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Projects Proposed by Faculty of Science for the 10th call

Epigenomics and evolution of sex determination in vertebrates
Lukáš Kratochvíl & Michail Rovatsos

Sex chromosomes represent an outstanding example of the convergence at the genomic level. They evolved likely more than 40-times independently just in amniote vertebrates (mammals, reptiles and birds), in many cases probably from the ancestral environmental sex determination, where sex chromosomes are not present. In many cases, the same pair of ancestral autosomes started playing the role of sex chromosomes, e.g. the XX/XY sex chromosomes of viviparous mammals including humans share gene content with ZZ/ZW sex chromosomes in lacertid lizards. The project aims to uncover sex chromosomes and to determine their gene content in yet unstudied vertebrate lineages, to test homology of sex chromosomes across and within particular lineages using cytogenetic and molecular approaches. Also, it will focus on the convergent evolution during differentiation of sex chromosomes with the respect of gene content, particularly loss of genes from degenerated Y and W chromosomes and the effect of sex chromosome differentiation on the expression of sex-linked genes, in order to uncover how particular lineages cope with the loss of gene copies during degeneration of unpaired sex chromosomes. The project has also a practical aspect: to find a reliable technique for molecular identification of sex of individuals in endangered or commercially valuable species of vertebrates.

 
Relevant team publications since 2015:

Rovatsos M., Kratochvíl L. 2017. Molecular sexing applicable in 4,000 species of lizards and snakes? From dream to real possibility. Methods in Ecology and Evolution (doi: 10.1111/2041-210X.1271).

Rovatsos M., Praschag P., Fritz U., Kratochvíl L. 2017. Stable Cretaceous sex chromosomes enable molecular sexing in softshell turtles (Testudines: Trionychidae). Scientific Reports 7: 42150.

Johnson Pokorná M., Altmanová M., Rovatsos M., Velenský P., Vodička R., Rehák I., Kratochvíl L. 2016. The first description of the karyotype and sex chromosomes in the Komodo dragon (Varanus komodoensis). Cytogenetic and Genome Research 148: 284-291.

Rovatsos M.,Vukić J., Johnson Pokorná M., Altmanová M., Moravec J., Kratochvíl L. 2016. Conservation of sex chromosomes in lacertid lizards. Molecular Ecology 25: 3120-3126.

Rovatsos M., Vukić J., Kratochvíl L. 2016. Mammalian X homolog acts as sex chromosome in lacertid lizards. Heredity 117: 8-13.

Altmanová M., Rovatsos M., Kratochvíl L., Johnson Pokorná M. Minute Y chromosomes and karyotype evolution in Madagascan iguanas (Squamata: Iguania: Opluridae). Biological Journal of the Linnean Society 118: 618–633.

Johnson Pokorná M., Kratochvíl L. 2016. What was the ancestral sex-determining mechanism in amniote vertebrates? Biological Reviews 91:1-12.

Rovatsos M., Johnson Pokorná M., Kratochvíl L. 2015. Differentiation of sex chromosomes and karyotype characterisation in the dragonsnake Xenodermus javanicus (Squamata: Xenodermatidae). Cytogenetic and Genome Research 147:48-54.

Rovatsos M., Johnson Pokorná M., Altmanová M., Kratochvíl L. 2015. Female heterogamety in Madagascar chameleons (Squamata: Chamaeleonidae: Furcifer): differentiation of sex and neo-sex chromosomes. Scientific Reports 5: 13196.

Rovatsos M., Vukić J., Lymberakis P., Kratochvíl L. 2015. Evolutionary stability of sex chromosomes in snakes. Proceedings of the Royal Society of London B – Biological Sciences 282: 20151992.

 

Electrochemical Bio(sensors) for Sensitive Detection of Organic Xenobiotic Compounds
Ass
oc. Prof. RNDr. Vlastimil Vyskočil, Ph.D.

Monitoring of detrimental organic xenobiotic compounds in the environment and in simple clinical samples is one of the most important tasks of modern analytical chemistry. Electrochemical techniques are especially suitable for large-scale environmental and clinical monitoring of electrochemically active xenobiotics because they are inexpensive, extremely sensitive, and they present an independent alternative to so far prevalent spectrometric and separation techniques. Development of sufficiently sensitive and selective electrochemical methods for determination of various environmentally and clinically important biologically active organic substances is the main task of our UNESCO Laboratory of Environmental Electrochemistry.

In current electroanalytical chemistry, there is an ever-increasing need for new electrode materials characterized by broader potential window, higher signal-to-noise ratio, biocompatibility, mechanical stability enabling their application in flowing systems, and resistance toward passivation. The last requirement is especially important because electrode fouling is probably the biggest obstacle to more frequent applications of electroanalytical techniques in environmental/clinical analysis.

In consequences to the above-mentioned facts, the proposed post-doc project should be focused on following innovative strategies:

–          application of non-traditional electrode materials (silver amalgam, boron-doped diamond, micro-structured forms of carbon) in combination with modern extraction techniques (micro solid-phase extraction, single-drop micro-extraction, gas-diffusion micro-extraction, hollow-fiber extraction) for increasing the sensitivity of the analyte determination

–          testing of new electrode materials (boron-doped diamond powder, diamond-like carbon, nano-structured forms of carbon and gold) as perspective alternatives to the traditional ones

–          development of miniaturized smart sensors and devices for field measurements and/or measurements in microliter-volume samples

–          application of DNA biosensors utilizing the DNA–analyte interaction for increasing the sensitivity of the analyte determination

The candidate will be expected to carry out the development and testing of novel electrochemical bio(sensors) and strategies for sensitive determination of selected organic xenobiotic compounds. Special emphasis will also be placed on the investigation of mutual interactions between DNA and the studied xenobiotics. The investigated analytes will be (but not limited to) pesticides, anticancer drugs, tumor biomarkers, and chemical carcinogens. The project involves active collaboration with the research groups of Assoc. Prof. Miroslav Fojta (Institute of Biophysics of the CAS, Brno), Assoc. Prof. Tomáš Navrátil (J. Heyrovský Institute of Physical Chemistry of the CAS, Prague), and Assoc. Prof. Alexander Kromka (Institute of Physics of the CAS, Prague).

Contact person and supervisor of the project:

Assoc. Prof. RNDr. Vlastimil Vyskočil, Ph.D.

Head of the Group of Electrochemical Biosensors and Bioelectrochemistry UNESCO Laboratory of Environmental Electrochemistry

Department of Analytical Chemistry Faculty of Science
Charles University
Hlavova 8, 128 43 Prague 2, Czech Republic
tel.: +420-221 951 599, fax: +420-224 913 538, e-mail: vlastimil.vyskocil@natur.cuni.cz
web: https://www.natur.cuni.cz/chemistry/analchem/research-and-science/groups/laboratory-of-environmental-electrochemistry

 
Tethering complex exocyst in plant morphogenesis and defence
Viktor Žárský, Department of Experimental Plant Biology at the Faculty of Science, Charles University

Plant morphogenesis is based essentially on the regulation of cell division plane and orientation or localization of cell elongation – i.e. on processes of polarized secretion, where along with the cytoskeleton, regulators of membrane vesicles traffic play a crucial role. Our laboratory at the Department of Experimental Plant Biology contributes decisively to the characterization of the exocyst vesicles tethering complex involved in the secretion pathway localization by mediating first phase of specific contact between the vesicle and target membrane. Localized secretion is also one of the basic plant defence mechanisms after the microbial pathogen attack and not surprising also in this context exocyst plays important roles. Based on the best candidate interests we will specify details of the experimental program together.  In any case the project will have to do with the characterization of functions of specific isoforms of exocyst subunits EXO70 – a very plant specific feature of the complex.

Topic relevant papers of last two years (2016 and 2017):

Zhang C, Brown MQ, van de Ven W, Zhang ZM, Wu B, Young MC, Synek L, Borchardt D, Harrison R, Pan S, Luo N, Huang YM, Ghang YJ, Ung N, Li R, Isley J, Morikis D, Song J, Guo W, Hooley RJ, Chang CE, Yang Z, Žárský V, Muday GK, Hicks GR, Raikhel NV. Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis. Proc Natl Acad Sci U S A. 113:E41-50, 2016.

Bloch D, Pleskot R, Pejchar P, Potocký M, Trpkošová P, Cwiklik L, Vukašinović N, Sternberg H, Yalovsky S, Žárský V. Exocyst SEC3 and Phosphoinositides Define Sites of Exocytosis in Pollen Tube Initiation and Growth. Plant Physiol. 172(2):980-1002, 2016 ( to this report a short teaser was published in the Science).

Vukašinović N, Žárský V. Tethering Complexes in the Arabidopsis Endomembrane System. Front Cell Dev Biol. May 19;4:46. doi: 10.3389/fcell.2016.00046. 2016.

Pečenková T, Sabol P, Kulich I, Ortmannová J, Žárský V. Constitutive Negative Regulation of R Proteins in Arabidopsis also via Autophagy Related Pathway? Frontiers in Plant Science vol. 7, Article 260; ;7: doi: 10.3389/fpls.2016.00260. 2016.

Vukašinović N, Oda Y, Pejchar P, Synek L, Pečenková T, Rawat A, Sekereš J, Potocký M, Žárský V. Microtubule-dependent targeting of the exocyst complex is necessary for xylem development in Arabidopsis. New Phytol. 213(3):1052-1067, 2017 - doi: 10.1111/nph.14267, 2016.

Sabol P, Kulich I, Žárský V. RIN4 recruits the exocyst subunit EXO70B1 to the plasma membrane. J. Exp. Bot.; , in press, doi: 10.1093/jxb/erx007, 2017.

Rawat A, Brejšková L, Hála M. Cvrčková F, Žárský V. The Physcomitrella patens exocyst subunit EXO70.3d has distinct roles in growth and development, and is essential for completion of the moss life cycle. New Phytol. in press DOI: 10.1111/nph.14548, 2017.

Pečenková T, Pleskot R, Žárský V. Subcellular Localization of Arabidopsis Pathogenesis-Related 1 (PR1) Protein. Int. J. of Mol. Sci., 18, 825; doi:10.3390/ijms18040825, 2017.

Pečenková T, Janda M, Ortmannová J, Hajná V, Stehlíková Z, Žárský V. Early Arabidopsis root hair growth stimulation by pathogenic strains of Pseudomonas syringae. Annals of Botany in press, 2017.

Sekereš J, Pejchar P, Šantrůček J, Vukašinović N, Žárský V, Potocký M. Analysis of exocyst subunit EXO70 family reveals distinct membrane polar domains in tobacco pollen tubes. Plant Physiol. 173: 1659-1675, doi:10.1104/pp.16.01709, 2017.

Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen. Plant Physiol. 174:223-240, doi:10.1104/pp.16.01282, 2017 (to this and previous report a commentary was published in Plant Physiology).

 

Modeling of nanoparticle diffusion and transport in macromolecular environment
(postdoc project proposal)

Diffusion of nanoparticles in an environment containing macromoecules is much more complicated process than simple diffusion in pure solvents which is commonly described in textbooks. Examples of such environments are synthetic polymer gels or a crowded environment of proteins inside a cell. Friction experienced by the diffusing molecules in such environment does not follow the well-known Stokes-Einstein relation: small diffusants are more faster, while sticky diffusants are slower than what could be calculated from macroscopic viscosity. Therefore the term nanoviscosity has been coined in the last decade. Many experimental works addressing nanoviscosity are available in literature but suitable theoretical models are still scarce. The goal of this project is to design simplified (coarse-grained) models of nanoparticle diffusants in macromolecular environments, and to use computer simulations as a theoretical tool to study their spatial distribution and diffusion properties. The project is a part of a larger research project focused on modeling of partitioning and diffusion of small molecules in polymeric gels.

The applicant's task will be to design the simulation models, to carry out the simulations and to analyze the simulation data. The results will be used for fundamental understanding of the physical process, as well as for interpretation of experimental results from collaborating teams.

Profile of an ideal candidate:

  • Completed PhD at the time of application, but not more than 10 years since its completion, fulfilment of other conditions prescribed by the University (required)
  • Good knowledge of English (FCE equivalent or better)
  • Strong background in soft matter and statistical mechanics
  • Experience with molecular simulation, programming and Linux OS

Project supervisor: Dr. Peter Košovan
Contact: peter.kosovan@natur.cuni.cz +420-221-591-290
Soft Matter research group (http://web.natur.cuni.cz/~kosovan1/softmatter/)
Department of Physical and Macromolecular Chemistry
Faculty of Science, Charles University, Prague
Hlavova 8, 128 43 Prague, Czech Republic

 

Determining the cascade of cell loss in Alzheimer’s disease
Mgr. Petr Telenský, PhD, Department of physiology
Contact: telep@centrum.cz, +420 221 951 772

Annotation:

Despite decades of effort, clinical trials for treatment strategies aimed at reducing amyloid burden in patients suffering from Alzheimer’s disease did not result in an effective cure. This prompted the necessity to re-evaluate the dominant hypothesis that accumulation of beta-amyloid in the brain is the initiating cause of Alzheimer’s disease. A major obstacle in determining the cause of neurodegenerative process in Alzheimer’s disease is the lack of knowledge on the cascade of cellular loss in specific brain structures and neuronal subpopulations. Furthermore, quantitative description of the changes in specific glial subpopulations in the course of the neurodegenerative process is completely lacking. Filling this knowledge gap became practically possible only recently with the development of the Isotropic Fractionator technique and with the discoveries of novel neuronal and glial nuclear markers. Therefore, the goal of this project is to validate novel nuclear markers for the isotropic fractionator technique and to map the cascade of loss of specific brain cell subpopulations during the course of the neurodegenerative process in the novel transgenic rat model strain Tgf-344AD. This project is expected to have a substantial impact on our understanding of Alzheimer’s disease etiology.

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