Stijn Hendrik Peeters

Index

• About
• Current Projects
• Past Projects
• Skill summary
• Bibliography
• Link to personal (non-work) projects

About

I am an ambitious (micro) biologist who is easy to work with and a team player. I have a broad interest in all things biology, from biochemistry to bioinformatics. I am particularly skilled in the creation and analysis of -omics datasets, from sample to publication-ready figures. I am also no stranger to meta-genomics, genome assembly, etc. I have been involved in the cultivation and characterization of over 70 novel Planctomycetes, resulting in skills pertaining to cultivation and phylogeny. I have ample experience with light (brightfield, confocal, fluorescent) and transmission electron microscopy. I am looking to apply these skills on a new and exiting projects together with a motivated and experienced group of scientists.

Current projects

Starvation response in Kuenenia stuttgartiensis

In this project we turn of the inflow of nutrients resulting in immidiate starvation, due to the effective concentration of nitrite in the bioreactor system being ~0. Response of bacterium is followed by transcriptomics, metabolomics and electron microscopy.

Membrane sub-proteome of Kuenenia stuttgartiensis

Kuenenia stuttgartiensis is an anammox bacterium, a bacterial family that all share a similar bacterial organella called the anammoxosome. This compartment houses its energy metabolism and is therefore thought to be analogous to the eukaryotic mitochondium. We have very little idea which proteins reside in which membrane, as we have not yet discovered any targetting mechanism. In order to examine protein abundances in each membrane, we set out to separate each membrane and perform quantitative proteomics.

Bacterial operon prediction

There are quite a few operon prediction tools out there, but none suited my need. I have used both genomic distances between genes as well as transcriptome data to predict operon structures.

Past projects

Cell division of Planctomycetes

Investigation of non-model cell division in Planctopirus limnophila, which lacks most the normally essential cell division machinery. We genetically modified this bacterium to delete the remaining "essential" cell division genes, which did not affect their abnormal cell division.

Ammonia and nitrite transporters in Kuenenia stuttgartiensis

By limiting either free [nitrite] or [ammonia] in the growth media of Kuenenia stuttgartiensis, we examined the expression levels of all transcripts, but with a focus on nutrient transporters. These are of especial interest because nutrient have to pass three double membranes instead of two, due to the unsual intracellular organelle called the anmmamxososome.

The quest for a molecular signal that targets the anammoxosome of anammox baceteria

I used a machine learning approach similar to Medema et.al., but used a RNA based approach instead of a protein based approach. Did not yield any convincing results. In order to restart a similar project, we need a higher number of confirmed annammoxosomal proteins. This could achieved in the near future, as described above.

Core genome database for anammox bacteria

I often found myself looking at a gene and then wondering wether the gene had any relevance beyond just the bacterial strain I was investigating. To find the relevance of a gene in the larger scope of it's family, I clustered all protein products. The original annotation of each gene was attached to each cluster, and a representative of each of these clusters was used further identify domains present in each cluster. This information was added to a database, and can be queried for any search term. This way, any protein of interest can be quickly examined for presence in other anammox species.

Skills

1. Research of biological topics with(in) a team
2. Various types of light microscopy (brigh field, fluorecent, confocal etc
3. Computational analysis of large sets of images
4. Transcriptomics, proteomics, metabolomics, genomics, from sample to figure
5. Coding pipelines that take raw data and produce figures, with minimal user input
6. Cloning in B. subtilis and E. coli
7. Lab scale bioreactor systems
8. Antibody techniques, precipitation, blotting, etc.
9. Electron microscopy sample preparation: High pressure freezing, epon embedding, ultramicrotome sectioning
10. R/python programming languages
11. Linux/bash
12. LaTeX / html, markdown languages

Bibliography

Reviews

Cell division

Transcriptomes

Species description and characterisation

This bibliography was generated with the aid of bibtex2html 1.95.