[SocBiN] PhD student position in Bioinformatics (BOKU Vienna, Austria)

[Office BioTop]

PhD student position: Genomic and epigenomic analysis of a plant-based
expression platform for recombinant glycoproteins
 
This project is offered within the framework of the International PhD
Program „Biomolecular Technology of Proteins – BioToP” at BOKU -
University of Natural Resources and Life Sciences, Vienna, Austria.
 
Project description
The tobacco-related plant species Nicotiana benthamiana is emerging as
a promising host for the rapid, versatile and safe production of
biopharmaceuticals. Furthermore, N. benthamiana lines have been
established which permit the production of recombinant glycoproteins
with customized N- and O-glycan structures and thus superior biological
activities. 
 
The project will focus on a detailed genomic and epigenomic analysis of
a glycoengineered N. benthamiana line optimized for the production of
recombinant proteins and its comparison with wild-type plants. NGS
libraries will be generated from genomic DNA and mRNA isolated from
leaves and other organs. Computational analysis of the data obtained
with these sequencing libraries will then involve mapping of read-pairs
against the Nb-1 draft genome, with the aim of assessing the genetic
differences existing between Nb-1 and glycoengineered N. benthamiana, as
well as its progenitor line. For once, this information can be used to
reconstruct the genome sequence of glycoengineered N. benthamiana.
Secondly, these studies will yield a comprehensive assessment of the
genomic status of the currently most frequently used N. benthamiana
production line and reveal any genetic or epigenetic alterations
incurred during its generation. Special attention will be paid to the
identification and transcriptional activity of genes encoding cysteine
and serine proteinases, since degradation of recombinant proteins in
planta is largely due to members of these protease families. Particular
emphasis will be also placed on the characterization of the N.
benthamiana complement of glycosyltransferases, glycosidases and prolyl
hydroxylases whose activities could potentially lead to the formation of
non-human N- and O-glycan structures or other protein modifications on
biotherapeutics. Altogether, the outcomes of this project will provide a
powerful resource for the further development of this attractive new
expression platform.
 
Required skills and qualifications
We are looking for a graduate student with a Master´s degree in
bioinformatics or in a related field, solid programming skills (e.g.
developing sequence analysis tools), experience with the analysis of NGS
data sets, understanding of lab methods and knowledge of
genomics/transcriptomics. 
 
For more detailed information about the project and the PhD program
BioToP please visit http://biotop.boku.ac.at
 
Application
The PhD Program BioToP will only consider applications that are
submitted using the official BioToP application forms. No other forms of
applications will be accepted. 
 
For application guidelines and download of forms please visit
http://biotop.boku.ac.at. 
 
Application Deadline: 31.10.2015
 
 
 


PhD Programme BioToP
"Biomolecular Technology of Proteins"
BOKU - University of Natural Resources and Applied Life Sciences
Muthgasse 18
A-1190 Vienna
Email:biotop at boku.ac.at
Web: http://biotop.boku.ac.at
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