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Chinese Hamster Ovary (CHO) cells are the most important production platforms of the biopharmaceutical industry. In the group of Professor Nicole Borth, at the University of Natural Resources and Life Sciences in Vienna (BOKU), we are performing extensive research on this important cell line. Our work spans from basic, ground-laying cell line characterization that looks into basic cellular function, up to the evaluation of novel techniques to improve the pipeline of cell line development or to boost bioprocess relevant properties. In this project we intend to implement a genome-wide deletion screen using CRISPR technology to further expand our knowledge on various genomic regions. Based on the collected insights, we aim to generate new CHO derived cell lines by large-scope gene editing, followed by in-depth characterization including the assessment of growth behaviour, productivity and model protein product quality. These are the specific challenges you´ll need to adress The main topic of your thesis will be the design of the library of gRNAs, along with the bioinformatic evaluation of sequencing results. The library of cells that bears the different gRNA pairs will be screened for deletions that i) are lethal, ii) reduce growth, iii) reduce productivity and iv) have no impact on any of these. The pipeline for this screen, whether based on PCR results from the population or whole genome sequencing or RNAseq needs to be developed and the appropriate statistical tests applied. Depending on your previous education, this can be combined with bioinformatics tasks from other projects or with wetlab work for cloning and delivery of the genome wide library. Within the three years of your PhD you will get the possibility to work in an inspiring and enjoyable environment with numerous possibilities for further education and personal development. Due to the direct collaboration with industrial partners you will not only expand your expertise, but already bridge your science to industry. That’s important to us As an ideal candidate you have completed a master’s degree in bioinformatics, biotechnology, computational biology or related fields. Research experiences in the following areas would be of advantage, but are not a prerequisite: Analysis of NGS sequencing data, including whole genome sequencing, RNAseq or ChIPseq Statistical evaluation of large scale data sets mammalian cell culture basic molecular biology techniques such as plasmid construction and cloning, PCR, RT-qPCR etc. application of CRISPR systems You should enjoy working in a team in an international and interdisciplinary environment. Furthermore, you should also be up to the challenge to tackle individual tasks independently and rise to become confident in your field of research.
Please send your cv and a motivation statement to firstname.lastname@example.org Start of project between 06/2020 and 09/2020