PhD in Modelling yeast metabolis and regulated cell death

Different yeast species play a vital role in industrial biotechnology for the sustainable production of a wide range of products, for example ethanol as a biofuel or protein ingredients for alternatives to animal-based products. However, also the lifespan of these yeast cells is finite, and their death negatively impacts processes: for example, with regards to process duration or product quality.

Therefore, we developed an approach that integrates the disciplines of fundamental cell and molecular biology, systems and synthetic biology with bioprocess and metabolic engineering to improve both our understanding of these cell death processes as well as the survival and performance of different yeast species in industrial bioprocesses.

In this project, you will:

• develop mathematical models on how yeast cell actors impact physiology and metabolism and how cell heterogeneity affects the cell population;
• develop highly curated and predictive enzyme constrained Genome scale models (ecGEMs) of Saccharomyces cerevisiae and Komagataella phaffii that incorporate regulated cell death (RCD) pathways;
• extensively model yeast metabolism during RCD under industrially relevant conditions;
• characterize molecular mechanisms and identify biomarkers. The models will be used to design strategies to postpone yeast cell death under industrially relevant conditions.

You will work here
A consortium at seven host institutes (Wageningen Universiteit, Universidade do Minho, Danmarks Tekniske Universitet, Austrian Centre for Industrial Biotechnology, Imperial College London, Università degli Studi di Milano Bicocca and Chalmers Tekniska Högskola) together with fifteen associated partners, ranging from start-up to large biotechnology companies and renowned research institutes aims to understand how yeast cells die under industrial process conditions and use this knowledge to improve biomanufacturing.

Your project, together with 12 other doctoral projects, will focus on a different aspect, but in strong synergy with the other projects. As such, each PhD will receive a strongly interdisciplinary training alongside performing exciting research. During this PhD project you will perform secondments to the Austrian Centre of Industrial Biotechnology (Austria) and Cambrium (Germany).

Your research is embedded within the chair Systems and Synthetic Biology and you will be supervised by Prof. Dr Maria Suarez Diez and Dr Edoardo Saccenti. Within the project, you will collaborate with the other consortium members of UPsYDe and especially the Laboratory of Bioprocess engineering (BPE) at Wageningen University, the laboratories of Dr. Briggite Gasser (Austrian Centre of Industrial Biotechnology) (Viena, Austria) and of Dr Pierre Salvy at Cambrium (Berlin, Germany).

Management/Office Assistent – Leerstoelgroep Gedragsecologie

Wat ga je doen?
Jij runt als Management/Office Assistent het secretariaat van de leerstoelgroep Gedragsecologie van Wageningen University & Research (WUR).

Jouw taken en verantwoordelijkheden zijn o.a.:

• Secretariële- en administratieve taken (overzicht houden van belangrijke deadlines; verwerken van gegevens in verschillende systemen)
• Aanspreekpunt voor medewerkers, studenten en gasten
• Ondersteuning leerstoelgroep (interne informatievoorziening; hulp bij (administratieve) vragen)
• Organisatorische taken (reizen boeken; plannen en organiseren van vergaderingen, bijeenkomsten en uitjes; communicatie: website en social media)
• HR taken (contractwijzigingen, aanmelding externe medewerkers/student-assistenten, controle tijdregistratie en verlof)
• Financiële taken (orders plaatsen en verwerken, budget management, controle uitgaven)
• Onderwijsondersteunende taken (vak- en cijferregistraties, bijhouden studentenadministratie)

Hier ga je werken
Informatie over leerstoelgroep Gedragsecologie vind je hier: Behavioural Ecology Group - WUR

Chemisch analist pesticiden

Word jij enthousiast van werken in het lab? Wil je met jouw werk bijdragen aan de veiligheid van ons voedsel? En lijkt het je leuk om dat te doen in een gezellig team waar hard gewerkt én gelachen wordt? Dan zijn wij op zoek naar jou!

Wij zoeken naar een enthousiaste en nauwkeurige chemisch analist die zich thuis voelt in een dynamisch laboratorium en graag de handen uit de mouwen steekt. Je komt terecht in een van de Pesticiden teams, waar we dagelijks voedsel analyseren op de aanwezigheid van pesticiden. Jouw werk draagt dus direct bij aan de voedselveiligheid voor mens en dier.

Als chemisch analist pesticiden voer je analyses uit waarbij je gebruik maakt van gestandaardiseerde protocollen. De nadruk ligt op instrumentele analyses met behulp van moderne meetsystemen op het gebied van LC-(HR)MS/MS en GC-(HR)MS/MS. De analyse- en onderzoeksresultaten worden gerapporteerd aan de projectleider. Als analist werk je in een analyseteam dat verantwoordelijk is voor het efficiënt uitvoeren en rapporteren van de analyses.

Jouw taken en verantwoordelijkheden bestaan onder andere uit:

• het opwerken van de monsters;
• het uitvoeren van metingen met behulp van onze moderne LC-(HR)MS/MS en/of GC-(HR)MS/MS systemen;
• het verwerken en interpreteren van de data;
• het opstellen van standaard operating procedures (SOPs).

Je bent dus bij het hele proces betrokken: van monsteropwerking tot rapportage. Dat maakt het werk afwisselend en leerzaam. Je werkt in een team van betrokken collega’s met wie je samen zorgt voor betrouwbare resultaten.

Jij komt te werken in een van de pesticiden teams (ongeveer 20 medewerkers per team) die zich dagelijks bezighouden met voedselveiligheid, in Wageningen. Professionele teams waar samenwerken, kwaliteit en werkplezier centraal staan.

Post Doc: Aphid-microbiome Interactions

As postdoc aphid-microbiome interactions at the Lab. of Entomology, you will be responsible for setting up methodologies and pipelines for microbiome analyses of aphids, converting complex data into comprehensive graphs and in building hypotheses on how the microbiome affects aphid physiology and behavior. The hypotheses will then be tested in bioassays and electrical penetration graph experiments with aphids, plants and microbial inoculants.

You will support the team in unraveling what role the microbiome plays in the broader context of aphid-plant interactions.

Your duties and responsibilities include:

• Setting up and executing bioassays with aphids, plants and microorganisms
• Analyzing 16S/ITS amplicon sequencing data
• Validating implications of the microbiome on aphid physiology and behavior

Your team
You will work in an international, multidisciplinary team of colleagues at the Lab. of Entomology and the Lab. of Virology in Wageningen.

You will work here
The Laboratory of Entomology focusses on the biology of insects with an emphasis on understanding ecological aspects in the context of the underlying physiological and molecular mechanisms. The Laboratory of Entomology consists of a team of ambitious scientists and lecturers. The education programme focusses on BSc, MSc and PhD levels and includes ecological, physiological and molecular aspects. You will work in close collaboration with the Laboratory of Virology, which focuses on plant viruses, arboviruses and insect viruses, aiming to unravel the molecular and ecological mechanisms underlying virus-host and virus-vector interactions.

Two PhD positions Functioning of intercropping systems -experimental & modelling

Then we have 2 PhD positions available, within the Dutch-Danish project Robotic Intercropping, within the focus areas ‘Agro-ecological Potential’ (position #1) and ‘Ecological Interactions Among Plants’ (position #2). As a Wageningen University PhD student within this project, you will contribute to the expansion of our knowledge on the functioning and role of intercrops, at the level of the whole system as well as the level of individual plants. You will collaborate with other researchers in the project team and contribute to project goals with your PhD study.

In your application, please state very clearly, at the start of your letter, whether you apply for position #1 or position #2. Application letters that do not contain this information will not be considered.

Position #1 - experimental
In this PhD study, you will evaluate and help optimize a highly diverse intercropping system. You will assess which combination of service crops and their management by robots can reduce the need for agricultural inputs, enhance biodiversity and diversity-mediated ecosystem services, while maintaining crop yields comparable to intensive agricultural systems. You will analyse the relation between different combinations of service crops and their effect on ecosystem services. You will do this in part with a Danish counterpart by making use of large multi-year field experiments that will be running in both Wageningen and Copenhagen locations.

Position #2 - modelling
In this PhD study, you will work on improving our understanding of competition between cash and service crop plants in intercrop systems, and the underlying driving eco-physiological mechanisms. You will use 3D plant modelling (so-called functional-structural plant modelling) to address questions and generate hypotheses on the interactions between plants, soil, environment and management such as leaf pruning and root cutting. For this, you will consider both above- and belowground processes. For the modelling you will make use of data obtained in the experiments, and you will also play a minor role in acquiring that data.

You will work here
You will be located at Wageningen University within the centre for Crop Systems Analysis (CSA) at Wageningen University. PhD position #1 will be supervised by Dr Luuk Croijmans, Dr Dirk van Apeldoorn, and Prof Dr Niels Anten. PhD position #2 will be supervised by Dr Franca Bongers and Prof Dr Jochem Evers. Both positions with also be co-supervised by Prof Dr Svend Christensen from Copenhagen University; also the leader of the project. Regular meetings will be organised within the focus area, and at the level of the whole project. Frequent visits to Denmark are envisaged, especially for PhD position #1.