BEYOND-THE-LIMIT RECRUITMENT

The main element of education at the Doctoral School of Exact and Natural Sciences (SDNSP) is the implementation of an individual PhD project in one of the scientific disciplines (Astronomy, Computer Science, Mathematics, Biological Sciences, Chemical Sciences, Physical Sciences, Earth and Environmental Sciences) that are covered by the school, under supervision of a faculty member chosen by the doctoral student.

Education at SDNSP includes courses in the form of specialization and monographic lectures, workshops, seminars, two-day symposiums as well as courses and trainings to improve the skills of doctoral students in teaching.

The graduate of the Doctoral School of Exact and Natural Sciences has a highly specialized education acquired under the supervision of leading scientists and is prepared to undertake independent scientific and teaching activities at universities and research institutes. In addition, the graduate will have gained extensive knowledge beyond the discipline in which he/she prepared his doctoral dissertation, as well as skills in conducting scientific and teaching activities

Education

Education program

The education lasts 4 years. It includes obligatory classes (no more than 300 hours in total during the whole period of education) and the implementation of an individual research program, carried out under the supervision of a supervisor.

IRK registration instruction

Instruction

Principal Investigator: prof. dr hab. Joanna Trylska

E-mail: joanna@cent.uw.edu.pl

Project description

Enzymes are biocatalysts that speed up chemical reactions. These reactions occur in cells, which form a crowded environment. Cells, apart from water and ions, contain many other molecules such as nucleic acids, proteins, ribosomes, lipids, and metabolites. In addition, the cellular environment is compartmentalized by phospholipid membranes. Membranes are used for cell protection, transport of compounds, and organizing cells’ interior space. All in all, a specific biochemical reaction occurs with background macromolecules that may occupy 30% of the volume in mammalian cells. Apart from physically restricting the space for the enzyme of interest, the crowders and the membranes also nonspecifically interact with the enzyme and its substrates. The confinement and interactions may affect the reaction rates as compared to dilute water conditions. In addition, such conditions also affect the binding and effectiveness of enzyme inhibitors that are used as drugs.

However, for ease of interpreting the results, in a laboratory test tube, enzymes are often studied in dilute buffer solutions, which do not reflect the physiologic conditions and cell context. So, to understand what controls enzymatic activity and obtain realistic reaction rates or inhibitor efficiencies, we will perform enzymatic assays accounting for complex surroundings.

Proteases are an important class of enzymes that cleave peptide bonds and are involved in many biological functions. Also, viral genomes encode proteases that cleave the viral protein chain precursors after they are translated by the host cell machinery. Since these proteases are key to viral replication, they have been viable drug targets. Drugs inhibiting proteases of the human immunodeficiency virus and hepatitis C virus (HCV) have been used in antiviral combination therapies in humans.

We will investigate the reactions catalyzed by two enzymes encoded by the HCV genome. This virus causes liver inflammation which can lead to serious liver damage and cancer. One of the HCV enzymes that we will focus on is called the NS3/4A protease and is a known drug target with several drugs approved for clinical use in the last decade. The second one is the NS2 protease with no approved drugs as yet, but it is a possible target to consider. These two proteases work at the endoplasmic reticulum membranes of the host cell. Our goal is to determine how membrane environment and macromolecular crowding affect the activity of these two hepatitis C virus proteases crucial for viral replication. We will also investigate how the membrane and crowded surroundings affect the efficiency of two drugs binding to NS3/4A. As membrane mimics we will use micelles, lipid vesicles and nanodiscs, which are nanoscale lipid bilayers. As crowder molecules, we will use synthetic polymers such as polyethylene glycol, polysucrose, polyglucose, and proteins. The efficiencies of the reactions will be monitored by various techniques such as fluorescence spectroscopy, electrophoresis, chromatography, and microcalorimetry.

Requirement

The  call  is  open  to  all  those  who  are  not  PhD  holders  and  are  not  students  at  the  doctoral  schools.

- will hold an MSc degree in (bio)physics or a related discipline before Oct 1^st, 2023, i.e., at the time of starting the Doctoral School,

- have a background in biophysics and biochemistry,

- are knowledgeable and interested in biophysics and biochemistry methods such as fluorescence and circular dichroism spectroscopy, and microcalorimetry,

- are interested in enzymatic reactions, biological membranes, and crowded milieu,

- will apply for and do a six-month internship abroad in the USA,

- will comply with the rules of the Preludium BIS projects found on the National Science Centre Poland webpage.

In addition:

- experience in laboratory work, especially with peptides and proteins, will be beneficial,

- very good command of spoken and written English is a must, as well as teamwork skills and critical thinking.

Admission limit: 1

Recruitment schedule

• registration in the Internet Registration of Candidates, referred to as “IRK”, submitting an application to the IRK: 10 May  - 31 May 2023 
• qualification procedure:  01 June  -  07 June 2023
• announcement of the ranking list: until  16 June  2023
• accepting documents from qualified candidates: 19 June - 21 September 2023
• announcement of the list of accepted candidates: until 30 September 2023

Recruitment fee

The admission fee is PLN 200 and is paid to the candidate's individual account generated in the IRK system.

Form of the selection procedure

Evaluation of the following elements shall be taken into account in the selection process:

1) scientific activity of the candidate based on a CV or resumé, documented with scans of materials attached to the application for admission to the School;

2) interview with the candidate / qualification examination;

3) other achievements.

Language of the selection process, including the interview

The interview shall be carried out in Polish or English – in accordance with the candidate’s preferences presented in IRK. If the Polish language is selected, the interview may include parts in English.

Required documents

The candidate shall submit a School admission application only through the IRK. The application shall include the following:

1)     indication of the selected discipline in which the candidate plans to pursue education, PESEL number or passport number, nationality, contact information (residence address, e-mail address, telephone number), information whether the candidate agrees to receive administrative decisions by means of electronic communication, consent for processing of personal data for the purposes of the admissions procedure;

 2)    a scan of the graduation diploma of uniform master’s degree or postgraduate studies or an equivalent diploma obtained under separate regulations, or in the case of candidates pursuing education in the European Higher Education Area – a certificate of holding a master's degree or a statement that the diploma or certificate conforming the award of a master's degree will be delivered by 21st of September 2023, in the case of a diploma equivalent to a uniform master’s degree or postgraduate studies graduation diploma, a candidate shall justify such equivalence. In case the diploma was issued in a language other than Polish or English, the candidate shall attach its certified translation; 

3)   a resume or CV outlining the candidate’s scientific activity, including scholarly interests and achievements during the five calendar years preceding the application (if a candidate became a parent during this time, as evidenced by a scan of the child’s birth certificate attached to the application, this period shall be extended by two years for each child), including, but not limited to:

-        publications,

-        research and organizational work at student research groups,

-        participation in scientific conferences,

-        participation in research projects,

-        awards and honorable mentions,

-        research internships,

-        research skills training programs completed,

-        activities promoting science,

-        activity in science movement representative bodies,

-        average of their university grades,

-        professional career,

-        level of proficiency in foreign languages;

4)     scans of materials evidencing scientific activity mentioned in their CV and/or resume;

5)     a document confirming at least B2 proficiency level in English or a declaration of the level of proficiency in English allowing education at the School;

6)     the scan of a declaration by the planned supervisor, confirming their agreement to undertake the duties of a supervisor and of the number of doctoral students, for whom they perform the duties a designated supervisor, in accordance with the template constituting Appendix no.4 to the Resolution no. 17 of the Senate of the University of Warsaw of 20th January 2021 on rules of admission to doctoral schools at the University of Warsaw (the University of Warsaw Monitor of 2023, item 43), the candidate may also attach a scan of opinions of other academics about the candidate and their scientific activity. Template of the supervisor’s statement

7)     the photograph of a candidate’s face that allows for their identification;

8)     a declaration confirming whether the candidate was or is a doctoral student or a participant of doctoral studies or whether they have initiated a doctoral dissertation process or whether proceedings to award them a doctoral degree have been initiated – and if yes, the title of their doctoral dissertation or the research project prepared by a candidate, including the name and last name of the candidate’s tutor or supervisor;

9)    a declaration confirming that they have reviewed the Resolution no. 17 of the Senate of the University of Warsaw of 20th January 2021 on rules of admission to doctoral schools at the University of Warsaw (the University of Warsaw Monitor of 2023, item 43) and Articles 40 and 41 of the Code of Administrative Procedure;

10)  scanned transcripts of records of the graduate and postgraduate studies or the uniform Master’s degree studies, or equivalent documents (e.g. diploma supplement);

11)  abstract of the master’s thesis or master’s project in English (up to 3,000 characters with spaces);

Evaluation criteria

The committee shall evaluate the candidates by awarding them points for their competencies to  perform specific tasks in a research project and scientific achievements to date. On the basis thereof, the committee shall rank the candidates according to the following criteria:

 a) competencies to perform specific tasks in a research project (70% of the final score)

• 3 points - very good
• 2 points – good
• 1 point – poor
• 0 points - no competencies

 b)  publication track record, including publications in renowned scientific papers / magazines (30% of the final score)

•  4 points – prominent
• 3 points - very good
• 2 points – good
• 1 point – poor
• 0 points - no publication track record

Scholarships

PRELUDIUM BIS doctoral scholarships shall amount to:

• PLN 4266.00 gross per month, until the month in which a PhD student’s mid-term evaluation is performed at the doctoral school and
• PLN 5119.00 gross per month, after the month in which a PhD student’s mid-term evaluation is performed at the doctoral school and

shall be awarded pursuant to the Act on Higher Education and Science of 20 July 2018.

Recruitment Legislation and Acts to Know

• Resolution no. 17 of the Senate of the University of Warsaw of 20 January 2021 on rules of admission to doctoral schools at the University of Warsaw (consolidated text: the University of Warsaw Monitor of 2023, item 43)

• Resolution no. 7 of the Rector of the University of Warsaw of 31 March 2023 on the admission procedure fee for carrying out the qualification procedure to the doctoral school at the University of Warsaw (the University of Warsaw Monitor of 2023, item 126)