Position available at the Snijder lab
The Snijder lab is looking for two talented students to join the team in fully funded Ph.D. positions (4 yrs). We are also looking for a postdoctoral fellow to join our team (1 yr with possible extension up to 3 yrs).
We study the structure and composition of viral antigens and their interactions with neutralizing antibodies, with a special focus on vaccine design. In particular, we work with systems such as dengue virus, ebola virus and influenza to explore the role of N-linked and O-linked glycosylation in viral antigen-antibody interactions. We use the state-of-the-art in mass spectrometry and cryo electron microscopy to map out the glycans on viral antigens and identify how they restrict binding by neutralizing antibodies through steric shielding and other mechanisms. Available research methods include glycoproteomics, single particle electron microscopy, native mass spectrometry and hydrogen-deuterium exchange mass spectrometry.
Furthermore, the Snijder lab is developing new protocols and methodology for mass spectrometry based de novo antibody sequencing. We are developing an efficient workflow based on LC-MS/MS methods from the field of bottom-up proteomics to derive experimental amino acid sequences straight from samples of purified monoclonal antibodies and aim to expand the methodology to polyclonal mixtures. We will benchmark our sequencing methods on a large panel of monoclonal antibodies, including functional validation of experimental output sequences in assays for antigen binding and epitope mapping. Also, we will pursue the analysis of targeted antigen-specific polyclonal mixtures of antibodies to follow immunizations and natural infections.
Ph.D. position 1: Exploring the role of glycosylation in viral antigen-antibody interactions.
This is a fully funded Ph.D. position for 4 years at Utrecht University in the Heck lab. Prior experience with mammalian cell culture and protein expression is appreciated. Start date: as soon as possible.
Ph.D. position 2: Developing new methods for de novo antibody sequencing by MS.
This is a fully funded Ph.D. position for 4 years at Utrecht University in the Heck lab. Prior experience with hybridoma cell culture and recombinant antibody production is appreciated. Start date: as soon as possible.
We are looking for candidates with a broad interest in structural virology, immunology and vaccine design. Candidates are encouraged to develop their own line of work in connection to the lab’s research interests as outlined above. We offer a guaranteed one-year contract with a possible extension for two additional years. Candidates are encouraged to apply for their own fellowship grants and will receive our full support in this. Prior experience with cryo electron microscopy, and with mammalian cell culture and protein expression is appreciated. Start date: as soon as possible.
These positions are funded by the Institute for Chemical Immunology. You will be working at Utrecht University in Utrecht, The Netherlands, under direct supervision of Joost Snijder in the Biomolecular Mass Spectrometry and Proteomics group of Albert Heck (who will also function as promotor for the PhD positions). To apply for any of the positions, please send a motivation letter, CV and the names and contact information of two references to firstname.lastname@example.org mention ‘application for ICI position’ in the subject.
March 26th 2018
Industrial, nutritional and therapeutic proteins have become key molecular entities used in the food industry and human/animal healthcare. Their role is rapidly increasing in this era of advanced biotechnology, with a large part of the newly approved drugs being already protein based. However, due to their large size, biology driven production, and complicated structural features therapeutic and nutritional proteins and industrial enzymes form some of the most challenging molecular entities to be functionally and structurally characterized. The main goal is to develop much-needed new analytical strategies enabling the separation, identification and quantification of all molecular forms of industrial enzymes, nutritional proteins and biotherapeutics in their intact native state. Distinctively, the novel analytical workflows to be developed within this program are aimed at the genuine intact proteins and will allow us to simultaneously establish structure-function relationships of proteoforms and aggregation states of proteins. The consortium is a collaboration between Utrecht University (Heck-lab), Leiden University Medical Center (Wuhrer-lab) and the companies DSM, FrieslandCampina and Roche. The project is (co)financed by the Netherlands Organisation for Scientific Research (NWO).
PhD1 (LUMC) will develop different native separation technologies for offline/online coupling to mass spectrometry using different types of industrial enzymes. The analytes will be enzymes exhibiting highly diverse and challenging modifications such as glycosylation and glycation. DSM will provide enzyme activity assays for demonstration of proof-of-concept for structure-function determination, materials and expertise and support in native enzyme analytical characterization.
PhD2 (UU) will further develop and employ high-resolution native mass spectrometry methods to characterize the complexity of dairy proteins, including the characterization of isoforms and co- occurring post-translational modifications. Integration of the gathered data with information measured by more conventional bottom-up, non-native approaches will be a prime objective. FrieslandCampina will provide support with in vitro digestion assays and immunological assays.
PhD3 (UU) will develop, and online couple, native separation and mass spectrometry methods applied to biopharmaceuticals such as immunoglobulins, fusion proteins and other antibody-based formats. Roche will provide expertise and materials for (affinity) columns and glyco-enzymes. Roche will in addition provide in-kind support with functional assays.
The three PhD students will work together in a team with principal investigators and post-docs of the involved groups and companies, and take secondments in industry to learn, but also transfer, new technologies. The PhD students will be appointed at the involved academic institutes, for a period of 4 years, and become embedded in the graduate schools and will perform practical work at both the UU and LUMC to allow a broad analytical technology toolbox development for structure-function determination of the different types of proteins.
We seek motivated students with a degree in Chemistry, Biology or Pharmaceutical Sciences with an interest and background in protein biochemistry and analytical method development and like to work in a team. Please send your applications (CV, letter of motivation and 2 references) in before May 1, 2018 via e-mail to Corine Heuzer (PA of Albert Heck) at email@example.com. Enquiries about the positions can be made to Manfred Wuhrer (M.Wuhrer@nulllumc.nl) or Albert Heck (firstname.lastname@example.org).
Looking for a Postdoctoral Fellow:
In this project we aim to identify soluble factors present in melanoma patients’ plasma, that are responsible for systemic immune suppression, which hampers T cell activation upon checkpoint inhibitor treatment. In a collaborative effort with the NKI/AVL we will analyze systemic treatment naïve plasma samples by deep proteomic profiling from stage III melanoma patients that have progressed to stage IV. Changes in the profile of the identified proteins will be tested in an independent cohort of 100 melanoma patients treated with ipilimumab+nivolumab from whom we have collected baseline plasma samples.
For more information please contact Maarten Altelaar email@example.com