Doctoral (PhD) student position in Evolutionary selection of DNA structures for detection and inhibition of pathogens

Do you want to contribute to top quality medical research?

To be a doctoral student means to devote oneself to a research project under supervision of experienced researchers and following an individual study plan. For a doctoral degree, the equivalent of four years of full-time doctoral education is required.

The Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet conducts research and teaching within immunology, infection biology, cell biology and cancer. MTC have about 40 research groups and our key words are multidisciplinary, bridging, national and international collaborations. 

The research team

We are looking for a Doctoral student to work in Erik Benson’s research team (a part of Birgitta Henriques Normark's Research Group) based at Scilifelab campus Solna. The team focuses on using DNA nanotechnology to develop libraries of DNA structures with large diversity. We use these structures to perform selection experiments combined with sequencing to find the structures with the best properties. The goal is to develop alternatives to antibodies and to understand what factors control the specific cell uptake of DNA. As a member of the team, you become a part of the Scilifelab community and the unit for microbiology-bacteriology at the Karolinska Institute.

The doctoral student project and the duties of the doctoral student

Antibodies are essential for modern research, diagnostics, and therapies but face challenges with batch-to-batch variations and slow deployment against new pathogens. Aptamers, constructed from DNA or RNA, provide an alternative with rapid synthesis and chemical incorporation, though they generally bind weaker than antibodies. However, their binding strength can be greatly enhanced through avidity by scaffolding multiple aptamers to fit target epitopes. We have developed a system for evolutionarily selecting DNA structures that pattern multiple aptamers to discover multivalent aptamers. In this research project the student will work to design DNA nanostructure libraries and perform selection against pathogenic targets of viral and bacterial origin. The selection process will be monitored by high throughput sequencing paired with custom bioinformatics and high throughput structure prediction tools. Promising candidate structures will then be produced individually and profiled for their binding to their target by SPR and integrated in prototype diagnostic tests. Promising candidate structures will also be profiled for their capacity to inhibit their pathogen targets.

What do we offer?

A creative and inspiring environment full of expertise and curiosity. Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. As a doctoral student you are offered an individual research project, a well-educated supervisor, a vast range of elective courses and the opportunity to work in a leading research group. Karolinska Institutet collaborates with prominent universities from all around the world, which ensures opportunities for international exchanges. You will be employed on a doctoral studentship which means that you receive a contractual salary. Employees also have access to our modern gym for free and receive reimbursements for medical care.

Eligibility requirements for doctoral education

In order to participate in the selection for a doctoral position, you must meet the following general (A) and specific (B) eligibility requirements at latest by the application deadline.

It is your responsibility to certify eligibility by following the instructions on the web page Entry requirements (eligibility) for doctoral education.

A) General eligibility requirement

You meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:

1. have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
2. have satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the advanced/second-cycle/master level, or
3. have acquired substantially equivalent knowledge in some other way in Sweden or abroad.*

Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.

*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.

B) Specific eligibility requirement

You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:

• Show proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school.

Follow the instructions on the web page English language requirements for doctoral education.

Verification of your documents: Karolinska Institutet checks the authenticity of your documents. Karolinska Institutet reserves the right to revoke admission if supporting documents are discovered to be fraudulent. Submission of false documents is a violation of Swedish law and is considered grounds for legal action.

(A) and (B) can only be certified by the documentation requirement for doctoral education.

Skills and personal qualities

We are looking for a creative, self-driven candidate who is interested in developing new methods in life-science. The candidate should be comfortable working both in a wet-lab and using computational tools to analyze data and draw conclusions. You should be well-organized, with excellent communication skills, and able to work effectively within a multidisciplinary team.

In addition to the aforementioned requirements for the position:

• A Master’s degree in, Biomedicine, Biotechnology, Bioinformatics, Bioengineering, Physics, Chemical engineering or a related field (or equivalent upon starting the position).
• Experience in a biochemistry wet-lab setting.
• Experience with DNA sequencing and sequencing data analysis.
• Proficiency in English (written and spoken).
• Strong interpersonal skills and positive references from previous research environments.

Meritorious for the position:

• Experience with Affinity profiling of binders.
• Experience with DNA sequence design.
• Experience with inhibition assays.
• Competency in computational analysis (preferably python).

Terms and conditions

The doctoral student will be employed on a doctoral studentship maximum 4 years full-time.

Application process

Submit your application and supporting documents through the Varbi recruitment system. Use the button in the top right corner and follow the instructions. We prefer that your application is written in English, but you can also apply in Swedish.

Your application must contain the following documents:

• A personal letter and a curriculum vitae
• Degree projects and previous publications, if any
• Any other documentation showing the desirable skills and personal qualities described above
• Documents certifying your general eligibility (see A above)
• Documents certifying your specific eligibility (see B above)

Selection

A selection will be made among eligible applicants on the basis of the ability to benefit from doctoral education. The qualifications of the applicants will be evaluated on an overall basis.

Karolinska Institutet uses the following bases of assessment:

• Documented subject knowledge of relevance to the area of research
• Analytical skill
• Other documented knowledge or experience that may be relevant to doctoral studies in the subject.

All applicants will be informed when the recruitment is completed.

https://bensonlab.se/

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