Institute of Macromolecular Chemistry AS CR, v. v. i. (IMC), according to the Act No 283/1992 Sb and the Statutes of ASCR and the Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), announce a selective procedure for (http://www.biocev.eu/)

Scientific Researcher/Postdoctoral fellow position

For the BIOCEV research program 4 „Biomaterials and Tissue Engineering“, project 4.1.3. „Polymeric Biomaterials for Regenerative Medicine“.

Topic: Bioactive coatings for cardiovascular grafts.

Job description: The research activity will by focused on coating model substrates, such as, polymeric blood vessel prostheses currently used by cardiovascular surgery, scaffolds prepared by decellularization of biological blood vessels or heart valves, and neurovascular stents, with artificial fibrin gels containing various bioactive molecules capable of specific interactions with selected cells. The coating should provide a graft with bloodcompatibility and support the creation of natural endothelium on its surface. As most current artificial grafts fail after some time in organism, the development of bioactive coatings is an essential objective for several interdisciplinary projects seeking to new generation of cardiovascular grafts. The researcher’s activity will include the optimization of the coating structure and composition in response to experimental results provided continuously by collaborating teams of cell biologists (Institute of Physiology ASCR, Prague), designer of the grafts (Faculty of Biomedical Engineering CTU in Prague and Acandis GmbH, Germany) and medical doctors (Institute for Clinical and Experimental Medicine, Prague, Institute of Hematology and Blood Transfusion, Prague, and Dept. of Thoracic, Cardiac and Vascular Surgery, University Hospital Tuebingen, Germany).

Requirements:

• PhD degree of biochemistry, molecular and cell biology, biomaterials, or biomedical engineering with orientation to interactions between biomaterials and biological systems.
• Research experience of biochemical methods is important; experience of microscope techniques (SEM, confocal microscopy) or cell culturing is welcome.
• English, written and spoken, advanced level
• High self-motivation and team work
• Ability of an independent scientific work, flexibility and willingness to learn new research fields
• Organization skills

Contract type: Full time job, 1 year contract, expected extension to 3-year contract
The position is open to start between January and February 2018
Place of work: Institute of Macromolecular Chemistry AS CR, Dept. of Bioactive Polymers (BIOCEV group), BIOCEV, Vestec near Prague.

Application should contain:

• A cover letter summarizing the applicants’ career, past research accomplishments, statement of motivation, and research interests (1-2 pages),
• Curriculum vitae with a list of publications, patents, scientific awards etc.; with impact factors if available, together with WOS citation index without autocitation, cumulative IF and H-index
• Recommendations of the previous supervisor or head of department / R & D team and another respected person in the field

The entire application should be sent as one single PDF via e-mail riedel@imc.cas.cz

Close date: December 10, 2017;

Contacts: For detail information about the topic contact Ing. Tomas Riedel, PhD. (riedel@imc.cas.cz).

Open vacancy: Postdoctoral fellow in remote sensing at Global Change Research Institute (Brno, Czech Republic)

The Global Change Research Institute of Czech Academy of Sciences (CzechGlobe) is looking for a postdoctoral fellow in optical remote sensing of natural and man-managed ecosystems.

CzechGlobe remote sensing laboratory is a dynamic research group focusing mainly on remote sensing of vegetation functioning with an overlap towards imaging spectroscopy of urban landscapes, soils and waters (http://www.czechglobe.cz/en/institute-structure/research-sector/ii-domainecosystems-analysis/#odpz). It has direct access to the airborne carrier equipped with hyperspectral (VNIR, SWIR and TIR) imaging spectrometers, an airborne and terrestrial LiDAR systems and other state-of-the-art laboratory equipment (http://www.czechglobe.cz/en/about-us/infrastructure-elements/).

We are offering a full-time 2-year postdoctoral fellowship with an expert focus on one of the following topics: 1/ synergic use of the airborne visible-, near-, short-wavelength and thermal infrared hyperspectral images with airborne and terrestrial LiDAR measurements for operational retrieval of forest physiological traits towards better understanding the eddy-covariance flux tower observations or 2/ interpretation of airborne thermal infrared image data, with support of other hyperspectral and LiDAR observations, to assess potentials of urban vegetation in mitigation of high temperature events in cities.

We require:

• PhD in remote sensing or any related biological and physical sciences
• Active knowledge of remote sensing physical principles, quantitative interpretational methods and current air-/space-borne optical sensors
• Regular publications in impact peer-reviewed scientific journals
• Proactive and autonomous approach to scientific challenges

We welcome:

• Interdisciplinary linkage between remote sensing and other biological and physical sciences (plant physiology, eddy-covariance flux measurements, physics and mathematics, forestry and agriculture, etc.)
• Experience in radiative transfer or in dynamic vegetation modelling
• Practical skills in optical airborne/field measurement techniques

We offer:

• Opportunity of new creative scientific development
• Access to modern airborne, ground and laboratory instrumentation
• Flexible working time conditions
• Perspective scientific career with a prospect of follow-up position

Further detailed information can be obtained from Dr. Olga V. Brovkina <brovkina.o@czechglobe.cz>. In case of interest, please send your full scientific CV and your motivation letter until 1st October 2017 at the email address: jobs@czechglobe.cz (email subject: „ RS postdoctoral fellow“).

Laboratory of Genome Integrity http://www.img.cas.cz/research/jiri-bartek/

PhD position – cell/molecular biology

Project title: Molecular mechanisms for maintaining the integrity of human genome under conditions of replication stress
Supervisor: Jana Dobrovolná (jana.dobrovolna@img.cas.cz)
Co-suprevisor: Pavel Janščák (pavel.janscak@img.cas.cz)

Project description: The project will focus on molecular mechanisms involved in processing of highly genotoxic RNA:DNA hybrids, called R-loops, that are suspected to play role in cancer development. The candidate will identify the proteins associated with R-loops under conditions of chemically- and oncogene-induced replication stress and study their role in maintenance of genome stability. The project offers training in a broad range of molecular, cell biological and biochemical techniques. The student will also undergo short-term trainings at the Institute of Molecular Cancer Research of the University of Zurich where he/she will be exposed to front-line research in the field of DNA repair and cancer.

Candidate’s profile (requirements): M.Sc. or equivalent in biochemistry or molecular/cellular biology, good English, independent thinking, strong interest in basic research and experimental work.

Laboratory of Cell Differentiation http://www.img.cas.cz/research/petr-bartunek/

Project 1

Project title: Zebrafish models for normal and malignant hematopoiesis
Supervisor: Petr Bartůněk (bartunek@img.cas.cz)

Project description: This project aims at understanding the molecular mechanisms underlying cell fate determination and differentiation of blood cell progenitors as well as studying processes involved in cell transformation of leukemic cells. The candidate will further develop ex vivo and in vivo techniques and employ already established methods like hematopoietic cell transplantation, embryo microinjection, in situ hybridization, immunohistochemistry, flow cytometry, RNAseq, ChIPseq and advanced live animal imaging including light-sheet microscopy.

References: Svoboda et al. Blood. 2014; 124(2):220-8, Svoboda et al. Nat Protocols. 2016; 11(5):1007-20.

Candidate’s profile (requirements):
 MSc or equivalent in cell and/or developmental biology.

Project 2
Project title: Zebrafish models of human cancer
Supervisor: Petr Bartůněk (bartunek@img.cas.cz)

Project description: This project will focus on establishment of new models of human cancer and will aim at understanding the process of tumor initiation, propagation and spreading in vivo. This knowledge will be used to design therapeutical strategies that will be further tested in zebrafish. The candidate will employ established methods and techniques like embryo microinjection, tumor cell transplantation, drug treatment, high-throughput microscopy, whole body and MALDI imaging.

Candidate’s profile (requirements):
 MSc or equivalent in cell and/or developmental biology.

Laboratory of Molecular Pharmacology http://www.img.cas.cz/research/jaroslav-blahos/

Project title: Novel mechanism of Cannabinoid Receptor 1 regulation by SGIP1
Suprevisor: Jaroslav Blahoš (jaroslav.blahos@img.cas.cz )

Project description: We plan to open position for Ph.D. students in a project of Cannabinoid Receptor 1 regulation by molecular partner SGIP1. This molecule was discovered in our lab as an interacting partner of the receptor. This interaction has profound effect on the receptor signaling. The techniques planned will combine DNA recombination, protein chemistry, pharmacological functional tests of various intracellular signaling pathways, cell biology tools including fluorescence microscopy, TIRF, BRET and FRET.

Laboratory of Leukocyte Signalling http://www.img.cas.cz/research/tomas-brdicka/

PhD position – immunology

Project title: Regulation of leukocyte signalling by membrane adaptor proteins
Supervisor: Tomas Brdicka (tomas.brdicka@img.cas.cz)

Project description: The project will focus on the regulation of myeloid cell signalling by adaptor protein PSTPIP2. This protein is a known suppressor of neutrophil inflammatory response and its absence in mice results in autoinflammatory disease similar to several human disorders. The candidate will explore the molecular mechanism of how this protein suppresses inflammatory signalling in neutrophils and other leukocytes of myeloid lineage and how it prevents the development of autoinflammatory disorder. The project will include analysis of leukocyte development, migration, immune response and signalling pathways using genetically modified mouse models and cell lines. The candidate will also be involved in projects exploring function of other adaptor proteins involved in the regulation of leukocyte signalling and inflammation.

Candidate profile: The candidate must hold a Master degree (or be close to its completion) in immunology, molecular/cell biology, biochemistry or in related field of life sciences. The applicant must have a strong interest in immunology and related biomedical sciences. Ability to communicate in English is required.

Laboratory of Mouse Molecular Genetics http://www.img.cas.cz/research/jiri-forejt/

PhD position – cell/molecular biology

Project title: The role of PRDM9 allelic variation and activity for hybrid sterility in mice
Supervisor: Emil Parvanov (emil.parvanov@img.cas.cz)
Co-suprevisor: Jiří Forejt (jiri.forejt@img.cas.cz)

Project description: Explore the role of the zinc finger array of PRDM9 protein for mouse hybrid steriliy and determine the state of the PRDM9-dependent histone modifications and their relation to hotspot formation and distribution. The study will include the combination of classical genetic crosses, cytological observations, ChIP-seq experiments and so on.

Candidate’s profile (requirements): M. Sc. or equivalent in genetics or cell biology. The candidate should have solid background in molecular biology and genetics and basic skills in methods of mouse genetics.

Laboratory of Integrative Biology http://www.img.cas.cz/research/martin-gregor/

Project 1

Project title: Intestinal barrier dysfunction and epithelial-immune cell interactions in plectinopathy
Supervisor: Martin Gregor (martin.gregor@img.cas.cz)
Co-supervisor: Alžběta Kalendová (alzbeta.kalendova@img.cas.cz)

Project description: Inflammatory bowel disease (IBD) is characterized by compromised intestinal barrier function in association with excessive activation of the mucosal immune system. Using mouse model of plectinopathy we show that absence of plectin, a highly versatile cytolinker, in intestinal epithelium aggravates experimentally induced colitis and potentiates associated carcinogenesis. The major goal of this project is detailed analysis of molecular mechanism underlying governing role of plectin in intestinal barrier maintenance. In addition, we will study the impact of plectin deficiency on initiation and progression of colorectal cancer. We will further develop mouse model with tissue-specific plectin ablation in myeloid cell lineage and characterize it with respect to plectin-controlled epithelial-immune cell interactions. Understanding the mechanisms involved in the plectin-deficiency-mediated pathogenesis of IBD and colorectal cancer is necessary to define new targets for disease screening and strategies for its prevention and treatment. The successful candidates will learn and utilize advanced cellbiology, molecular-biology, physiology and imaging techniques, while developing and analyzing various mouse models.

Candidate profile: We are seeking outstanding self-motivated candidates with master's degree in molecular biology, physiology, biochemistry or related fields. We are offering research at a state-of-the-art equipped institute with experienced colleagues, international working environment and international collaborations.

Project 2

Project title: Cytoskeleton-dependent regulation of cell-cell contacts in simple epithelia
Supervisor: Martin Gregor (martin.gregor@img.cas.cz)

Project description: The ongoing project is focused on understanding how cytoskeletal cytoarchitecture regulates cell-cell contacts (such as tight and adherens junctions, or desmosomes) in simple epithelia of GIT and biliary tracts. Successful candidate will analyze established CRISPR/Cas9 knockout cell lines in 2D and 3D (organoid) cultures. This project will use advanced microscopy techniques (including 3D time-lapse and super-resolution microscopy), biophysical methods and biochemical analysis of signaling pathways. The part of the project is in collaboration with Center for Medical Physics and Technology, Erlangen (traction force microscopy and magnetic tweezers experiments). The project is supported by recently awarded funding.

Candidate profile: We are seeking outstanding self-motivated candidates with master's degree in molecular, cellular or developmental biology, biochemistry or biophysics. We are offering research at a state-of-the-art equipped institute with experienced colleagues, international working environment and international collaborations.

Laboratory of Cellular and Viral Genetics http://www.img.cas.cz/research/jiri-hejnar/

Project title: Functional characterization of avian sarcoma and leukosis virus receptors
Supervisor: Daniel Elleder (elleder@img.cas.cz)

Topic: Avian sarcoma and leukosis virus (ASLV) served historically as a key model in both virus and cancer research. Our laboratory has long tradition with this model. More recently, we have identified and further characterized some of the cellular receptor molecules employed by the virus for entry into host cells. The current project will aim at elucidating the function that these receptor molecules play in the biology of the chicken cell, and how it impacts the cytopathic effects of the virus infection. The work will be mostly using molecular biology and virology techniques, but will also involve bioinformatic methods (their prior knowledge is not required). We will try to identify selection pressures exerted during avian evolution on the receptor molecules. We will also try to identify endogenous receptor ligands. Lastly, we will try to identify how new virus subgroups are formed by recombination with chicken endogenous retroviruses. Further reading: 1. J Virol, 2005, 79:10408; 2. J Virol, 2004, 78:13489; 3. Virology, 2006, 344:25; 4. J Virol, 2016, PMID: 27881654; 5. Genome Biology, 2015, 16:164.

Candidate profile: M.Sc. or similar degree in molecular genetics or related field. Highly motivated.

Laboratory of Biology of the Cell Nucleus http://www.img.cas.cz/research/pavel-hozak/

Project 1

Project title: Contribution of (pre)lamin A – phosphoinositides complexes to intranuclear order
Supervisor: Pavel Hozák (pavel.hozak@img.cas.cz)

Project description: Lamins are intermediate filament proteins present in nuclear lamina and, to less extent, in the nuclear interior. They are involved in a variety of nuclear functions, such as regulation of gene expression, DNA replication, DNA repair, chromatin organization, and cellular ignalling. Mutations in lamins cause severe disease – laminopathies. While interactions and functions of lamins in lamina are extensively addressed, much less is known, about the lamin pool in the nuclear interior. Our preliminary data demonstrate that lamin A forms a complex with nuclear myosin I and a phosphoinositide phosphatidylinositol 4,5-bisphosphate. This project focuses on detailed characterization of these complexes by biochemical, structural and advanced microscopy methods using various experimental models. The project will implement molecular biology and biochemistry methods as well as the state-of-the-art imaging techniques including fluorescence, confocal and super-resolution (SIM, STED, STORM) microscopy. The project is supported by recently awarded funding from the Grant Agency of the Czech Republic.

Candidate profile: M.Sc. (Mgr.) degree or equivalent in molecular/cellular biology or biochemistry, good English, independent thinking, strong interest in basic research and experimental work, dedication to learn and develop new techniques.

Project 2

Project title: Phosphoinositides compartments in the cell nucleus – their structure and functions
Supervisor: Pavel Hozák (pavel.hozak@img.cas.cz)

Project description: Phosphoinositides are phosphorylated species of phosphatidylinositol. They are present at all membranous structures within a cell (plasma membrane, ER, GA, endosomes and various vesicles) where they direct membrane trafficking and serve as signalling molecules. Surprisingly, phosphoinositides localize also to the cell nucleus, which is internally absent of membrane. We have previously demonstrated that phosphatidyl inositol-4,5-bisphosphate (PIP2) is present in the nucleolus as well as carbon-rich patches which we termed the lipid islets. We have shown that nucleolar PIP2 stimulates activity of RNA polymerase I and other transcription factors such as UBF and fibrillarin and thus modulates transcription of rDNA genes. In the nucleoplasm, lipid islets associate with RNA polymerase II and their absence negatively affects transcription of proteincoding genes. The exact mechanism, however, remains largely unknown. This project focuses on finding (i) the detailed composition of lipid islets as well as (ii) defining a cross-talk between various phosphoinositides within the nucleus, (iii) defining direct protein interacting partners of phosphoinositides, and (iv) elucidating the mechanism by which the phosphoinositides modify nuclear processes, e. g. RNA polymerase II transcription.

The PhD project will implement molecular biology and biochemistry methods as well as the state-ofthe-art imaging techniques including fluorescence, confocal and super-resolution (SIM, STED) microscopy. The project is supported by funding from the Grant Agency of the Czech Republic.

Candidate profile: M.Sc. (Mgr.) degree or equivalent in molecular/cellular biology or biochemistry, good English, independent thinking, strong interest in basic research and experimental work, dedication to learn and develop new techniques.

Project 3

Project title: Identifying the interactions of chromatin and the nuclear periphery
Supervisor: Jindřiška Fišerová (jindriska.fiserova@img.cas.cz)
Co-supervisor: Pavel Hozák (hozak@img.cas.cz)

A nuclear periphery involves a nuclear envelope with a lamina tightly attached to the inner nuclear membrane and nuclear pore complexes facilitating nucleocytoplasmic transport. The nuclear periphery plays a crucial role in chromatin organisation, regulation of gene transcription, gene silencing or in mediating the communication between the nucleus and the cytoplasm. The importance of the nuclear periphery is also demonstrated by number of diseases (called envelopathies) resulting from a mutation in genes encoding for one of the peripheral protein such as lamin or emerin. The structure of the nuclear periphery as well as the role of proteins associated with the periphery in the above mentioned processes is fragmentary. This project focuses on those topics and aims to further uncover the biochemical interactions at the nuclear periphery. The PhD project will implement the state-of-the-art imaging techniques including super-resolution (SIM, STED) as well as molecular biology and biochemistry methods for in-depth studies of the role of periphery associated proteins in chromatin organisation.

Candidate’s profile (requirements): M.Sc. (Mgr.) degree or equivalent in molecular/cellular biology, good English, independent thinking, strong interest in basic research and experimental work.

Laboratory of Eye Biology http://www.img.cas.cz/research/zbynek-kozmik-biocev/

Project title: The role of transcription factors and enhancers in mouse embryonic development
Supervisor: Zbynek Kozmik (kozmik@img.cas.cz)

Project description: Position is available in the area of developmental biology. Project will focus on the role of transcription factors in vertebrate eye development using laboratory mouse as a model system. The methods used will include gene knockouts using Cre/loxP and Crispr/Cas9 technologies, gene expression studies of mutant mice by in situ hybridization, immunohistochemistry and RNA-seq. Gene regulatory networks will be interrogated using ChIP-seq and reporter gene assays in cell lines and transgenic animals. In addition, genetically modified mice will be generated using CRISPR/Cas9 approach in order to investigate enhancer redundancy (shadow enhancers).

Candidate profile: Eligible candidates should have M.Sc. or equivalent in molecular, cell and developmental biology or biochemistry. We seek candidates with interest in experimental work using laboratory mice as a model.

Laboratory of Transcriptional Regulation www.img.cas.cz/research-groups/zbynek-kozmik

Project title: Evolution of developmental control mechanisms
Supervisor: Zbynek Kozmik (kozmik@img.cas.cz)
Project description: Position is available in the area of evolutionary-developmental biology (evodevo).

Project will focus on animal eye evolution. Evolution of genes and gene regulatory networks will be studied using selected animal models available in the laboratory (zebrafish, amphioxus, annelid worm, cnidaria). The methods used will include bioinformatics, gene isolation, gene expression studies by in situ hybridization, transgenesis and gene knockouts using Crispr/Cas9 system.

Candidte profilea: Eligible candidates should have M.Sc. or equivalent in molecular, cell, developmental, evolutionary biology or biochemistry. We seek candidates with independent thinking, strong interest in basic research who are willing to allocate significant amount of their time for experimental work in the wet lab.

Laboratory of Structural Biology http://www.img.cas.cz/research/pavlina-rezacova/

Project title: Extending the LEDGF/p75 interactome
Supervisor: Pavlína Řezáčová (pavlina.rezacova@img.cas.cz)

Project description: LEDGF/p75 is an epigenetic reader and an attractive therapeutic target involved in HIV integration and the development of mixed lineage leukemia (MLL) fusion-driven leukemia. Although highly relevant in the light of ongoing LEDGF/p75 drug development, its physiological function is not completely understood. We are seeking highly motivated PhD students that would investigate various aspects linked with both LEDGF/p75 physiological and pathological roles using protein biochemistry, biophysics and structural biology. Čermáková, K., et al., Validation and structural characterization of the LEDGF/p75-MLL interface as a new target for the treatment of MLL-dependent leukemia. Cancer Research, 2014. 74 (18): 5139 Těšina, P., et al., Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif. Nature Communications, 2015. 6: 7968

Laboratory of Transgenic Models of Diseases http://www.img.cas.cz/research/radislav-sedlacek/

Project 1

Project title: Elucidation of the biological role of Tiki, Wnt-specific Metalloproteases
Supervisor: Radislav Sedláček (radislav.sedlacek@img.cas.cz)

Project description: The project focuses on TIKI1 and especially TIKI2 (TRABD2A and TRABD2B genes) whose biological role in mammals is still purely understood. TIKIs function as negative regulators of the Wnt signaling pathway, mediating cleavages of N-terminal residues of a subset of Wnt proteins. Phylogenetic analysis shows that Tiki1 and Tiki2 orthologues are highly conserved among vertebrate and mammalian species although the Tiki1 is missing in rodents. The role of Tiki proteases will be studied in mouse and human systems and the work will start with the analysis of our TIKI2 –deficient mice. The aim of this study is to describe the pathophysiologic roles of TIKI2 (TIKI1).

Candidate’s profile: M.Sc. (Mgr.) degree or equivalent in molecular/cellular biology or biochemistry, a good command of English, independent thinking but also team player, strong interest in basic research and experimental work, ability to work with animals (rodents – training will be provided).

Laboratory of RNA biology http://www.img.cas.cz/research/david-stanek/

Project title: Evolution of RNA splicing
Supervisor: David Staněk (stanek@img.cas.cz)

Project description: RNA splicing is a crucial step in gene expression during which non-coding introns are removed and exons are joined together. Introns have been found in all eukaryotic organisms but their function and origin remains mysterious. However, recently discovered unicellular marine predators contain new class of introns. This offers a unique opportunity to study a completely unexplored world in the RNA universe and reveal fundamental principles of intron evolution and function. This is a collaborative project with experts on unicellular organisms from the Institute of Parasitology and involves both bioinformatics as well as molecular biology approaches.

Candidate profile: M.Sc. in molecular, cellular or developmental biology, parasitology or bioinformatics.

Laboratory of Adaptive Immunity http://www.img.cas.cz/research/ondrej-stepanek/

PhD position in cell biology (with a taste of immunology)

Project 1

Project title: It is troublesome without BBSome
Supervisor: Martina Huranová (martina.huranova@img.cas.cz)

Project description: Primary cilium and immunological synapse are related structures. Both organelles concentrate sensory and signaling receptors of multiple signaling pathways. In addition, structural and functional establishment of these structures is dependent on polarized protein transport and remodeling of actin cytoskeleton. Bardet-Biedl syndrome (BBS) is a severe multiorgan disease (ciliopathy) caused by loss-of-function mutations in several BBS related proteins. BBSome is a complex of eight BBS proteins and regulates two key processes during ciliogenesis. First, BBSome transports multiple receptors to the ciliary membrane. Second, BBSome inhibits activity of RhoA GTPase, which regulates F-actin polymerization. The herein project aims to understand how BBSome regulates actin remodeling during ciliogenesis. Second part of the project will focus on the role of BBSome in the formation of the immunological synapse between T cells and antigen-presenting cells. The PhD candidate will analyze BBS4 deficient mice and generate and analyze BBS7 and BBS4 deficient cell lines. The experimental approaches will include fluorescence microscopy and superresolution microscopy, techniques of biochemistry and molecular biology and immunological assays.

Offer: We can offer enthusiastic, well-equipped research environment and sufficient funding. The research focuses on solving emerging questions in cell and developmental biology.

Candidate profile: M.Sc. or equivalent in cell biology, molecular biology or related fields. We are looking for a highly motivated and enthusiastic student with a strong commitment to science, wet lab experience (e.g. MSc. project), good laboratory practice and ethics. Previous experience with cell cultures, animal models, fluorescence microscopy, and/or methods in molecular/cell biology and biochemistry is an advantage.

Project 2

Project title: Track the Tregs
Supervisor: Ondřej Štěpánek (ondrej.stepanek@img.cas.cz)

Project description: Regulatory T cells (Tregs) are crucial players in establishing self-tolerance. However, some aspects of Treg biology are still poorly understood. It is unclear how highly self-reactive T cells decide between negative selection and Treg conversion in the thymus. The PhD candidate will address the role of Foxp3 transcription factor in this cell-fate decision checkpoint using transgenic animal models. Second part of the project will focus on the analysis of the role of pathogen specific Tregs during infection using monoclonal Tregs and Listeria monocytogenes infection. Third part of the project will analyze the heterogeneity of Treg population in the steady-state and during various disease conditions (infection, cancer, and autoimmunity).

Offer: We can offer enthusiastic environment of a young research team, well-equipped research environment and sufficient funding. The research focuses on solving emerging questions in immunology.

Candidate profile: M.Sc. or equivalent in immunology, cell biology, developmental biology or related fields. We are looking for a highly motivated and enthusiastic student with a strong commitment to science, wet lab experience (e.g. MSc. project), good laboratory practice and ethics. Previous experience with animal models and immunological research is an advantage.

Project 3

PhD position in cell biology

Project title: Molecular mechanisms of inflammation.
Supervisor: Peter Draber (Peter.Draber@img.cas.cz)

Project description: Inflammation is a principal mechanism of body defense against invading pathogens and its proper mounting is critical for clearing infection. At the same time, the hyperactivation of pro-inflammatory pathways might lead to severe autoimmune disorders and cancer. The initial activation of the immune system requires pro-inflammatory mediators, such as TNF, IL-1, and IL-17. The binding of these cytokines to their receptors on cell surface triggers formation of complicated signaling complexes. Very tight regulation of these complexes is required to ensure adequate activation and termination of inflammatory signaling. However, the precise molecular mechanisms guiding the assembly and activity of these signaling complexes are still largely enigmatic. At first, the candidate will identify novel components of several pro-inflammatory signaling complexes (including IL-17 receptor signaling complex) using mass-spectrometry analysis. Subsequently, roles of the newly identified components will be studied in vitro by analyzing knockout cell lines generated by Crispr-Cas9 technology. Finally, the candidate will focus on the role of these molecules in vivo using animal models. Altogether, the successful candidate should finish her/his PhD study with deep theoretical knowledge in the field of inflammation and be highly skilled to perform up-to-date molecular biology methods and analysis of mouse models.

Candidate profile: M.Sc. or equivalent in cell biology, biochemistry, molecular biology, or a related field. We are looking for a highly motivated and enthusiastic candidate with deep interest in science. Prior laboratory experience is advantageous.

Laboratory of Germ Cell Development http://www.img.cas.cz/research/zdenek-trachtulec/

Project title:
Supervisor: Zdeněk Trachtulec (zdenek.trachtulec@img.cas.cz)

PhD project: Investigation of the relationship between the alleles of some genes and low copy number repeat variation in various mouse and rat models of reduced fertility. The applied methods will include: fertility phenotyping (dissections, sperm count and malformation assays), fluorescent and light microscopy (cytology and histology of testes and ovaries)), genotyping, gene expression analyses.

Research Topic: The PRDM9 (PR-domain 9) protein is an epigenetic factor important for both male and female fertility that determines the sites of meiotic recombination. PRDM9 variants contribute to non-allelic homologous recombination leading to genomic disorders and were found in sterile men. We identified mouse Prdm9 as the first vertebrate hybrid sterility gene. Prdm9 participates in our rodent models of complete sterility, time-dependent (semi)sterility reduced sperm count, and mild meiotic arrest.

Candidate profile: M.Sc. or equivalent in molecular genetics and/or reproductive biology, experience in work with rodents, basic bioinformatics, active English

Guest group of Genome Dynamics and Neurodegeneration

Project title: The mechanistic interplay between DNA strand break repair, RNA processing, and human neurological disease
Supervisor: Hana Hanzlikova (h.hanzlikova@sussex.ac.uk)
Co-supervisor: Keith Caldecott (k.w.caldecott@sussex.ac.uk)

Project description: DNA single-strand breaks (SSBs) are the most frequent DNA lesions arising in cells and are a major threat to cell survival and genetic integrity, as indicated by the elevated genetic deletion, embryonic lethality, and neurological disease observed if single-strand break repair (SSBR) is attenuated1. Based on our recent exciting data2 we will address the extent to which the impact of SSBs extends to other neurodegenerative diseases and to normal human ageing. In addition, the project will address the mechanisms by which SSBs trigger neurodegeneration, and will employ cutting edge techniques in molecular and cellular biology, including genome editing by CRISPR-Cas9 technology. The successful applicant will join a dynamic and well-funded laboratory with training opportunities in laboratories in both Prague and the UK.

An overview of research in the Caldecott lab can be found at www.sussex.ac.uk/lifesci/caldecottlab. 1. Caldecott, K.W. Single-strand break repair and genetic disease. Nat. Rev. Genet. 9, 619–631 (2008). 2. Hoch, N.C., Hanzlikova, H. et al. XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia. Nature. 541(7635), 87-91 (2017)

Candidate’s profile (requirements): The successful applicant will be highly motivated, enthusiastic and willing of working within a multidisciplinary team. Previous experience with methods in molecular and cell biology and biochemistry, eukaryotic cell cultures and fluorescence microscopy will be an advantage.

PALS postdoc position: X-ray optics and spectroscopy for plasma diagnostics

The candidate is supposed to work predominantly on the following topics:

• X-ray diagnosis of high-power laser-matter interaction
• Development and implementation of advanced spectroscopic and imaging schemes
• Participation in interaction experiments at high-power laser system PALS
• Computational evaluation of extended sets of experimental data
• Modeling of the laser-matter interaction based on computer codes

Requirements:

• PhD in physics or related field
• Excellent computational skills needed for application of simulation tools (physical optics, plasma hydrodynamics, atomic and PIC codes)
• Experience in X-ray physics and instrumentation is a plus (but not mandatory)
• Good knowledge of spoken and written English

Job conditions:

• The opportunity to participate in unique scientific projects
• Collaboration with a strongly motivated scientific team
• Career growth, professional education
• Competitive and motivating salary
• 5 week holidays and other employee benefits

Applications containing CV, cover letter, contacts of references, and any other material the candidate considers relevant, should be sent to Dr. Libor Juha, Laser Plasma Department, Institute of Plasma Physics, Czech Academy of Science, Za Slovankou 3, 182 00 Prague 8, Czech Republic; juha@ipp.cas.cz

PALS postdoc position: Laser-plasma chemistry

The candidate is supposed to work predominantly on the following topics:

• Laser induced dielectric breakdown (LIDB) in gases: from laser sparks to plasma filaments
• Diagnostics of plasmas formed in gases, liquids (i.e., laser cavitation) and heterogeneous systems by focused high-power laser beams
• Analysis of chemical consequences of LIDB and related phenomena: laboratory simulation of high-energy-density events related to the origins of life
• Investigating the relationship between physical characteristics and chemical changes in laser-produced plasmas
• Collaboration with theorists modelling the chemical change in various laser-plasma-chemical systems

Requirements:

• PhD in physical chemistry, chemical physics, plasma physics, plasma chemistry, astrobiology or related field
• Experience in plasma diagnostics, laser-plasma interaction and/or plasma chemistry
• Skills in high-power-laser science and technology represent a plus (but not mandatory)
• Good knowledge of spoken and written English

Job conditions:

• The opportunity to participate in unique scientific projects
• Collaboration with a strongly motivated scientific team
• Career growth, professional education
• Competitive and motivating salary
• 5 week holidays and other employee benefits

Applications containing CV, cover letter, contacts of references, and any other material the candidate considers relevant, should be sent to Dr. Libor Juha, Laser Plasma Department, Institute of Plasma Physics, Czech Academy of Science, Za Slovankou 3, 182 00 Prague 8, Czech Republic; juha@ipp.cas.cz

PALS postdoc position: Secondary charged particle beams at the PALS facility

The candidate is supposed to work predominantly on the following topics:

• Performing experimental campaigns at the PALS facility
• Diagnostics and instrumentation for characterization of charged particle emission
• Laser wakefield acceleration of electron beams
• Laser driven acceleration of proton and ion beams
• Probing dense plasmas by fast charged particles
• Data analysis

Requirements:

• PhD in plasma physics, particle physics, accelerator physics
• Experience in particle diagnostics, beam instrumentation, and particle detectors
• Skills in data analysis and high-power-laser science and technology represent a plus (but not mandatory)
• Good knowledge of spoken and written English

Job conditions:

• The opportunity to participate in unique scientific projects
• Collaboration with a strongly motivated scientific team
• Career growth, professional education
• Competitive and motivating salary
• 5 week holidays and other employee benefits

Applications containing CV, cover letter, contacts of references, and any other material the candidate considers relevant, should be sent to Dr. Miroslav Krůs, Laser Plasma Department, Institute of Plasma Physics, Czech Academy of Science, Za Slovankou 3, 182 00 Prague 8, Czech Republic; krus@ipp.cas.cz

PALS doctoral / postdoc position: Physics of high-power iodine laser system

The candidate is supposed to work predominantly on the following topics:

• Alignment of the iodine laser beamline
• Determining and optimizing output pulse parameters (energy, pulse width, contrast, etc.)
• Participation in interaction experiments at high-power laser system PALS
• Measuring the PALS beam wavefront by means of the wavefront sensor
• Improvement of the wavefront using adaptive optics
• Modeling of the beam parameters in ZEMAX software or GLAD code

Requirements:

• Master degree or PhD in optics, laser physics or related field
• Experienced in laser beam alignment and diagnostics
• Experienced in simulation in ZEMAX software or GLAD code
• Experienced in programming in C++ is a plus (but not mandatory)
• Good knowledge of spoken and written English
• Expected feeling as a team player

Job conditions:

• The opportunity to participate in unique scientific projects
• Collaboration with a strongly motivated scientific team
• Career growth, professional education
• Competitive and motivating salary
• 5 week holidays and other employee benefits

Applications containing CV, cover letter, contacts of references, and any other material the candidate considers relevant, should be sent to Dr. Jan Dostál, Laser Plasma Department, Institute of Plasma Physics, Czech Academy of Science, Za Slovankou 3, 182 00 Prague 8, Czech Republic; dostal@ipp.cas.cz

For the project “Repeatome dynamics in the earliest evolutionary stages of apomictic plants”, funded by the Czech Science Foundation, we seek to the earliest possible date a highly motivated

PhD student in Cytogenetics

The project (duration 3 years) is aimed at a better understanding of mechanisms underlying the transition from sexual to apomictic reproduction. Apomixis is tightly connected with hybridization and polyploidization. Despite a great potential in agriculture, the genetic mechanisms of apomixis are still poorly understood. Hybridization causes genetic instability including a restructuring of the repeatome, the fastest evolving part of plant genomes. Bursts of transposable elements due to hybridization-induced genomic shock may trigger a switch to apomixis. In the project, sexual and apomictic Hieracium species will be investigated in an extensive breeding program, comparing artificial hybrids with natural apomicts of the same parentage as a model of hybrid speciation that may lead to the formation of apomictic lineages.

An interdisciplinary and international team of researchers from the Institute of Botany (www.ibot.cas.cz/en/) of Czech Academy of Sciences and the Department of Botany of the Charles University in Prague (www.cuni.cz/UKEN-1.html) will tackle this complex biological question from various angles (cytogenetics, genomics, embryology, reproductive biology).

Responsibilities of the PhD candidate include karyotyping of plants, in situ hybridization (FISH, GISH) with a main focus on the localization of parental-specific repetitive elements using probes derived from NGS data as cytogenetic markers to investigate genome repatterning following hybridization. Further tasks include data processing and interpretation, presentations at international conferences and publications in IF journals.

Experience with karyological and cytological techniques, preferably in plants, is desired. The candidate should have an excellent command of English. Personal features should include reliability, patience, technical accuracy, flexibility, good social skills and the readiness to learn.

We offer creative work, the chance for personal development, a pleasant working atmosphere in a marvellous environment (Pruhonice Park, UNESCO World Heritage Site, www.pruhonickypark.cz/en/the-pruhonice-park/), and an excellent infrastructure at the Laboratory of Molecular Cytogenetics and Karyology (http://www.ibot.cas.cz/en/scientific-groups-and-laboratories/laboratory-of-molecular-cytogenetics-and-karyology/) under the leading of Dr. Alexander Belyayev. The PhD candidate will be enroled at Charles University in Prague, one of the oldest universities in Europe.

For more information, please contact Dr. Judith Fehrer (fehrer@ibot.cas.cz). Applications containing a motivation letter, a short CV and two references should be sent until 22. January 2017 to ibot@ibot.cas.cz.

In the project “Repeatome dynamics in the earliest evolutionary stages of apomictic plants” funded by the Czech Science Foundation,

a Postdoc Position in Bioinformatics

is available at the Institute of Botany (www.ibot.cas.cz/en/) of Czech Academy of Sciences. Project begin is January 2017; the position is for 3 years and shall be filled as quickly as possible, with an option to be prolonged after the end of the project.

The project is aimed at a better understanding of mechanisms underlying the transition from sexual to apomictic reproduction. It brings together an interdisciplinary and international team of researchers who will tackle a complex biological question from various angles (cytogenetics, genomics, embryology, reproductive biology).

Tasks involve the de novo identification and quantification of genomic repeats from high-throughput sequencing data in the non-model hawkweed genus Hieracium in order to investigate genome repatterning following hybridization. The successful applicant will be involved in experimental design and statistical analysis, collaborate with wet-bench biologists and help to integrate the results into the bigger picture.

Prerequisites are a PhD in Biology, Genomics, Bioinformatics or a related field with at least two years of experience in Bioinformatics (preferably with a background in eukaryote genomes), a profound interest in the topic, the capacity to work independently as well as to contribute creatively to a team, and the proven ability to publish in renowned IF journals.

We offer an excellent infrastructure and a friendly working atmosphere in a marvellous environment (Pruhonice Park, UNESCO World Heritage Site, http://www.pruhonickypark.cz/en/the-pruhonice-park/) in the close vicinity of Prague and an option to become engaged in the future establishment of a central Bioinformatics unit at the Institute of Botany.

For more information, please contact Dr. Judith Fehrer (fehrer@ibot.cas.cz).

Applications containing a motivation letter, a short CV, a full publication list and two references should be sent until 15. January to ibot@ibot.cas.cz.

Open postdoc / research fellow positions at The Institute of Plasma Physics in Prague, Tokamak Department

The Tokamak department of the Institute of Plasma Physics of CAS, Prague, Czech Republic is seeking candidates for postdoc / research fellow positions. The successful candidate will work within the Theory and modelling group. Positions are open in the following areas:
1. Integrated modelling, support of COMPASS experiments.
2. Tokamak edge and scrape-off layer modelling.
Apply by November 10, 2016.
Detailed description
The Tokamak department of the Institute of Plasma Physics (see http://www.ipp.cas.cz) is a major thermonuclear research laboratory in the Czech republic, located in Prague, which operates a compact tokamak—COMPASS. The Theory and modelling group of this department is focused on supporting COMPASS experiments by simulations as well as on contributing to international fusion research. Primary topics include integrated / transport modelling, edge and scrape-off layer physics, MHD or magnetic perturbations. We are currently aiming at expanding the group by two fellows, who would carry out research in the above listed areas.
The successful candidates will be responsible for performing research in one of the areas, closely linked to experiments on COMPASS and other tokamaks. Strong international collaboration is expected, primarily within EUROfusion laboratories.
The contract will be for 2 or 3 years with a possible prolongation or a subsequent permanent contract. The application deadline is November 10, 2016. Requirements
· Doctoral degree in physics, computational physics or similar.
· Experience in magnetic thermonuclear fusion research, preferentially in theory and modelling.
· Strong computer science skills: numerical methods, programming (Python and Fortran preferred), data analysis.
· Proficient English spoken and written.
Contacts
Please address your questions and applications (cover letter + CV) to Jakub Urban,urban@ipp.cas.cz, +420-26605-3396.

Deputy Director for Czech Centre for Phenogenomics, Vestec, Czech Republic The Czech Centre for Phenogenomics (CCP) is currently seeking a Deputy Director to serve as part of the management team and co-leading a Phenotyping Module. Requirements

The Global Change Research Institute CAS seeks a postdoctoral research fellow with the focus on analysis of eddy covariance data. The main task will be to analyze and interpret data from eddy-covariance measurement in different sites and to publish the results. The position is available from summer 2016. Requirements

The Global Change Research Institute CAS seeks a research fellow with the focus on analysis of eddy covariance data. The main task will be to analyze and interpret data from eddy-covariance measurement in different sites and to publish the results. The position is available from summer 2016. Requirements

Position in social and policy analysis of ecosystem services. The Global Change Research Centre (CzechGlobe), Academy of Sciences of the Czech Republic, Department of Human Dimensions of Global Change, seeks a postdoc research assistant or junior scientist with the research focus in the areas of valuation of ecosystem services, behavioral and socio-economic aspects of ecosystem services, cost-benefit analysis and agricultural economics and policy. Requirements

The Global Change Research Centre, Academy of Sciences of the Czech Republic, seeks a postdoc research fellow or junior scientist with the following research focus: Interpretation of data measured at the Atmospheric Station Křešín u Pacova. The Atmospheric Station Křešín u Pacova is a new monitoring and research infrastructure that started operation in 2013. It consists mainly of a 250 m tall tower and is a monitoring point for greenhouse gases, selected aerosol properties and gaseous pollutants. Ancillary meteorological measurements are conducted, too. The Atmospheric Station offers broad opportunities for multidisciplinary research focused on climate change, air composition and air quality. Requirements

Institute of Plasma Physics of the Czech Academy of Science, Prague, Czech Republic, is seeking a talented, motivated scientific software developer. Our team develops high-quality scientific software within the international fusion community. The candidate will primarily work with Jakub Urban and the CODAC team on software for integrated simulations in plasma physics and on data acquisition and handling software for large fusion experiments, applied to the COMPASS tokamak and future experiments like ITER or JT-60SA. Requirements

Institute of Plasma Physics, AS CR, v.v.i., seeks candidates for Junior researcher positions in the Department of Materials Engineering. Our research focuses in interaction of plasma with materials, in particular plasma spraying and spark plasma sintering. Further details on our research may be checked at www.ipp.cas.cz/Mi/ Requirements

The Global Change Research Centre, AS CR, v. v. i., in accordance with the Act No.283/1992 On the Academy of Sciences of the Czech Republic, as amended by the Act No. 420/2005, and in accordance with the Statute of the Academy of Sciences of the Czech Republic, announces an open competition for the position of the research fellow with the focus on analysis of eddy covariance data. Requirements

The Global Change Research Centre, AS CR, v. v. i., in accordance with the Act No.283/1992 On the Academy of Sciences of the Czech Republic, as amended by the Act No. 420/2005, and in accordance with the Statute of the Academy of Sciences of the Czech Republic, announces an open competition for the position of the postdoctoral research fellow with the focus on analysis of eddy covariance data. Requirements