Sweet Crosstalk

Recruitment

Recruitment is closed: we have hired 15 great ESRs! More news soon

Living the sweet life

We are recruiting for 15 Marie Curie Early Stage Researcher (PhD) positions within the Sweet Crosstalk Network on understanding the molecular-level role of glycans at the human mucosa–microbiota interface

Sweet Crosstalk is a multidisciplinary European Training Network built to address the challenge of understanding, at a molecular level, how glycans are involved at the human mucosa–microbiota interface, and how this correlates with human well-being. The research strategy of the Sweet Crosstalk programme focuses on optimal synergy between chemistry and biology. In the network the expertise ranges from chemical synthesis, biochemistry, structural biology to microbiology and cell biology.

Our 7 academic groups are all renowned leaders in the glycoscience and microbiome fields, whereas the complementary 4 companies are specialized in glycan-based diagnostics and prophylactic therapies. Under their guidance, the Early Stage Researchers trained in this network will become the new generation of innovative scientists with expert knowledge and skills in interdisciplinary glycoscience and human microbiome research. Pursuing a PhD within the Sweet Crosstalk Training Network is an excellent starting point for a career at both top European research institutions as well as the healthcare/biotech job market.

We are currently looking for talented and motivated candidates to become Sweet Crosstalk PhD students. Do you want to be trained as a scientific expert in innovative glyco- and microbiome science? Are you open-minded, curious, ready to explore new ways, and do you like the challenge of working in a dynamic international network with 15 PhDs at seven leading European academic research institutes and four life science companies, covering different aspects of innovative glyco- and microbiome science? Then apply!

Quickly jump to descriptions of available PhD research projects: ESR1 & ESR8 (Wennekes, Netherlands); ESR2 & ESR3 (Juge, UK); ESR4 (Overkleeft, Netherlands); ESR5 & ESR6 (Molinaro, Italy); ESR7 & ESR10 (Salonen, Finland);  ESR9 (Rovira, Spain);  ESR11 (Cani, Belgium); ESR12 (Beauprez, Belgium); ESR13 (Vigsnæs, Denmark); ESR14 (Mercenier, NL); ESR 15 (Field, UK)

The Sweet Crosstalk Network offers:

  • highly competitive & attractive salary and working conditions in accordance with the Marie Skłodowska-Curie Action regulations for Early Stage Researchers
  • The standard length for the PhD positions is a 3-year-MSCA contract, but for several ESR positions in the Sweet Crosstalk ITN funding for an additional 4th year will be provided by the host institution (see website for details)
  • challenging research projects to lead to a dissertation (PhD thesis) at high profile universities, research institutions and companies located around Europe.
  • the opportunity to become an expert in the field of glyco- & microbiome science and hold a unique position within the European labour market
  • training in state-of-the-art scientific skills and transferable managerial skills
  • participation in network-wide training activities, courses, workshops and conferences
  • intersectoral secondments to gain work experience and training in several academic institutes and an industrial setting

What is a secondment?: a research training period of several months spent by an ESR/PhD student at the premises of a different research institute or company in the Sweet Crosstalk ITN. The secondment will involve physical mobility of the ESR/PhD to the other ITN partner. During the secondment, a you receive supervision and training at the premises of the receiving partner.

Requirements for all candidates:

In accordance with the very strict EC Marie Skłodowska Curie Actions (MSCA) Sweet Crosstalk ITN rules you must meet the following two eligibility criteria for your ESR/PhD position(s) of interest (so, please do not respond if you are not eligible):

Eligibility criteria 1: Candidates did not reside or carry out their main activity (e.g. reside, work, studies) in the country of the PhD host institution for more than 12 months during the 3 years immediately prior to project’s application deadline (time spent as part of a procedure for obtaining refugee status under the Geneva Convention, compulsory national service and/or short stays such as holidays are not taken into account).

Eligibility criteria 2: Candidates are in the first four years of their research careers upon the starting date of their appointment to an ESR/PhD position (full-time equivalent research experience, measured from the date when a researcher obtained the degree entitling him or her to embark on a doctorate) and have not been awarded a doctoral (PhD) degree.

Profile of candidates, are you:

  • in possession of a Master degree that fits the research area(s) of the ESR position(s) of your interest, such as a degree in the field of molecular life sciences, chemistry, chemical biology, biochemistry, cell biology, molecular biology, microbiology, life sciences/medicine, pharmaceutical sciences, biotechnology, OR will you obtain such a Master degree by September 2019?
  • an excellent student who has obtained high grades during your studies?
  • do you have an inquisitive mind-set, accuracy, focus and are you self-reliant?
  • willing to undertake trans-national mobility to perform research abroad?
  • proficient in the English language (both oral and written)?
  • able to work and collaborate within an international multidisciplinary team? Excellent communication skills and cooperation skills are required
  • interested in molecular life sciences in general and glyco- & microbiome science in particular?
  • fulfilling all the requirements and eligibility criteria?

Then apply now for one of our 15 PhD research projects via the online application form.

The deadline for applications is the 21st of June, 2019.

Application procedure:

  • Please submit your application via the application form on our website.
  • Apply for a maximum of two (1st and 2nd preference) of our 15 PhD positions.
  • Only complete applications will be considered.
  • Applications and enclosures that are received after the application deadline of 21st of June, 2019 12:00 PM CEST will not be considered.
  • All applications will be checked for eligibility criteria 1 & 2. You may be asked to submit further details.
  • Eligible applications will be evaluated according to a standardised evaluation sheet.
  • Selected candidates will be invited for an interview (Skype or in person).
  • Selected candidates may be invited for a second interview (Skype or in person).
  • Candidates will be notified of the outcome.

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Sweet Crosstalk ITN ESR (PhD) project descriptions & vacancy details:


ESR1 Project with Dr. Tom WennekesUtrecht University, the Netherlands; Science fields: (Bio-)Organic Chemistry/ Chemical Biology

Host institution: Utrecht University (the Netherlands)

Main supervisor: dr. Tom Wennekes

Co-supervisor(s): Prof. Geert-Jan Boons, Prof. Nathalie Juge (Quadram Institute, UK), Prof. Antonio Molinaro (University of Naples Federico II, Italy)

PhD duration: 48 months

Desired start: June-September 2019

ESR1 PhD project:  Developing multifunctional mucin O-glycan-based arrays and chemical probes: profiling mucin glycocode dynamics and glycan-binding proteins in the presence of mucosal microbiota

Background: Interactions between the host and the gut microbiome are essential for the establishment and maintenance of gut health. Mucin O-glycans dominate this microbiota-host interface and are thus ideally positioned to modulate these interactions. However, only a rudimentary understanding of the function of O-glycans and their dynamics at a molecular level is available at this interface. This hampers the development of early diagnostics and glycotherapeutics for personalized microbiome health based on this crucial class of biomolecules. Mapping these mucin O-glycans, their glycan protein-interactions, carbohydrate-active enzymes and their dynamics in the presence of microbiota members will therefore be crucial to understand how the complex bacterial communities in our gut influences human physiology in health and disease. This projects aim is to develop and validate a state-of-the art molecular toolbox for achieving this.

Project description: In this project you will develop a chemo-enzymatic synthesis of defined complex O-glycan epitopes that are relevant at the human gut microbiota interface. These epitopes will be incorporated via smart chemistry approaches (e.g. cleavable linkers) into multivalent representations to study glycan epitope consumption by microbiota co-cultures. Isotope labelled versions of these epitopes will be used in LC/ion-mobility-MS analysis of mucin O-glycan samples to quantitatively profile their composition. Finally, by attaching the O-glycan epitopes onto glycoarray chips in various combinations you will screen for glycan-binding proteins present in microbiota samples. During your PhD project you will receive training and acquire expertise in advanced organic chemistry, chemo-enzymatic glycosylations, array printing, chemical biology techniques, advanced oligosaccharide purification & structural characterisation (NMR, MS ion-mobility) techniques, and basics in cell biology & microbiology.

Planned secondments:  1) Quadram Institute (3 months); Biological evaluation of epitope constructs; 2) University of Naples Federico II (3 months): NMR-based structural characterization of epitope-glycan-binding protein complexes; 3) Company Nutrileads (1 month): Evaluating the commercialization of developed technology.

For more information on this ESR vacancy contact: t.wennekes@uu.nl

 

 



ESR2 Project with Prof. Nathalie Juge @ Quadram Institute, UK; Science fields: Biochemistry/ Analytical Chemistry

Host institution: Quadram Institute Bioscience (UK)

Main supervisor: Prof. Nathalie Juge

Co-supervisor(s): Dr. Tom Wennekes (Utrecht University, the Netherlands), Prof. Antonio Molinaro (University of Naples Federico II, Italy)

PhD duration: 36 months

Desired start: September 2019

ESR2 PhD project:  Deciphering the intimate relationship between mucin glycosylation and gut bacteria

Background: Beneficial interactions between the host and the gut microbiome are essential for the establishment and maintenance of gut health. The epithelium lining the gastrointestinal tract provides a habitat to gut microbes that can use mucin glycans as adhesion sites or source of nutrients. An alteration in mucin glycosylation is associated with a dysbiosis of the gut microbiota and the development of colitis. It is therefore important to determine the mechanisms underpinning gut bacteria-host interactions at the mucosal surface so be able to develop strategies to restore gut homeostasis.

Project description: In this project, you will investigate the interaction between bacteria and mucins by profiling native mucin O-glycan composition from various cell lines and tissues in relation to microbiota composition and use advanced labelling approaches to visualize mucin O-glycans fluorescently in vitro (cell lines) or in vivo (mouse models). During your PhD project you will receive training and acquire expertise in molecular microbiology (anaerobic growth assays, co-cultures; in vitro colon fermentation), mucin purification, mass spectrometry-based glycomics (MALDI-ToF MS & ToF/ToF-MS), experience in animal handling and tissue processing, advanced bioimaging techniques (fluorescence and confocal microscopy, imaging flow cytometry). mammalian cell and tissue culture. Training will embrace research practice and theory, management, communication (to scientific and lay audiences), intellectual property, teamwork and technical writing. The student will present his/her work to internal seminars and to relevant International meetings. The possible commercial issues relating to the impact of this research on human health will be highlighted and the student will be encouraged to participate into outreach activities.

Planned secondments: 1) Utrecht University (3 months); evaluation of bacterial species on mucin O-glycan arrays/beads 2) University of Naples Federico II (2 months): evaluation of cell surface polysaccharides from major mucin-degraders; Company Glycom (1 month): gain industrial experience on pipeline for oligosaccharide production

For more information on this ESR vacancy contact: nathalie.juge@quadram.ac.uk

 

 



ESR3 Project with Prof. Nathalie Juge @ Quadram Institute, UK; Science fields: Biochemistry/ Analytical Chemistry

Host institution: Quadram Institute Bioscience (UK)

Main supervisor: Prof. Nathalie Juge

Co-supervisor(s): Prof. Patrice Cani (Universite Catholique de Louvain, Belgium), Dr. Louise Vigsnaes (Glycom, Denmark)

PhD duration: 36 months

Desired start: September 2019

ESR3 PhD project:  Defining the molecular mechanisms underpinning host O-glycan recognition by gut bacteria

Background: The complex microbial community (microbiota) inhabiting the large intestine has a profound effect on health and physiology, providing benefits such as modulation of immune development, digestion of complex carbohydrates, and inhibition of pathogen colonization. However, abnormalities in microbiota composition (dysbiosis) have been implicated in several disease states. One major factor shaping the composition and physiology of the gut microbiota is the availability of dietary and host glycans into the intestine. In addition to carbohydrates from the diet, some gut bacteria have the ability to utilise host glycans such as human milk oligosaccharides (HMOs) (in infants) or host O-glycans present on mucins (in adults) as a source of nutrient.

Project description: The overall aim of the project is to gain mechanistic insights into the receptors involved in the interaction between bacteria/probiotics and host glycans. Specific objectives include 1/ to characterise the kinetics of interaction between major host O-glycan structures (mucin oligosaccharides, HMOs) and gut bacterial cell surface proteins (adhesins, lectins) and 2/ unravel the metabolic pathways involved in mucin/HMO glycan degradation/utilisation by major gut symbionts. During your PhD project you will receive training and acquire expertise molecular microbiology (anaerobic growth cultures, cloning and heterologous expression, mutagenesis); recombinant protein purification; in vitro binding assays such as Surface Plasmon Resonance (SPR); Isothermal titration calorimetry (ITC); in vitro activity assays and carbohydrate analysis (Nuclear Magnetic Resonance (1H-NMR) or High-performance anion-exchange chromatography (HPAEC), metabolomics. Training will embrace research practice and theory, management, communication (to scientific and lay audiences), intellectual property, teamwork and technical writing. The student will present his/her work to internal seminars and to relevant International meetings. The possible commercial issues relating to the impact of this research on human health will be highlighted and the student will be encouraged to participate into outreach activities.

Planned secondments: 1) Universite Catholique de Louvain (3 months) metabolite analysis 2) Company Glycom (3 months) synthesis of novel oligosaccharides.

For more information on this ESR vacancy contact: nathalie.juge@quadram.ac.uk

 

 



ESR4 Project with Prof. Hermen Overkleeft @ Leiden University, the Neterlands; Science fields: (Bio-)Organic Chemistry/ Chemical Biology

Host institution: Leiden University (the Netherlands)

Main supervisor: Prof. Hermen Overkleeft

Co-supervisor(s):Dr. Tom Wennekes (Utrecht University, NL), Carme Rovira (University of Barcelona, ES)

PhD duration: 48 months

Desired start: June 2019

ESR4 PhD project:  Probing and perturbing glycosyl hydrolase activities at the mucosal-microbiota interface

Project description: You will investigate the glycosyl hydrolase (GH) activity spectrum in microbiota and the effect of inhibiting these enzymes with glycan-based hydrolase activity-based probes (ABP) and inhibitor panels. You will optimize these tools through a high-throughput screen for microbiota glycosyl hydrolase inhibitors. You will develop new GH ABPs, tailored to recognize and identify GH activities that characterize (gut) micro-organismal GHs and including enzymes evolved to remove oligosaccharides (endoglycosidases), furanosides (furanosidases) and higher-carbon sugars (e.g., sialosidases).Using an in-house glycomimetics library, encompassing over 400 structurally and configurationally unique iminosugars, you will screen in a fluorescence polarization ABPP using our ABP technology to look for compounds able to interfere with specific gut microbiome GH activities. To achieve this you will receive training in biochemistry, organic synthesis, assay development, medicinal chemistry, chemical biology.

Planned secondments:  1) University of Helsinki (2 months): Profile microbiota GH activity in gut microbiota; 2) University of Barcelona (3 months): Model novel ABP-GH binding conformations, 3) Company Inbiose (3 months): Develop screen for GHs and perform screening runs on Inbiose platform.

For more information on this ESR vacancy contact: h.s.overkleeft@chem.leidenuniv.nl

 

 



ESR5 Project with Prof. Antonio Molinaro @ University of Napoli Federico II, Italy; Science fields: Chemistry/ Structural Biology

Host institution: University of Napoli Federico II (Italy) – Enrollment in PhD school of Chemical Sciences

Main supervisor: Prof. Antonio Molinaro; Prof. C. De Castro; Dr. F. Di Lorenzo

Co-supervisor(s):Prof. Carme Rovira (University of Barcelona), Dr. Anne  Salonen (University of Helsinki)

PhD duration: 36 months

Desired start: June-July 2019

ESR5 PhD project:  Full structural determination of LPS from Gram negative microbiota.

Project description: Science: 1) Selective extraction and purification of endotoxin from selected mucosal microbiota Gram negative bacteria, such as Bacteroides vulgatus, Akkermansia muciniphila et al.; 2) Determination of core oligosaccharide and O-antigen primary structure; 3) Structural determination of lipid A; 4) Insights into 3D structure of bacterial lipopolysaccharides. Training: Expertise in basic knowledge on microbiology (bacterial culture); expertise in organic chemistry, chemical biology techniques, analytical chemistry, carbohydrate chemistry, state-of-art NMR spectroscopy and MS spectrometry, computational methods for building 3D complex carbohydrate structures.

Expected Results: 1)Full structural details of bacterial lipopolysaccharides involved in the cross-talk with eukaryotic interactor; Structure-activity relationship of lipid A/oligo/polysaccharide moieties and their interaction with eukaryotic receptor; 3) establishment of a LPS archetypal structure from bacteria at mucosal interface and use of it for diagnostic purposes (i.e., dysbiosis vs. symbiosis).

Planned secondments: 1) University of Helsinki, Collection of key microbial strains, growth and accumulation of dried bacterial pellet (3 months) 2) University of Barcelona (3 months) Computational approaches towards the understanding of 3D structural of bacterial LPS; 3) Iceni Diagnostics (3 months) Development of glycomolecules based on bacterial LPS skeleton of therapeuthic use.

For more information on this ESR vacancy contact: molinaro@unina.it

 

 



ESR6 Project with Prof. Antonio Molinaro @ University of Napoli Federico II, Italy; Science fields: Chemistry/ Structural Biology

Host institution: University of Napoli Federico II (Italy) – Enrollment in PhD school of Chemical Sciences

Main supervisor: Prof. Antonio Molinaro; Prof. A. Silipo ; Dr. R. Marchetti.

Co-supervisor(s): Dr. Tom Wennekes (Utrecht University ), Prof. Patrice Cani (Universite Catholique de Louvain)

PhD duration: 36 months

Desired start: September-October 2019

ESR6 PhD project:  Screening of microbial glycoconjugates eukaryotic interactors for an effective comprehension of dialogue at mucosal level

Objectives: Science: 1) Extraction, purification of a series of LPSs from mucosal bacterial strains; 2) Selective LPS chemical fragmentation/ modification and following derivatization; 3)NMR studies of binding of selected LPS fragment with eukaryotic lectins; 4) Epitope mapping of the binding region of the LPS fragment. Training: Expertise in organic chemistry, chemical biology techniques, analytical and organic chemistry, carbohydrate chemistry, NMR spectroscopy particularly devolved in non canonical NMR experiments devoted to study of carbohydrate protein interaction (STD-NMR, tr-NOE based, w-LOGSY based); computational methods for building 3D carbohydrate

Expected Results: 1) Identification of key eukaryotic lectins involved in the dialogue between the host and microbe at mucosal level; 2) identification of LPS and other bacterial glycoconjugate epitopes involved in the physical binding with GBs; 3) Thorough understanding of key molecular actors of interactions at molecular level between bacterial endotoxins with eukaryotic counterpart.

Planned secondments: 1) Universite Catholique de Louvain (4 months) collection of eukaryotic lectins from mucosal surface in pathological state, i.e., metabolic disorders such as obesity and diabetes, 2) Quadram Institute Bioscience  (3 months) test binding of LPS to C-type lectins (cell reporter lines  and recombinant proteins) by flow-cytometry analysis; 3) Company Nutrileads (2 months) assessment structure-activity relationship of various carbohydrate-based immunomodulatory molecules

For more information on this ESR vacancy contact: molinaro@unina.it

 

 



ESR7 Project with Dr. Anne Salonen @ University of Helsinki, Finland; Science fields: Microbiology/ Biochemistry

Host institution: University of Helsinki (Finland)

Main supervisor: Dr. Anne Salonen, Dr. MD Ilkka Kalliala

Co-supervisor(s): Prof. Nathalie Juge (Quadram Institute), Dr. Tom Wennekes (Utrecht University)

PhD duration: 36 months

Desired start: September-October 2019

ESR7 PhD project:  Molecular characterization of cervicovaginal mucus-microbiota interactions in health and in relation to cervical carcinogenesis

Project description: Cervicovaginal mucus and commensal microbiota are integral components of the female reproductive track. Their fluctuations in response to internal and external factors can markedly impact the physiology and support either health or pathological sequelae of the reproductive organs. For example, elevated bacterial mucus-degrading enzymatic activity has been detected in women with cervical carcinoma. In this project, you will study the cervicovaginal mucus-microbiota interactions at molecular level by characterizing mucin O-glycans and carbohydrate-active enzymes in relation to e.g. to microbiota and development and treatment of cervical cancer. The samples have been collected and your tasks include coordinating their analysis for integration and interpretation of multivariate datasets derived from mass spectrometry, next generation sequencing, bio-chemical measurements and questionnaires. Successful candidate will have skills in R or other language for data analysis, and basic understanding of biochemistry. During your PhD project you will receive training and acquire expertise in data analysis, molecular biology and microbiology, enzymatic assays, organic chemistry and chemical biology techniques

Planned secondments: 1) Quadram Institute (3 months): Isolation & sequencing of glycan content in vaginal samples, 2) Utrecht University (3 months): Chemical probe-based detection of vaginal glycosylhydrolases/glycan-binding proteins 3) Company Inbiose (2 months): Screen for vaginal glycosyltransferases/glycosylhydrolases.

For more information on this ESR vacancy contact: anne.salonen@helsinki.fi

 

 



ESR8 Project with Dr. Tom WennekesUtrecht University, the Netherlands; Science fields: (Bio-)Organic Chemistry/ Chemical Biology

Host institution: Utrecht University (the Netherlands)

Main supervisor: Dr. Tom Wennekes

Co-supervisor(s): Prof. Geert-Jan Boons, Dr. Anne Salonen (University of Helsinki), Prof. Hermen Overkleeft (Leiden University)

PhD duration: 48 months

Desired start: June-September 2019

ESR8 PhD project:  Getting a grip on microbial lectins, glycosyl transferases and hydrolases with smart chemical probes

Background: Key to comprehending glycocode-based crosstalk at the mucosa-microbiota interface is through molecular understanding the microbial proteins binding/recognizing and processing the glycan (glycocode) structures at this interface during their life-cycle: production by glycosyltransferases (GT) and removal by glycosidases (GH). Finally, Human and microbial glycocode readers (lectins/ adhesins; GB) recognize the glycocodes and translate this molecular-level information into appropriate responses from the host and microbiota. The chemical biology approach of this ESR project offers a unique strategy for dissecting this complexity by asking the ‘right’ focused molecular-level question, i.e. targeting only one specific protein/enzyme class, and devising a tailor-made chemical approach– a smart bioactive molecular tool – to answer them.

Objectives: You will develop a panel of GH & GT inhibitors that perturb microbial glycan metabolism. In addition you will develop a metabolic labeling toolbox to label microbial glycans in microbiota  and also equip them with photocrosslinker for microbial GB discovery. To achieve this you will receive training in advanced organic synthesis, chemical biology techniques, confocal fluorescence microscopy, microbial FACS, computational modeling glycan-protein interaction advanced sequence, NMR analysis of identified novel glycan-GB interaction, basics bacterial genetics, microbiology and protein expression and purification.

Planned secondments: 1) Company Inbiose (3 months): Identification of novel glycosylhydrolases, recombinant expression and purification; 2) University of Barcelona (2 months): Computational simulation of active site binding glycosidase inhibitors/probes; 3) University of Naples Federico II (2 months): NMR analysis of novel glycan-lectin interaction

For more information on this ESR vacancy contact: t.wennekes@uu.nl

 

 



ESR9 Project with Prof. Carme Rovira @ University of Barcelona, Spain; Science fields: Chemistry/ Computational Biology

Host institution: University of Barcelona (Spain)

Main supervisor: Prof. Carme Rovira

Co-supervisor(s): Prof. Hermen Overkleeft (University of Leiden), Prof. Antonio Molinaro (University of Naples Federico II).

PhD duration: 36 months

Desired start: October 2019

ESR9 PhD project:  Computer simulation of structure and dynamics of glycans & glycan-binding enzymes at the human mucosal microbiota

Project description: In this project you will develop and improve current programs/approaches to map the conformational energy landscape of sugar-like molecules and use these methods to extract energetic and conformational properties of inhibitors and activity-based proves for glycoside hydrolases (GHs) of the gastrointestinal mucus. In parallel, you will use molecular dynamics, quantum mechanism/molecular mechanics (QM/MM) and metadynamics techniques and to elucidate molecular mechanisms of enzymes that bind/recognize and process glycans at the mucosa-microbiota interface. Finally, you will analyse the conformational dynamics of mucose complex glycans that are being characterized experimentally by our consortium partners. The project will be performed in a world leading group of computational biochemistry, in close interaction with experimental research groups and industrial partners of the SCT consortium.  The techniques/tools you will receive training and acquire expertise include ligand docking, structure and sequence alignment, molecular dynamics, ab initio simulations, QM/MM and metadynamics methods.

Planned secondments: 1) Leiden University (3 months): design of inhibitors of GH activities at mucosal–microbiota interface; 2) University of Naples Federico II (2 months): NMR-based structural characterization of epitope-glycan-binding protein complexes; 3) Company Glycom (1 month): evaluating the industrial applications of the developed methodology.

For more information on this ESR vacancy contact:  c.rovira@ub.edu and visit the group web pagehttp://www.ub.edu/sqpbio

 

 



ESR10 Project with Dr. Anne Salonen @ University of Helsinki, Finland; Science fields: Microbiology/ Biochemistry

Host institution: University of Helsinki (Finland)

Main supervisor: Dr. Anne Salonen, Dr. Katri Korpela

Co-supervisor(s):Prof. Antonio Molinaro (University of Naples, Italy) and Patrice Cani (Universite Catholique de Louvain, Belgium)

PhD duration: 36 months

Desired start: September-October 2019

ESR10 PhD project:  Human milk oligosaccharides and intestinal endotoxins: Role of glycans in shaping early life microbiota and immune development

Background: Early life microbiota is an important factor for long-term human health. We have established a large birth cohort that focuses on the drivers and health consequences of gut microbiota development in Finnish children  (https://helmitutkimus.com/helmi-in-english/). Project description: This PhD project focuses on glycans that play key roles in gut microbiota and immune development in infancy. Specifically, the project aims to 1) Study human milk oligosaccharides (HMOs) in relation to microbiota development 2) Isolate key Gram negative early colonizers and characterize their immunological and metabolic effects 3) Structural characterization of dominant endotoxins (LPS) in the infant gut.

Profile: You have a MSc degree on microbiology, biochemistry or related field. During your PhD project you will receive training and acquire expertise in microbiota analysis, bacterial culture, cell culture, analysis of immunological and metabolic parameters in animal model, analytical and organic chemistry, carbohydrate chemistry, NMR spectroscopy.

Planned secondments: 1) Company Glycom (3 months): Identification of HMOs from breast milk samples 2) Universite Catholique de Louvain (2 months): Investigate physiological effects of key isolated strains in animal model, 3) University of Napoli (2 months): Structural determination of LPS from selected samples and strain(s)

For more information on this ESR vacancy contact: anne.salonen@helsinki.fi

 

 



ESR11 Project with Prof. Patrice Cani @ UCLouvain, Belgium; Science fields: Integrative Physiology/ Metabolomics

Host institution:  UCLouvain (Belgium)

Main supervisor: Prof. Patrice D. Cani

Co-supervisor(s):Dr. Anne Salonen (University of Helsinki Finland), Prof. Antonio Molinaro (University of Naples Federico II, Italy)

PhD duration: 36 months

Desired start: September-October 2019

ESR11 PhD project: Studying and modulating the mucosal-gut microbiota interface and its impact on the pathophysiology of obesity and related cardiometabolic disorders such as type 2 diabetes

Project description: In this project we will use different models (in vivo and in vitro) to understand the cellular and the molecular mechanisms influenced by intestinal microbes and their metabolites. To decipher the key features regulating physiology and metabolism we will focus on the gut to peripheral organs axis (liver, adipose tissue and brain).  The focus will be on the investigation of physiopathology diseases or the onset thereof such as altered gut barrier function and, systemic low-grade inflammation and immune system influencing host response. Hereby, we will modulate the microbiota composition of mice by using innovative nutrients, next generation beneficial bacteria or specific bacterial components in the context of obesity and cardiometabolic disorders. During your PhD project you will receive training and acquire expertise in 1) integrative physiology (expertise in laboratory animals handling, 2) in vivo gut microbiota/bacterial components administration 3) gut microbiota analysis, 4) transcriptomic and metabolic parameter assessments on different tissues (gut, fat pads, brain, liver, muscles), 5) histological analysis (gut, adipose tissue, liver morphology, mucus layer thickness and goblet cells).

Planned secondments: 1) University of Helsinki, Finland (2 months): Characterization of specific microbes in microbiota upon treatment, 2) Quadram Institute Bioscience (QIB), UK (3 months): Assessment of the mucins from intestinal samples / relevant glycocodes, 3) Company Glycom, Denmark (3 months): Analysis of potential undigested prebiotic fibers.

For more information on this ESR vacancy contact: Patrice.cani@uclouvain.be

 

 



ESR12 Project with Dr. Joeri Beaprez @ Inbiose, Belgium; Science fields: Biochemistry/ Molecular Biology

Host company: Inbiose (Belgium)

Partner organisation for PhD degree: Ghent University (Belgium)

Main supervisor: Dr. Joeri Beaprez

Co-supervisor(s): Prof. Hermen Overkleeft (Leiden University), Dr. Tom Wennekes (Utrecht University)

PhD duration: 36 months

Desired start: June-July 2019

ESR12 PhD project:  Characterization of novel microbiota-derived glycosyltransferases and glycosylhydrolases

Project description: The goal of this project is to build novel screening principles for glycan active enzymes, by setting up several novel techniques. First novel enzyme synthesis principles will be developed and novel assaying techniques set up. In a second phase potential enzyme candidates will be identified via next gen sequencing of different sources of microbiota and bio-informatics tools. Finally, the novel identified enzymes will be cloned and synthesized via high throughput cloning and the developed enzyme synthesis methodology, after which the enzymes will be characterized with the new assay technique. This will form the basis to build completely novel glycans in vitro as well as in vivo. During your PhD project you will receive training and acquire expertise in high throughput cloning techniques, protein expression and purification, biochemical assay and screening technique development, bio-informatics, structure-function relationship determination, analytical biochemistry, and laboratory automation

Planned secondments: 1) Leiden University (3 months): Chemo-enzymatic synthesis of precursors to use in screening; 2) Utrecht University (2 months): Analysis of in vitro synthesized glycans.

For more information on this ESR vacancy contact: Joeri.Beauprez@inbiose.com

 

 



ESR13 Project with dr. Louise Kristine Vigsnæs @ Glycom A/S, Denmark; Science fields: Biochemistry/ Analytical Chemistry

Host institution: Glycom A/S (Denmark)

Partner organisation for PhD degree: Denmark Technical University

Main supervisor: dr. Louise Kristine Vigsnæs

Co-supervisor(s): Prof. Nathalie Juge (Quadram Institute, UK), Dr. Anne Salonen (University of Helsinki)

PhD duration: 36 months

Desired start: September-October 2019

ESR13 PhD project:  Impact of human glycans on gut barrier function and mucosal microbiota

Background: The gut microbiota is important for human health; however, when the composition is disrupted by e.g. environmental factors unfavourable bacterial signals can arise impacting gut permeability and immune responses. Human glycans (e.g. human milk oligosaccharides (HMOs)) are complex structure that can beneficially modulate the gut microbiota and the bacterial metabolite profile leading to improvement in the gut barrier.

Project description: The overall aim of the project is to investigate the role of human glycans (e.g HMOs) on mucin-degrading bacteria from either healthy and disease, gut barrier and immune function. Specific tasks will include i) labelling of selected glycans in order to identify the metabolic pathway in mucin-degrading bacteria ii) examining the impact either direct or indirect of selected glycans on gut permeability and immune function. During your PhD project you will receive training and acquire expertise in the structure and biology of human glycans such as HMOs; isotope labelling; mammalian cell and tissue culture; fluorescence and confocal microscopy; microbiota culturing and sequencing; development of intervention.

Planned secondments: 1) Quadram Institute (5 months); cell and tissue culturing analysing gut barrier function. 2) Utrecht University (2 months); Chemical biology techniques and probes. 3) Technical University of Denmark (4 months)

For more information on this ESR vacancy contact: louise.vigsnaes@glycom.com

 

 



ESR14 Project with dr. Annick Mercenier@ Nutrileads, the Netherlands; Science fields: (Bio-)Organic Chemistry/ Analytical Chemistry

Host institution: Nutrileads (the Netherlands)

Main supervisor: dr. Annick Mercenier & dr. Marcela Aparicio

Co-supervisor(s): dr. Tom Wennekes (Utrecht University, NL), dr. Nathalie Juge (Quadram Institute, UK), dr. Anne Salonen (University of Helsinki, Finland)

PhD duration: 36 months

Desired start: June-September 2019

ESR14 PhD project:  Unravelling the structure-function of pectin derived polysaccharides by studying the interaction of purified and modified variants with the host immune system and their impact on the human gut microbiota.

Project description: In this project you will develop an effective purification scheme of the pectic polysaccharides variants and you will perform chemo-enzymatic synthesis of defined motives of these variants. Using a collection of these variants and motives, you will study their impact on immune cells, the microbiota and the gut barrier aiming at unravelling the mechanisms underlying these effects. You will also identify which bacterial species and their enzymes are involved in their fermentation. To this end you will use select in vitro assays and confirm findings by a limited number of in vivo preclinical studies.

During your PhD project you will receive training and acquire expertise in glycan purification and chemo-enzymatic synthesis, assays used to characterize immune reactions, identification of receptors involved in the recognition of pectin polysaccharide derivatives. Moreover, you will analyse the impact of pectin derivatives on the gut microbiota becoming familiar with the methodology used in this key area (from bacteria DNA/RNA extraction to BioIT analysis of the results). Moreover, you will be exposed to the different assays used to study the gut barrier. Samples from clinical trials will be available to evaluate translation form preclinical results to the human situation.

Planned secondments: 1) Utrecht University (5 months): Chemo-enzymatic synthesis, purification and characterization; 2) University of Helsinki (4 months): different aspects and methodology of microbiota analyses; 3) Quadram Institute (3 months): impact on gut barrier and interaction with gut mucus.

For more information on this ESR vacancy contact: annick.mercenier@nutrileads.com

 

 



ESR15 Project with Prof. Rob Field @ Iceni Dignostics, UK; Science fields: Chemical Biology/ Analytical Chemistry

Host institution: Iceni Diagnostics (Norwich, UK)

Partner organisation for PhD degree: University of East Anglia

Main supervisor: Prof. Rob Field

Co-supervisor(s): Prof. Nathalie Juge (Quadram Institute, Norwich, UK), Prof. Antonio Molinaro (University of Naples Federico II, Italy)

PhD duration: 36 months

Desired start: September-October 2019

ESR15 PhD project:  Carbohydrate detection as the basis of new diagnostics for infectious diseases

Project description: In this project you will develop chemical tools and analytical methods with which to assess glycan/glycan-binding protein interactions with pathogenic microorganisms. Through engagement with Sweet Crosstalk partners, you will identify and prioritise synthetic glycans and/or LPS-derived glycans and/or glycan-binding proteins for evaluation. Your goal will be to devise practical glycan or glycan binding protein detection methods, suitable for use in point-of-care diagnostics, and that both detect and distinguish between pathogens. As such, the project would suit someone with a background in chemistry/biochemistry, who is keen to work across disciplines and to embrace the challenges and opportunities of developing new tools/products and approaches for infectious diseases R+D.

During your PhD project you will receive training and acquire expertise across chemical glycobiology, including carbohydrate and bioconjugation chemistry, structural characterisation techniques (HPLC, NMR, MS), nanoparticle technology, ELISA and lateral flow assay development, and microbiology. Working with the company will provide awareness of translational and market research, commercialisation activities, diagnostics test development and validation.

Planned secondments: 1) University of Napoli (3 months): Determination of O-glycan epitopes and their potential use in diagnostics, 2) Quadram Institute (3 months): Evaluation of diagnostic tests prototypes using co-cultures & microbiota samples.

For more information on this ESR vacancy contact: rob.field@icenidiagnostics.com

 

 


 

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