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1 funded PhD position (DC5) in MSCA Doctoral Networks - Istanbul

13 Mar 2023

Job Information

Organisation/Company
BAHÇEŞEHİR ÜNİVERSİTESİ
Department
Biophysics
Research Field
Biological sciences » Biological engineering
Technology » Biotechnology
All
Researcher Profile
First Stage Researcher (R1)
Country
Turkey
Application Deadline
Type of Contract
Temporary
Job Status
Full-time
Offer Starting Date
Is the job funded through the EU Research Framework Programme?
H2020 / Marie Skłodowska-Curie Actions
Reference Number
3
Marie Curie Grant Agreement Number
101073316
Is the Job related to staff position within a Research Infrastructure?
No

Offer Description

1 Doctoral Candidate position (DC5) at BAHÇEŞEHİR ÜNİVERSİTESİ (BAU) Istanbul is available in the framework of the Marie Skłodowska Curie - Doctoral Networks (MSCA-DN) project “Targeting RNA as an approach for treating retinal disease” (RETORNA). 

RETORNA proposes breakthrough research, distributed in 10 individual projects, performed by 10 Doctoral candidates (one of them being the DC5), in the following countries: IrelandSpainNetherlandsTürkiyeGermany and Italy. 

DC5 will be hired by BAHÇEŞEHİR ÜNİVERSİTESİ (BAU) and working mainly in the lab (https://durdagilab.com/in Istanbul, with various secondments in RETORNA consortium.

Get to know the lab:

We are applying computational chemistry methods to biological systems in our research group. Our inter-disciplinary research focuses on protein engineering and analyses of their structural/functional dynamics, ligand- and structure-based drug design, high throughput virtual screening, machine learning, text mining, investigation of molecular mechanisms of protein/drug, protein/protein and protein/DNA interactions and optimizations protocols for rational drug design. For this aim, together with applications of molecular modeling tools such as homology modeling, 3D-QSAR, molecular docking, molecular dynamics (MD) simulations, PMF computations, and applications of cheminformatic tools; we are also developing programing codes for several biological problems.

 

RETORNA summary description:

RETORNA aims to treat retinal diseases (RD) by using RNA therapy. Among the research objectives, we will study different types of RNA that are expressed in retinal cells. By observing bioinformatic models, cell and tissue cultures, animal models, and human patients, we will be able to create RNA profiles for different RD. This screening will identify several targets that will be used as therapeutic approaches. Then, selected RNAs will be used to treat different RD, such as macular degeneration and retinitis pigmentosa.

The proposed doctoral network (DN) will provide an innovative, international, multi/interdisciplinary platform to train young scientists in the field of vision science. 

For more information about RETORNA: https://cordis.europa.eu/project/id/101073316

 

Details of the individual project DC5:

Title of the DC5 project: Designing of novel aptamer-based AT1R targeted therapeutics against retinal degeneration

Host supervisor: Dr. Serdar Durdagi (BAHÇEŞEHİR ÜNİVERSİTESİ, Türkiye)

 

Objectives:

It is shown that retinal microglia express angiotensin II type-I receptor (AT1R), thus its endogenous ligand Ang-II may activate directly AT1Rs on microglia to induce an activation response and may lead to increase retinal inflammatory factors production. Thus, targeting this activation pathway in diseases such as DR can be useful for the identification of novel therapeutic agents. Since the therapeutic effects of aptamers on neurodegenerative diseases are well characterized, in the  proposed project, virtual aptamer libraries will be constructed and these libraries will be screened at the binding sites of the AT1R.

For this aim, we will write a Python script to generate libraries of oligonucleotides with lengths of 5 up to 10 (i.e., from 1024 (pentanucleotide) to 1048576 (decanucleotide) that will be all probable combinations of A, T, G, and C nucleotide sequences). Then, these oligonucleotides will be screened at the binding pocket of the AT1R and top-docking scored oligonucleotides will be used in molecular dynamics (MD) simulations. By this way, dynamic behavior of the protein-oligonucleotide complexes will be studied and binding free energies will be computed and sorted. As final step, based on binding free energy results (i.e., PBSA), top-scored oligonucleotides will be used in the designing the rigid and structural part of aptamer. In this step, the structural part of the aptamer will be designed by elongating the oligonucleotide using de novo designing techniques. This structural part of the aptamer will help in maintaining the optimal binding conformation of the recognition part of the aptamer. Moreover, computational predictions will be tested by in vitro experiments.

 

Expected Results:

Novel therapeutic aptamer sequences will be identified, designed and tested using target-driven approaches. Validation of the results will be carried out with our collaborators (i.e., Dr. Zohreh Hosseizadeh).

The core component of the proposed research is the ability to run multiple simulations, analyze them and communicate results between labs of Dr. Durdagi and Dr. Hosseizadeh. DC5 will be trained in protein-ligand interactions, machine-learning based design of therapeutics and subsequent virtual optimization. The DC5 will be also trained in development of new free-energy simulation techniques and programing/code writing.

 

Secondments are foreseen during the 36 months project.

Requirements

Research Field
All
Education Level
Master Degree or equivalent
Skills/Qualifications

Candidates reseachers must:

  • have MSc level training in computational biology or similar topics such as Chemistry, Biological Sciences, Physics, Biotechnology, Bioengineering or any other field that matches the DC5 project 
  • possess scientific skills for the project and research experience 
  • possess a good working level of English: candidates must demonstrate during the interview a good ability to understand and express themselves in both written and spoken English, sufficiently high to fully benefit from the experience 
  • be highly motivated
  • be creative and possess a high level of independency
Specific Requirements

1. Master degree with thesis

2. Python knowledge is desirable but not mandatory

The following 2 specific requirements (3 and 4) are not mandatory at the moment of application, but the selected candidate will have to proceed with acquiring the requirements in the first months of the contract: 

3. GRE result of at least 151 in the quantitative score type or GMAT result of at least 465 in total

4. English Proficiency Result Certificate (YDS:65, TOEFL:79, YÖKDIL:65) is required.(For English Language Education Program; YDS: 80, YÖKDIL: 80, TOEFL: 96)

Other desired skills:

1. Experience of computational drug design and optimization

2. Ability to learn new concepts and methods are recommended

3. Good basic knowledge of theoretical chemistry

Languages
ENGLISH
Level
Good
Research Field
Biological sciences » Biological engineering

Additional Information

Benefits

RETORNA fellows will be employed according to the rules for Doctoral Candidates in MSCA DNs and the general regulations of each hosting institution.

The monthly financial package will include the following gross researcher allowances:

1) Living allowance of € 3,400.00 (country correction coefficient applies)

2) Mobility allowance of € 600.00

3) Family allowance of € 660.00 if applicable.

The final net monthly amount depends on the country destination and the family situation.

The guaranteed PhD funding is for 36 months starting from autumn 2023.

Other benefits:

The selected candidates together with other 9 doctorates that will be selected will benefit from a large variety of activities foreseen for them. DCs at RETORNA will be provided with a unique multi-disciplinary and multi-sectoral training. First and foremost, DCs will be trained as scientists, each of them in their host institution, at their research secondments, and through local and network wide events. Next, thanks to the partnership between academic and non-academic entities, DCs will receive multi-sectoral inputs from both worlds. This will happen via lectures and workshops in our varied training program in which all DCs will participate.

Eligibility criteria
  • candidates can be of any nationality
  • must comply with the following mobility rule: researchers are required to undertake trans-national mobility (i.e., move from one country to another) and participate in all the activities foreseen by the project when taking up the appointment (trainings, summer courses, annual meetings, lectures, participation in conferences, public activities).
  • possess a Master degree or an equivalent that allows the access to the doctoral program in the BAHÇEŞEHİR ÜNİVERSİTESİ - BAU (read the requirements)
  • be, at the date of recruitment, a doctoral candidate (i.e. not already in possession of a doctoral degree). Researchers who have successfully defended their doctoral thesis but who have not yet formally been awarded the doctoral degree will not be considered eligible.
  • not have resided or carried out their main activity (work, studies, etc.) in the country of the recruiting beneficiary for more than 12 months in the 3 years immediately before the recruitment date. Short stays, such as holidays, are not taken into account.
Selection process

The RETORNA selection procedure is open, transparent, merit-based and in line with the Code of Conduct for the Recruitment of Researchers and the European Charter for Researchers.

The criteria for recruitment of DCs will respect the principles of non-discrimination contained in The Charter of Fundamental Rights of the European Union.

It is the policy of the RETORNA project to promote and give equal opportunities regardless of gender and stimulate gender balance.

Documents required

Interested candidates should submit the following documents via email to andreea.craciun@ucv.es, indicating in the e-mail title "RETORNA - DC5 application":

  • a detailed CV, including – if applicable – relevant publications
  • a motivation letter, indicating why you wish to conduct this research project
  • two (2) letters of reference
  • transcripts of bachelor and master degrees
  • English certificate (if the candidate possess one)

We encourage candidates to send any other certificates, representative publications, academic references or links demostrating the experience and interest in the project. 

All documents must be named as "type of document_NameSurname" (i.e. Motivation letter_Andreea Craciun")

Selection process

The selection process will foreseen the following steps:

1.  Eligibility: the RETORNA recruitment committee will check that each application is complete and that applicants fulfil the eligibility criteria described in the previous section.

2. Evaluation: each eligible application will be assessed by the principal investigator. The principal investigator will select up to four candidates for the following steps:

a. Online interviews: online interviews will be scheduled, in person interview will be organized where possible. Short-listed candidates will be invited for an online interview with the supervisor responsible for the research project DC5. At least one member of the recruitment committee will attend the online interviews.

b. Selection results: our recruitment committee will notify short-listed candidates of the results.

c. Hiring process and enrollment: the selected candidate will be put in touch with the principal investigator and the HR Department of the hosting institution to initiate the hiring procedure.

Applicants who have not been successful but who have received a positive evaluation will be put on a waiting list to cover possible withdrawals and future positions.

    Additional comments

    Recruitment calendar:

    • Deadline for applications: 13th of April 2023
    • Eligibility and Evaluation: 14th of April 2023 
    • Online Interviews: April 2023
    • Notification to candidates: first week of May 2023
    • Hiring process: May - July 2023
    • Start date of the fellowship: September 2023

    Work Location(s)

    Number of offers available
    1
    Company/Institute
    BAHÇEŞEHİR ÜNİVERSİTESİ
    Country
    Turkey
    State/Province
    Istanbul
    City
    Istanbul
    Postal Code
    34538
    Street
    Batman Sok 66

    Where to apply

    E-mail
    andreea.craciun@ucv.es

    Contact

    State/Province
    Türkiye
    City
    Istanbul
    Street
    Batman Sok 66
    Postal Code
    34734