Industrial PhD: Developing fluorescent aptamer sensors for high-throughput screening of secretory phenotypes in droplets

Applications are invited for an Industrial PhD at Graduate School of Science and Technology, Aarhus University, Denmark, within the Nanoscience programme. The successful candidate will be part of an application for an industrial PhD from the Innovation Fund Denmark. The position is available most likely from 1 February 2019 or later.


Title:
Industrial PhD: Developing fluorescent aptamer sensors for high-throughput screening of secretory phenotypes in droplets


Research area and project description:
One of the main goals of synthetic biology is to re-engineering organisms to produce valuable biomolecules and chemical compounds in a cheaper and more efficient way. With recent progress in DNA synthesis and assembly, genome editing and automation we have become highly efficient at designing and building production strains. However, this has generated a new bottleneck, since the throughput with which we create libraries now exceeds the throughput with which we can phenotypically assess the strains we generate. It has recently been shown that fluorescent RNA aptamers can be used to screen for efficient production strains in a microfluidics platform1. RNA aptamers can be selected to bind to an extremely wide range of target molecules, making aptamers remarkable general sensors. Sensors based on fluorescent aptamers have been described and quantitative dose-response relationships have been established for many of these aptamers2,3,4.

The aim of this project is to develop a highly flexible high-throughput screening platform to significantly shorten the timelines needed to select production cell lines with optimal yields and phenotypes in the context of Novo Nordisk projects. In this project, we want to establish the use of fluorescent aptamer sensors to measure extracellular protein and/or metabolite titers in nanodroplets to enable fast and flexible high-throughput screening of yeast and cell lines. The project will first consist in selecting specific fluorescent aptamer sensors for one or more defined model proteins/metabolites in the Andersen Lab (andersen-lab.dk) at Aarhus University, then testing their applicability in nanodroplets and finally validating the selected cell lines in the high-throughput microfluidics platform at Novo Nordisk.

For more information about doing an industrial PhD research project, see both the website of Aarhus University and of Innovation Fund Denmark.


References:

  1. Abatemarco, J. et al. RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes. Nat Commun 8, 332 (2017).
  2. Paige, J. S., Nguyen-Duc, T., Song, W. & Jaffrey, S. R. Fluorescence Imaging of Cellular Metabolites with RNA. Science 335, 1194–1194 (2012).
  3. Strack, R. L., Song, W. & Jaffrey, S. R. Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. Nat. Protoc. 9, 146–155 (2013).
  4. Jepsen, D. E. M., Sparvath, S. M., Nielsen, T. B., Langvad, A. H., Grossi, G., Gothelf, K. V., Andersen, E. S. Development of a genetically encodable FRET system using fluorescent RNA aptamers. Nat. Commun. 9, 18 (2018).


Qualifications and specific competences:
We search for highly motivated individuals to work on a highly ambitious project at the interface of basic research and application in industrial setups. Applicants for the PhD position must have a relevant Master’s degree within nanoscience, molecular biology or related fields.

Candidates should have experience and expertise in at least one of the following areas:

  • Biochemistry and molecular biology techniques.
  • Bioinformatics analysis of sequencing data.
  • Microfluidics and fluorescence analysis methods.

Furthermore, applicants are expected to:

  • Be independent, critically thinking, and have good project management skills.
  • Have strong cooperation and communication skills.
  • Have good command of the English language, both spoken and written.


Place of employment and place of work:
The project is conducted in close collaboration between the Andersen Lab for Biomolecular Design (andersen-lab.dk) at the Interdisciplinary Nanoscience Center (inano.au.dk), Aarhus University, and the Diabetes Research Unit at Novo Nordisk A/S. Since it is an Industrial PhD project, the PhD candidate will be employed at Novo Nordisk (Copenhagen) and enrolled at Graduate School of Science and Technology/GSST (Aarhus). The Industrial PhD candidate is expected to split the time equally between the company and the university, i.e. work equally in both places – the actual scheduling will be decided within the framework of the project.    


Contacts:
Applicants seeking further information are invited to contact:

Ebbe Sloth Andersen, Associate Professor, Interdisciplinary Nanoscience Center, Aarhus University, email: esa@inano.au.dk

Vera Schramke, Senior Scientist, Diabetes Research Unit, Novo Nordisk A/S, ves@novonordisk.com


 

Application procedures

Before you apply

Information and attachments:

Please be aware that you must have all relevant appendices, attachments, addresses for referees, etc. ready when you apply, as the entire application must be uploaded to the system in one go.

Documentation of language skills:

The English language requirement at Graduates School of Science and Technology is comparable to an “English B level” in the Danish upper secondary school (“gymnasium”).

English language qualifications comparable to an “English B level” is documented by one of the following tests:

  • TOEFL test, minimum score: 560 (paper-based test) or 83 (internet-based test). The paper-based test must have a “total score”. From August call 2019, GSST no longer accepts the paper-based test.
    Aarhus University does not accept the TOEFL ITP test. Aarhus University’s TOEFL code is 8935. You must request that the test centre send your test results to Aarhus University, in order to enable verification of your test results.
  • IELTS (academic) test, minimum average score: 6.5 points
  • Cambridge English Language Assessment:
    Cambridge Certificate of Proficiency (CPE)
    Cambridge English: Certificate of Advanced English with grade A,B or C (CAE)
    Cambridge English: First Certificate  with grade A (FCE)

When to take the test and how to upload the documentation:
The test result must not be more than two years old at the time of application.

The English language test should be taken before applying for admission and uploaded under “language skills documentation” in the online application form.

It is possible to apply for admission before you have taken the test. In this case documentation stating that you have signed up for a test (please state expected submission date) must be uploaded. If the test result is not part of the original application the test result is to be sent to sphd@psys.au.dk no later than one month after the application deadline.

The following applicants are exempted from documenting their English qualifications/taking a test:

  • Applicants with citizenship from the following countries: Australia, Canada, Ireland, New Zealand, United Kingdom, United States, or one of the Nordic countries (Denmark, Finland, Iceland, Norway or Sweden).
  • Applicants with a Bachelor’s or Master’s programme completed in Australia, Canada, Ireland, New Zealand, United Kingdom, or United States. In this case, please upload your Bachelor’s or Master’s diploma under the section ”Language skills documentation”.
  • Applicants with a Bachelor’s or Master’s programme completed at Aarhus University for which the requirement was English B level at the time of admission. In this case, please upload your Bachelor’s or Master’s diploma under the section” Language skills documentation”.
  • Applicants able to document that English was the language of instruction during the whole period of their Bachelor’s and/or Master’s programme. This must be documented by uploading an official document from the institution stating this under “language skills documentation”. The onus is on the applicant to provide this information as GSST will not pursue information regarding language of instruction for any programmes or institutions.

The programme committee may request further information or invite the applicant to attend an interview.


How to apply:

1)      Find the application form:
Go to http://talent.au.dk/phd/scienceandtechnology/opencalls/
Choose August 2018 Call with deadline 1 August 2018 at 11.59 PM MET.
You will be directed to the call, and must choose the programme 'Nanoscience'

2)      Fill in the following information:

  • Personal information
  • Academic background
  • Admission
  • Financing (if any)
  • Study: In the dropdown menu you must choose the project: "Developing fluorescent aptamer sensors for high-throughput screening of secretory phenotypes in droplets"
  • Source (how you found out about the call)

Next to some of the information fields you will find a number. Click on the number to get further directions on how to fill in the information field/what information is needed.

3)      Application attachments:
Please be aware that you cannot submit the application if one or several of these documents have not been uploaded.

If you wish to upload more than one document under each section, you must scan/merge all documents into one large PDF file and upload this. Please note that we reserve the right to remove scientific papers, large reports, theses and the like. Instead you can indicate a URL where the information is available.

Please note that all information in the application must be in Danish or English.

As a minimum all applications must include (pdf-files only, max. 20 MB, no zip):

  • One reference (template for references)
  • Curriculum vitae,
  • Motivation (max. 1 page)
  • Transcripts and diploma(s)
    Project description (½-4 pages). For technical reasons, you must upload a project description. When - as here - you apply for a specific project, please simply copy the project description above, and upload it as a PDF in the application. If you wish to, you can indicate an URL where further information can be found. Please note that we reserve the right to remove scientific papers, large reports, theses and the like.
  • Documentation of language skills if required.

After submission of the application, you will receive a confirmation e-mail with an application ID, you should use for reference if needed. The e-mail will also include a link to the application – GSST urges you to check that all mandatory data, marked with an asterisk (*), is registered correctly and all attached files are readable. In case of significant errors, you should reply to the confirmation e-mail with the correct details before the application deadline.

GSST reserves the right to verify the authenticity of your educational diploma and transcripts:

  • Request additional information to verify an application.
  • Reject the application if it is proven, or if the University has reasonable belief, that the information provided is false or if the applicant refuses to provide the requested information, whether or not an offer has already been made. 
  • For further information on applying, assessment procedures, etc. please see the GSST application guide here.  

Please note:

  • The programme committee may request further information or invite the applicant to attend an interview.
  • Admission is contingent upon full external funding from Innovation Fund Denmark, thus, if approved by GSST, it will be a conditional approval until full external funding is secured.

All interested candidates are encouraged to apply, regardless of their personal background.