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Written by Marek Kincl on . Posted in PRF.

Instructions to filling HAP (Academic Staff Performance Evaluation) at FSc USB, April 2022

Dear faculty members with at least 20% affiliation at the Faculty of Science USB,  please fill in the web form for Academic Staff Performance Evaluations (HAP) till Apr 19, 2022.

The evaluation applies to all academic staff who have a faculty affiliation of at least 20% (sum of faculty jobs including grants). Academic staff who are not involved in teaching or students’ supervision (i.e. educational activities) are not academic staff and are not subject to HAP. Technicians are also not academic staff (but if they aspire to move to an academic position from 1 July 2022, it is possible to apply to fill in the HAP).

Instructions:

Login to https://hap.jcu.cz with the same name and password as for STAG (IDM). If you cannot log in and you have academic employment >= 20% at the FSc, contact the portal administrator E. Krlín, This email address is being protected from spambots. You need JavaScript enabled to view it. .

 Notes on the evaluation at the FSc:

  1. For all blocks or questions, the period for which data are to be completed is always indicated.
  2. Teaching data is pre-filled using information from STAG - but needs to be checked and corrected. Please only include teaching, testing, course credits (‘zápočet’) done by you, i.e. do not include the work of Ph.D. students who have been involved in teaching, for example. Teaching is recorded on a subject-by-subject basis (each lecture and tutorial on a separate line).
  3. Examined students - each examined student on a course is listed only once. Their numbers are pre-filled according to STAG.
  4. The number of hours of weekly teaching can be a decimal number (with a decimal comma or a dot).
  5. The size of the grant project is judged by the total funding over the life of the project.
  6. In the field “Supervised Ph.D. students “list only students in the standard period of study.
  7. Leave blank items that do not apply to you.
  8. Fill in only the activities that you have carried out during your time at the Faculty of Science of USB. If you have performed activities within your employment at the FSc USB that are not on the USB records (e.g., reviewing thesis at other universities), please specify in the description.
  9. Import of scientific outputs (mainly articles) into HAP is done from OBD (bibliographic database). If you do not see some of your 2021 publications to be registered in RIV (country’s evidence of results), contact Jana Maxerová <This email address is being protected from spambots. You need JavaScript enabled to view it.> to verify/complete the publication’s entry in OBD. Without this step, the publication will not be registered in RIV, not reflected in the assessment of the FSc/JU.
    Fill in the missing output in HAP - the journal IF and category median do not need to be filled in, it will be supplied.
  10. Do not forget to enter "Number of citations in a given year (excluding 1st order self-citations)" at the end of section 2a), i.e. how many times your lifetime publications (regardless of affiliation) were cited by other authors in 2021. For instructions on how to find the number of citations in the Scopus and Web of Science databases, see https://web.prf.jcu.cz/veda/publikace/citace.html
    If you joined the FSc USB during the reporting period (2021 for publications) or later, you may also list performance from the other workplace prior to joining the FSc under the "Other" tab.
  11. In the “Academic offices and management activities” tab, the item “Deputy Head of the Department (faculty unit)” may be checked by the heads of sections of departments or other persons whose managing workload corresponds to this role.
  12. The 2019 and 2020 forms can be viewed but cannot be edited retroactively. If, with respect to the evaluation of academic staff and their placement in salary grades according to the new USB Salary Code, you wish to add critical information omitted at these forms, please add it in the HAP 2021 form, “Other relevant activities” tab as “Additional information” indicating the relevant year of the information. 

Practical notes for/from the evaluation:

  1. If HAP writes you e.g. 0.92+1.85 hours taught instead of 1+2 according to STAG, it means that one of the 13 weeks of the semester was dropped due to a holiday. Therefore, the output is reduced by a ratio of 12/13. If you substituted and taught 13 times, correct the values to 1+2. Otherwise keep the pre-filled values.
  2. When converting block instruction to hours/week, use a 13 week semester. Block 4 hours/sem = 4/13=0.31 hours/week.
  3. The corresponding author may indicate "I am the guarantor" in section 2a).
  4. If the teaching is provided by several persons present at the same time (practical/field classes, seminars led by two people), the same teaching can be reported by several persons (with an explanation of the indication of duplicated teaching in the "Other relevant activities" tab).

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Read more …Instructions to filling HAP (Academic Staff Performance Evaluation) at FSc USB, April 2022

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Written by Marek Kincl on . Posted in PRF.

Publication records, number of citations

Number of citations + setting of ORCID account and links with Publons.com (connected with Web of Science)

Instructions for determination of the number of citations in the given year (without 1st order autocitations), i.e. how many times in a given year (e.g. 2019) your lifelong publications (regardless of affiliation) were cited by other authors.
For the purpose of Academic Staff Performance Evaluations the result of either of the two sources below can be used:

SCOPUS - the instructions are easy,
If you search by name, make sure you select only records with your publications. If you search in Scopus by entering your ORCID (in this way, the Research Officer can search for your citations), verify that the record contains all your publications.

Web of Science - acceptable procedure, requires individual subtraction of self-citations from few newest papers.
Web of Science - older, complicated procedure.

Tutorials to create and maintain your ORCID record up to date

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Written by Blanka Bodnárová on . Posted in PRF.

Kurz galerie

Centre for Polar Ecology

Polar Ecology Course 2022

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Written by Ján Štěrba on . Posted in PRF.

nabídky kvalifikačních prací - offered topics (2)

Back to Dept. of Chemistry

Na této stránce je možné získat přehled o vypisovaných tématech diplomových prací na Katedře chemie jak v oborech chemických tak i v dalších příbunvých oborech. Díky výhodným podmínkám pro výzkum jsou výsledkem magisterských ale i bakalářských prací na našem ústavu nezřídka vědecké publikace. Jednou z velkých předností PřF JU je možnost (a nutnost) praktické práce již v bakalářském studiu. Pokud máte zájem o určité téma (i takové které není tady nabízené), kontaktujte přímo uvedeného školitele.
You can find offers of bachelor's and master's thesis at our department in chemistry and related fields. FSc USB allows (and requires) practical work already during the Bachelor studies. Thanks to the vast possibilities in research and up-to-date instrumentation, bachelor's and especially master theses usually result in publications in peer-reviewed journals. If you are interested in a specific topic (even a topic which is not offered here), contact please a potential supervisor.

Examples of topics of bachelor and master theses (or doctoral theses)

Pro zadání kvalifikační práce musíte odevzdat vyplněný a podepsaný zadávací protokol, s tím vám pomůže váš/-e školitel/-ka. Pro schválení musíte přinést vyplněný Zadávací protokol bakalářské/magisterské práce se všemi potřebnými podpisy, kromě podpisu vedoucího katedry, sekretářce Katedry chemie, Mgr. Kateřině Žižkové (Bud. C, 2. patro, 01 045, zizkok00 (at) prf.jcu.cz, tel. 38 777 6243). Krátký návod k vyplnění zadávacího protokolu najdete na našich stránkách.

Your supervisor will help you to fill in the assignment protocol, which you can find in documents - forms for students. Next, you need to get all the needed signatures, except the signature of the head of the department and hand in to the secretary of the Dept. of Chemistry (Mrs Zizkova, Bldg C, 1st floor, room 01 045, phone 38 777 6243). A short description helping you to fill in the assignment protocol can be found on our webpage.

Topic Supervisor
Modelling the effect of missense variants in intellectual disability and autism

Supervisor: Mgr. Michaela Fencková, PhD

Co-supervisor: Prof. Ivana Kutá Smatanová, Mgr. Petra Havlíčková

Single gene mutations represent the leading cause of intellectual disability (ID) and autism spectrum disorder (ASD). Missense variants that result in change of one amino acid (AA) in the protein sequence, contribute to disease risk to a similar or even greater degree than likely gene-disruptive mutations but their effect on protein structure and function is not known.

In this project, the student will use PyMOL molecular visualization and modeling system to introduce ~ 50 recurrent ID/ASD missense variants into high-resolution crystal structures of 10 proteins from RCSB Protein Data Bank and determine whether they affect folding and stability of the protein, its interaction with other proteins and molecules or alter the protein function. The results will lay down the basis for functional characterization of the underlying molecular and cognitive mechanisms in vitro and in our pre-clinical Drosophila model. If the student is motivated, he/she may be involved in initiation of these studies.
Glykomický a glykoproteomický profil tkání klíšťat a jiných krevsajících členovců s využitím bioortogonální a Click chemie a hmotnostní spektrometrie / Glycomic and glycoproteomic profile of ticks and other blood-feeding arthropods tissues using bioorthogonal and Click chemistry and mass spectrometry This email address is being protected from spambots. You need JavaScript enabled to view it. & Dr. Jarmila Štěrbová & Dr. Filip Dyčka
Analýza N-glykosylačních míst u proteinů krevsajících členovců (bioinformatika) / Analysis of N-glycosylation sites in proteins of blood-feeding arthropods (bioinformatics) This email address is being protected from spambots. You need JavaScript enabled to view it.
   
   
   
NMR structural studies on proteins of tick-borne pathogens

This email address is being protected from spambots. You need JavaScript enabled to view it. & This email address is being protected from spambots. You need JavaScript enabled to view it. (with the help of the Austro-Czech RERI-uasb NMR Center, JKU, Linz)
Elektronová mikroskopie fotosyntetických membrán a proteinových komplexů / Electron microscopy of photosynthetic membrane and protein complexes This email address is being protected from spambots. You need JavaScript enabled to view it.
  This email address is being protected from spambots. You need JavaScript enabled to view it. 

Role karotenoidů v ochraně fotosyntetických proteinů před tripletními stavy chlorofylu / The role of carotenoids in protection of photosynthetic proteins from chlorophyll triplet states

Molekuly chlorofylu jsou v autotrofních organismech vždy asociovány s karotenoidy. Funkcí fotosyntetických karotenoidů je jak rozšíření spektrálního okna pro sběr energie tak i ochrana organismu před kyslíkovými radikály, které jsou jinak nechráněným chlorofylem účinně generovány. Vlastnosti této ochranné funkce nejsou zřejmé zejména v případě systémů s 'nestandardními' karotenoidy jako mají některé eukaryotní řasy. V práci budou studovány jak přírodní komplexy, tak syntetické modelové systémy.
  This email address is being protected from spambots. You need JavaScript enabled to view it. 
 

Struktura pigment-proteinových komplexů fotosyntetických membrán a jejich funkce / Structure of pigment-protein complexes of photosynthetic membranes and their function

Světlosběrné komplexy jsou pravděpodobně nejdynamičtější součástí fotosyntetických membrán. Pigmenty pro sběr světelné energie jsou drženy proteinovou kostrou v přesných polohách a ve vysoké hustotě (až 0.5 M). Ačkoliv chybné postavení pigmentů může být pro fotosyntetický organismus smrtící, existuje mnoho variant kombinací druhů chlorofylů i karotenoidů. Klíčovou roli ve funkci výsledného komplexu má pak právě proteinový skelet, který lze zkoumat z bioinformatického nebo biochemického pohledu. Zaměřením práce může být jak teoretická analýza vlastností proteinů a srovnání s experimentem tak i sledování dynamiky fotosyntetické membrány v krátkém ( minuty) či dlouhém (dny a týdny) časovém horizontu.

 

  • Dr. Fencková: Modelling the effect of missense variants in intellectual disability and autism

  • Dr. Štěrba: Glycomic and glycoproteomic profile of ticks and other blood-feeding arthropods tissues using bioorthogonal and Click chemistry and mass spectrometry

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Written by Ján Štěrba on . Posted in PRF.

topics - entrance examination Biological Chemistry

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Topics - entrance exam - BSc Biological Chemistry

Mathematics

basic secondary school Mathematics, e.g., functions and graphs, equations, series, vectors, systems of equations

Chemistry

basic secondary school Chemistry, including calculations, e.g., basics of nomenclature of inorganic and organic compounds, basic calculations (molarity, molecular weight, …), periodic table and atomic structure, simple inorganic reactions, pH, basics of biochemistry (nucleotides and nucleic acids, aminoacids and proteins, saccharides). 

English language

 

Topics - entrance exam - MSc Biological Chemistry

Biochemistry

basic secondary school Chemistry, including calculations, e.g., basics of nomenclature of inorganic and organic compounds, basic calculations (molarity, molecular weight, …), periodic table and atomic structure, simple inorganic reactions, pH, basics of biochemistry (nucleotides and nucleic acids, aminoacids and proteins, saccharides). 

Biochemistry 1:

1.Introductory to Biochemistry: The origin of life; Mechanisms of molecular interactions, Metabolism.
2.Biomolecules: Amino acids; Peptides; Proteins; Carbohydrates; Lipids; Nucleic acids.
3. Enzyme catalysis I: Principles of catalysts and enzyme activity.
4. Enzyme catalysis II: Enzyme kinetics; Enzyme properties; Enzyme types.
5. Gene expression and proteosynthesis: Mechanisms of DNA replication; Transcription/the synthesis of RNA; Gene regulation in Procaryotes; Gene regulation in Eucaryotes; Translation/the synthesis of proteins; Posttranslational modification.
6. Biological membranes and membrane transport: Composition and structure; fluidity and assymmetry; transport across membranes; Methods in biomembrane research.
7. Introductory metabolism and bioenergetics: Metabolism; Thermodynamics of energetic metabolism; Biological oxidation; Coupled reactions; Experimental approach.
8. Energetic metabolism I: Carbohydrate metabolism; Compartmentation; Regulation.
9. Energetic metabolism II: The Citric acid cycle; Electron transport; Oxidative phosphorylation.
10. Energetic metabolism III: Lipid metabolism; Nitrogen utilization; Compartmentation.
11. Energetic metabolism IV: Photosynthesis and photosynthetic machinery; Photorespiration; the C4 cycle.
12. Biotransformation: Metabolism of xenobiotics; Mechanisms of biotransformation reactions; Enzymes in biotransformation, Compartmentation and physiological features.
13. Integration and regulation of energetic metabolism: Compartmentation of metabolic pathways; Functinal relatioships between pathways; Regulatory actions; Metabolic check points; Experimental approaches in metabolism.

Biochemistry 2:
1.Introductory to Biochemistry: The origin of life; Mechanisms of molecular interactions, Metabolism.
2.Biomolecules: Amino acids; Peptides; Proteins; Carbohydrates; Lipids; Nucleic acids.
3. Enzyme catalysis I: Principles of catalysts and enzyme activity.
4. Enzyme catalysis II: Enzyme kinetics; Enzyme properties; Enzyme types.
5. Gene expression and proteosynthesis: Mechanisms of DNA replication; Transcription/the synthesis of RNA; Gene regulation in Procaryotes; Gene regulation in Eucaryotes; Translation/the synthesis of proteins; Posttranslational modification.
6. Biological membranes and membrane transport: Composition and structure; fluidity and assymmetry; transport across membranes; Methods in biomembrane research.
7. Introductory metabolism and bioenergetics: Metabolism; Thermodynamics of energetic metabolism; Biological oxidation; Coupled reactions; Experimental approach.
8. Energetic metabolism I: Carbohydrate metabolism; Compartmentation; Regulation.
9. Energetic metabolism II: The Citric acid cycle; Electron transport; Oxidative phosphorylation.
10. Energetic metabolism III: Lipid metabolism; Nitrogen utilization; Compartmentation.
11. Energetic metabolism IV: Photosynthesis and photosynthetic machinery; Photorespiration; the C4 cycle.
12. Biotransformation: Metabolism of xenobiotics; Mechanisms of biotransformation reactions; Enzymes in biotransformation, Compartmentation and physiological features.
13. Integration and regulation of energetic metabolism: Compartmentation of metabolic pathways; Functinal relatioships between pathways; Regulatory actions; Metabolic check points; Experimental approaches in metabolism.

Molecular Biology

Introduction to molecular biology: History and application of molecular biology in today's science.
Molecular structure of genes and chromosome: Molecular definition of a gene, chromosomal organization of genes and noncoding DNA, structural organization of chromosomes.
Basic molecular genetic mechanisms, Replication of DNA: Understanding the central dogma of molecular biology and overview of basic molecular genetic mechanisms. Basic features of DNA replication in vivo.
Transcription and RNA processing, Translation and the genetic code: Principles of transcription in Prokaryotes and Eukaryotes, basic regulation of gene expression at transcriptional and postranscriptional level. Principles of translation, genetic code.
Mutation, DNA repair, and recombination: Molecular basis of mutations, induced mutagenesis, overview of repair mechanisms and principles of recombination.
Regulation of gene expression in Prokaryotes, Eukaryotes and the genetic control of development: Operon, molecular control of transcription in Eukaryotes, gene expression and chromosome organization, mechanisms of regulation of gene expression during development.
Molecular analysis of genes and gene products: Use of recombinant DNA technology to identify genes, molecular diagnosis of human diseases.
Recombinant DNA technology, the polymerase chain reaction: Cloning genes, principle of polymerase chain reaction and its applications.
Basic techniques of molecular biology: Overview of molecular biology techniques and their use in modern research.
Overview of molecular biology applications in modern basic and applied science: Summary of the course in context of using molecular biology in modern research.

General, Organic, and Analytical Chemistry

1. Atomic structure and the periodic table of elements
2. Chemical nomenclature, balancing equations
3. States of matter: gases, liquids, solids.
4. Chemical bonds and weak bonds
5. Solutions - chemistry and physical properties (solubility, solutions of acids and bases, buffer solutions)
6. Solutions - colligative properties
7. Chemical kinetics, mechanisms of reactions
8. Thermodynamics
9. Electrochemistry
10. Methods I: Chromatography, Spectrophotometry
11. Methods II: Potentiometry, Electrophoresis

• Atoms, molecules, bonding, polar and nonpolar molecules, intermolecular forces, solubilities, Lewis structures, preliminary ideas of resonance, arrow formalism, acids and bases.
• Introduction to orbitals, molecular orbital description of bonding, hybridization, structure of methane.
• Alkanes- conformational analysis, structural isomerism and nomenclature, alkyl groups.
• Alkenes- structure and bonding, nomenclature, E-Z notation, hydrogenation, relative stabilities. Alkynes- structure and bonding, relative stabilities, double and triple bonds in rings.
• Dienes and the allyl system, conjugation, introduction to the concept of aromaticity. UV spectroscopy.
• Stereochemistry- chirality, enantiomerism, R-S notation, diastereomerism, optical resolution.
• Ring systems- strain, stereochemistry of cyclohexane, conformational analysis of cyclohexane and its substituted derivatives, bicyclic and polycyclic compounds.
• Nuclear Magnetic Resonance (NMR) spectroscopy.
• Infrared (IR) spectroscopy.
• Alkyl halides, substitution reactions of alkyl halides- SN 2 and SN 1 mechanisms. Elimination reactions- E1 and E2 mechanisms.
• Overview of substitution and elimination reactions, oxidation of alcohols, rates and equilibria, syntheses.
• Acids and bases revisited. Additions to alkenes- mechanism of hydrogen halide additions, regiochemistry, resonance effects, carbocation stabilities, addition of other unsymmetrical reagents, hydroboration, dimerization and polymerization of alkenes.
• Carbocation rearrangements, addition of halogens to alkenes, oxymercuration, epoxidation and chemistry of oxiranes, cyclopropanation, carbenes, ozonolysis, alkene oxidations with permanganate and osmium tetroxide, addition reactions of alkynes.

Tools in the analytical laboratory; Fundamentals of precipitation titrations, acid-base titrations, complexometric titrations, redox titrations (including calculations of titration curves, detection of end points, applications); Theory of potentiometry (redox potential, electromotive force, electrodes of the first and second kind, redox electrodes, indicator and reference electrodes), applications of potentiometry (pH electrode, ion-selective electrodes, potentiometric titrations); Amperometric sensors, amperometric titrations; Coulometric Titrations; Conductometric analysis; Introduction to spectoscopy, instrumentation for molecular absorption spectroscpy in the UV-visible range, atomic spectroscopy, fluorescence spectroscopy, IR spectroscopy. Introduction to chromatographic techniques.

 

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