pro následné funkční období proběhne na zasedání sněmu AV ČR dne 10. 12. 2024.

Jedním z kandidátů na předsedu AV ČR je prof. RNDr. Libor Grubhoffer, CSc., dr. h. c. mult., který představí zaměstnancům krčského kampusu svou vizi o řízení AV ČR na jednání v úterý 22. 10. 2024 od 10:30 hod. v posluchárně Milana Haška na ÚMG.

Lecture „Metabolic dysfunction-associated steatotic liver disease: its modeling in mice and the effect of n-3 fatty acids“
2024-10-21 15:00 - 16:00 | Kinosal, Vídeňská 1083, Praha

Představení kandidáta na předsedu AV ČR - prof. RNDr. Radomír Pánek, Ph.D.
2024-10-16 09:30 - 10:30 | Posluchárna Milana Haška / Milan Hašek Auditorium
Dne 24. 3. 2025 skončí druhé čtyřleté období ve funkci předsedkyně AV ČR prof. RNDr. Evě Zažímalové, CSc. Volba kandidátky/kandidáta na předsedu AV ČR pro následné funkční období proběhne na zasedání sněmu AV ČR dne 10. 12. 2024.

Jedním z kandidátů na předsedu AV ČR je prof. RNDr. Radomír Pánek, Ph.D., který představí zaměstnancům krčského kampusu svou vizi o řízení AV ČR na jednání ve středu 16. 10. 2024 od 9:30 hod. v sále Milana Haška na ÚMG.

17th IMG PhD conference
2024-10-11 | Posluchárna Milana Haška / Milan Hašek Auditorium
Dear colleagues,
We would like to invite you to the 17th IMG PhD conference that will be on the 11th of October.
This year we will be hosting two international speakers: Mileidys Perez Alea, who will have a talk about ¨How to build a Start-up¨ and Elodie Chabrol, who will be talking about the world of ¨Science Communication¨.
We are opening the registration for everyone who is interested in attending the sessions we organized. You can find the program as well as information about the conference at the IMG website and the registration link below.
We are looking forward to seeing all of you and enjoying with us the up-coming conference.
Best regards,
Anton & Irina

Seminář Kristína Jamrichová, M.Sc.
2024-10-09 15:00 - 16:00 | Posluchárna Milana Haška / Milan Hašek Auditorium
“Investigating the Impact of Cullin-Dependent Degradation on Protein Homeostasis”
Cullin-dependent ligases (CRLs) regulate cellular homeostasis by targeting proteins for degradation. Mutations and alterations in the CRL substrate receptor FBXO38 have been linked to distal muscular atrophy, chronic obstructive pulmonary disease, and gender dysphoria. In our previous research, we demonstrated that FBXO38 controls centromeric chromatin density during spermatogenesis. We will present our progress in deciphering FBXO38 function, particularly in the context of protein homeostasis and ribosomal activity.

IEM CAS Institutional Seminar Series 10/2024
2024-10-03 14:00 - 15:00
Single-particle tracking of NMDA receptors at hippocampal synapses
Lecturer: Mgr. Petra Zahumenská / Department of Neurochemistry
Annotation: N-methyl-D-aspartate receptors (NMDARs) are ionotropic glutamate receptors essential for excitatory neurotransmission. These heterotetrameric complexes consist of two obligatory GluN1 subunits combined with two GluN2 (GluN2A-GluN2D) or GluN3 (GluN3A-GluN3B) subunits. The surface expression and subtype composition of NMDARs are tightly regulated through externalization, internalization, and lateral diffusion between synaptic and extrasynaptic regions.
In our study, we utilized the uPAINT (Universal Point Accumulation Imaging in Nanoscale Topography) microscopy technique to examine the surface dynamics of different NMDAR subtypes. uPAINT enables the tracking of individual NMDARs with a high spatial and temporal resolution by labelling them with fluorescent probes. This allows us to observe the distinct patterns of synaptic and extrasynaptic localization of GluN2A- and GluN2B-containing NMDARs in hippocampal neurons. Our approach combines the use of a small anti-GFP nanobody derived from a llama conjugated with an Atto647N fluorophore, along with the tdTomato-Homer1c marker, to define synaptic regions. This allows us to gain insights into the mobility and distribution of NMDAR subtypes at the synaptic level.
The seminar will take place on 3. 10. 2024 from 2 p.m. in the Turquoise Auditorium of the IEM CAS.
We look forward to your participation.

Seminář Marharyta Klianitskaya, Ing.
2024-10-02 15:00 - 16:00 | Posluchárna Milana Haška / Milan Hašek Auditorium
“Human Endogenous Retroviruses: Role in Negative Selection of T cells in the Thymus and Pathogenesis of Psoriasis”
Our research elucidates the role of human endogenous retroviruses (HERVs) in biological processes related to T cell immunity, autoimmunity, and the pathogenesis of psoriasis. HERVs are ancient viral elements integrated into the human genome. While most of these elements are rendered non-functional due to mutations and epigenetic silencing, some retain the ability to express themselves. Despite their foreign origin, the expression of these endogenous retroviruses does not typically trigger autoimmune disease.
The study employed single-cell RNA sequencing data from thymic tissues, revealing that a wide range of HERVs is expressed in thymic cells responsible for presenting autoantigens to T cells and for their subsequent negative selection. This suggests that some HERVs may be perceived by the immune system as autoantigens, and disruptions in the negative selection process could potentially lead to autoimmune diseases.
Psoriasis is a T cell-mediated chronic inflammatory skin disease that occurs in predisposed individuals carrying specific HLA-C alleles, which are crucial for presenting small peptides to T cells that survey for non-self peptides. RNA-seq data from psoriasis-affected tissues highlighted a significant correlation between elevated HERV expression and the development of the disease. These findings emphasize the potential role of HERVs in T cell-mediated conditions and offer new insights into the molecular mechanisms underlying psoriasis.

Researchers’ Night 2024 at the IEM CAS
2024-09-27 18:00 - 22:30
The mysterious world of experimental (bio)medicine
As night falls, our laboratories become a dark and magical place where the challenges of biomedicine become a reality. The darkness that surrounds the building creates a unique atmosphere. The light of microscopes shines through the darkness and reveals the secrets of life at the molecular and cellular level. Every click of the pipette, every flash of fluorescence and every record of information brings our scientists closer to their desired goal of discovering new diagnostic and therapeutic procedures that can change patients‘ lives worldwide.
Come and experience this feeling in person and visit selected experimental (bio)medicine laboratories. We look forward to welcoming you!
Programme
More information can be found on the official website (only available in Czech).

Noc vědců
2024-09-27 18:00 - 22:00

IEM CAS μLecture: Two-photon microscopy
2024-09-24 13:00 - 14:00
μLectures is a monthly seminar series designed to enhance researchers’ understanding of microscopy’s fundamental workings and principles. Each session, lasting 30 minutes, focuses on a specific concept or topic within microscopy. The practical information presented aims to deepen researchers’ comprehension of their microscopy experiments, giving them a better overview of the options available and enabling them to improve their experimental design and more effectively identify and resolve potential issues.
The topic of the September seminar will be two-photon microscopy. This technique is especially suitable for the imaging of processes in vivo. We will explain the two-photon microscopy principle, look at the advantages and disadvantages of this technique and what experiments it can be used for.
The seminar will take place on Tuesday 24. 9. 2024 from 1 p.m. in the Turquoise Auditorium of the IEM CAS. It will also be possible to join online using this link.
Registration is not required, but we will be happy if you can let us know if you plan to come (in person or via email iva.svecova@iem.cas.cz).

Holotomography Workshop - TOMOCUBE HT-X1
2024-09-24 09:00 - 2024-09-27 17:00 | IMG
Dear Colleagues,
Holotomography is an advanced imaging technique that uses a specialized microscope to capture high-resolution images of biological structures such as bacteria, cells, intracellular structures, or even entire organoids without the need for staining. This method allows for the acquisition of quantitative data, including dry mass measurements and various other parameters.
If you have ever considered exploring quantitative holotomography microscopy techniques or quantitative phase microscopy, this is an event you should not miss.
This workshop is designed for potential users and is fully dedicated to practically introducing holotomography as a quantitative microscopic technique. The method will be demonstrated through hands-on experience with the TOMOCUBE HT-X1 system.
The first half-day will take place a series of theoretical lectures, followed by three days fully dedicated to hands-on sessions. During these sessions, you will learn how to set up acquisitions, perform AI-boosted image segmentation, and analyze quantitative imaging data.
Led by one of Tomocube’s most advanced application specialists, Bruno Combettes, this workshop offers an excellent opportunity to discuss your experimental ideas and design with an expert in the method and system. It is also a unique chance to test your experimental design and ideas on the system, with expert guidance.
This event also provides an opportunity to gain valuable contacts for your future research work…
For any questions, please contact: ivan.novotny@img.cas.cz.

Představení kandidáta na předsedu AV ČR - PhDr. Pavel Baran, CSc.
2024-09-23 14:30 - 16:30 | Posluchárna Milana Haška / Milan Hašek Auditorium
Dne 24. 3. 2025 skončí druhé čtyřleté období ve funkci předsedkyně AV ČR prof. RNDr. Evě Zažímalové, CSc. Volba kandidátky/kandidáta na předsedu AV ČR pro následné funkční období proběhne na zasedání sněmu AV ČR dne 10. 12. 2024.

Jedním z kandidátů na předsedu AV ČR je PhDr. Pavel Baran, CSc., který představí zaměstnancům krčského kampusu svou vizi o řízení AV ČR na jednání v pondělí 23. 9. 2024 od 14:30 hod. v sále Milana Haška na ÚMG.

6th CCP Phenogenomics Conference
2024-09-17 - 2024-09-18 | Posluchárna Milana Haška / Milan Hašek Auditorium

IEM CAS Advanced Course on Preclinical Imaging
2024-09-16 08:00 - 2024-09-20 17:00
Basic information
The course aims to teach multimodal preclinical imaging techniques, including in vivo two-photon microscopy, in vivo multi-photon-based label-free techniques (SHG, THG, CARS), and magnetic resonance imaging (MRI) of small rodents. Participants will acquire theoretical knowledge and practical skills in various neuroimaging techniques, with a focus on intravital multi-photon microscopy and MRI principles. Emphasizing the importance of animal models in physiological research, the course guides participants through the entire process of conducting preclinical bioimaging experiments. It includes a detailed pipeline for analyzing brain tumour structures and functional parameters, covering cranial window surgery, two-photon microscopy usage, perfusion MRI and subsequent image analysis. Additionally, the workshop addresses the challenges in using animal models for research and provides access to field experts.
Intended audience
The course is designed for researchers (PhD candidates, Postdocs, Principal Investigators, etc.) with a serious interest in integrating in vivo imaging into their projects.
Methods
Two-photon fluorescent microscopy (functional calcium/voltage imaging, structural imaging), second harmonic generation (SHG), third harmonic generation (THG), coherent anti-Stokes Raman spectroscopy (CARS), high field magnetic resonance perfusion imaging (MRI), fluorescence lifetime imaging microscopy (FLIM)
Registration and more information can be found on our website.
