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Postdoctoral position in organisms detection from environmental DNA using CRISPR-Cas

100%, Zurich, fixed-term

The Laboratory of Ecosystem and Landscape Evolution and the Genome Engineering and Measurement Lab (GEML) at the ETH Zurich are looking for candidates to fill a post-doctoral position as part of the fully funded BRIDGE-Discovery project CRISPeD aiming at organisms detection. The Laboratory of Ecosystem and Landscape Evolution is an international research team with diverse scientific expertise and backgrounds, connected by the goal to understand biodiversity. We study the mechanisms that shape biodiversity patterns across spatial and temporal scales - in both terrestrial and aquatic ecosystems and their response to global changes. To make these connections, we collect data through biological monitoring, environmental DNA methods, remote sensing, and field sampling, and use these data to answer questions with statistical and process-based models of biological diversity. We are further committed to translating basic science findings and novel technologies into environmental applications, and thus engage in finding solutions to solve major environmental challenges. GEML is a knowledge and technology Hub aimed at syncing the scientific community with the rapidly evolving genome engineering methods and techniques. We develop, implement, optimise, and analyse cutting edge genome engineering workflows supporting a wide range of research projects at ETHZ, UZH, and the USZ. Our overarching goal is to deploy tools that can target unique genomic sites with the high activity and specificity required for  in vivo and  in vitro  applications, such as gene and cell therapy, and diagnostics.

Project background

Anthropogenic activities cause disruption to natural ecosystems, which can in turn impact the functioning of human societies. To ensure long-term societal well being, the monitoring of living organisms is becoming increasingly critical in a variety of domains from pathogens and pest detection to stock assessment and biodiversity protection. A critical challenge is to develop efficient data collection methods of potential biotic concerns that will allow informed management decisions. Engineered CRISPR-Cas reagents associated with a readout system are reported to allow the diagnosis of pathogens in medical samples. In the proposed project, we will generate a programmable approach for CRISPR-Cas to harness this technology and achieve organism detection in environmental DNA samples (eDNA), allowing fast and cost-effective tracking of multiple species’ occupancy overtime at multiple sites.

Job description

The position's responsibilities include bioinformatic development of the software to determine guide RNAs for target organisms, developping CRISPR-Cas laboratory protocols for the detection of target organisms of interest from environmental samples, supporting the collection of eDNA samples in the field and applying standard DNA extraction procedure, and increase the operational efficiency of the detection system.

Duration:
The position is initially for 24 months and extendable based on progress and evaluation of performance for up to a maximum of four years.

Your profile

You are a dedicated scientist with a doctoral degree in the field of molecular biology, biomedical engineering or related fields with the following expertise:

  • Experience in standard molecular biology techniques (cloning, PCR)
  • Expertise in bioinformatic and programming in python
  • Experience in the application of CRISPR-Cas protocols would be a plus
  • Expertise in field-collection of medical or environmental sample would be a plus
  • Independent planning, efficient execution and documentation of experiments
  • Excellent communication and writing skills and a strong attitude to work in a team
  • Ability to integrate efficiently various concepts from different disciplines

Please apply if you meet these criteria.

We offer

You will work together with a group of technicians, graduate students, and senior scientists to streamline and optimise experimental procedures in the CRISPR/eDNA research domain. Overall, the technology emerging from this project will provide the paradigm shift needed to vastly change the cost, speed and scale with which organisms can be surveyed through time allowing more informed solutions to multiple existing environmental problems.

You will work in an international vibrant team with the unique opportunity to continuously refine and expand your interpersonal and methodical skills. Read more about working at ETH and our benefits for employees.

ETH Zurich

ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find our university to be a place that promotes independent thinking and an environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we work together to develop solutions for the global challenges of today and tomorrow.
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Interested?

We look forward to receiving your online application with the following documents:

  •     CV (include complete list of publications and references we can contact)
  •     Motivation Letter
  •     Certificates with transcripts

Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered. Further information about the Laboratory of Ecosystem and Landscape Evolution and the Genome Engineering and Measurement Lab can be found on our websites.

Questions regarding the position should be directed to Prof. Loïc Pellissier (loic.pellissier@usys.ethz.ch) and Dr. Zacharias Kontarakis (zacharias.kontarakis@fgcz.ethz.ch) (no applications)

In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open environment that allows everyone to grow and flourish.

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