Student Profiles
The students 2008-2010: Alexander Baltz, Jiaxuan Chen, Fabian Bindel, Lukas Aeberhard, Rina Ahmed, Martina Weigt, Mathias Munschauer, Anna-Carina Jungkamp, Marlon Stoeckius (left to right)
Photo: Alexander Baltz/copyright: MDC
Here we introduce the MDC-NYU students and their joint projects with the Center for Genomics and Systems Biology and the Department of Biology at NYU.
Rina Ahmed (2009): Nematode microRNA evolution an its implications for adaptation
Supervisory team: Christoph Dieterich and Kris Gunsalus
Contact: rina.ahmed@mdc-berlin.de
In my PhD project, I will investigate the evolution of microRNA genes in the phylum of nematodes. For this, we will perform small RNA next-generation sequencing on a genus-wide level.
Alexander Baltz (2009): Biochemical characterization of the protein-mRNA interactome
Supervisory team: Markus Landthaler and Stephen Small
Contact: alexander.baltz@mdc-berlin.de
The aim of my PhD project is to investigate transcriptome-wide protein-mRNA interactions in mammalian cells and during development and differentiation in D. melanogaster.
Fabian Bindel (2010): Integrative analysis of cell metabolism and proteome in fast versus slow growing cells
Supervisory team: Stefan Kempa and Richard Bonneau
Contact: fabian.bindel@mdc-berlin.de
Cancer is a disease of imbalance in cell cycle regulation and consequently in cell growth. To acquire a cancer phenotype, a cell has to undergo a series of gene alterations which regulate cell proliferation, differentiation and apoptosis. Cancer cells can be characterized by their abnormal proliferation rate. Even if the in vivo concentration of the nutrients remain the same, some cancer cells are able to increase their proliferation rate.
My question is: What are the mechanisms that transform the metabolism to enable such altered proliferation rate?
The underlying feature behind different cell phenotypes is the different regulation of the metabolism despite the fundamental pathways being the same. These changes are reflected on the different molecular levels of a cell. To identify possible regulatory events changing a cell phenotypic behavior we will investigate the cell metabolism using stable isotope labeled substrates over different time spans. This allows us to monitor pathway activities in a dynamic way. Simultaneously, we will analyze the proteome to identify connections to an altered proliferation rate (e.g. isoform switching) by Stable Isotope Labeling by Amino acids in Cell culture (SILAC). Transcriptomic analysis (RNA-Seq) will be used for gene expression profiling. The combined data analysis of these different levels will further the identification of new potential targets for anticancer drugs.
Jiaxuan Chen (2009): Analysis of protein-protein interaction during embryogenesis in C. elegans
Supervisory team: Matthias Selbach and Fabio Piano
Contact: jiaxuan.chen@mdc-berlin.de
The aim of my PhD project is to study protein-protein interaction during early C. elegans development. Combining an in vivo SILAC approach and high-throughput quantiative mass spectrometry, I will investigate the binding partners of proteins that are important for C. elegans embryogenesis.
Anna-Carina Jungkamp (2009): Transcriptome-wide identification and characterisation of RNA-binding protein target sites in C. elegans
Supervisory team: Nikolaus Rajewsky and Fabio Piano
Contact: anna-carina.jungkamp@mdc-berlin.de
During my PhD project, I will study post-transcriptional regulation of gene expression in vivo. I will establish a technique to identify transcriptome-wide target sites of RNA-binding proteins in the nematode C. elegans. These data will then be combined with RNAi experiments, RNA-seq and high-throughput quantitative in vivo proteomics to study the function of particular RNA binding proteins. As a member of the BIMSB-NYU PhD Exchange Program, I have already visited Fabio Piano's lab to learn basic C.elegans techniques and during my PhD project and regular visits to his lab are planned. Some of the experiments are planned as joint projects with a PhD student in his lab.
Jungkamp AC; Stoeckius M; Mecenas D; Gruen D; Mastrobuoni G; Kempa S; Rajewsky N In vivo and transcriptome-wide identification of RNA binding protein target sites Molecular Cell 44 (5): 828-840 (2011-12-09)
Mathias Munschauer (2010): Investigation of translational regulation using small RNA sequencing
Supervisory team: Markus Landthaler and Christine Vogel
Contact: mathias.munschauer@mdc-berlin.de
The goal of my PhD project is to study translational regulatory mechanisms by in vivo crosslinking approaches and small RNA sequencing.
Marlon Stoeckius (2009-2011): High resolution transcriptome and proteome profiling during oocyte to embryo transition in C. elegans
Supervisory Team: Nikolaus Rajewsky and Fabio Piano
Contact: marlon.stoeckius@mdc-berlin.de
My PhD project was part of a long-standing collaboration with the lab of Fabio Piano at New York University. I spent several months in New York to learn C. elegans methods which enabled me to establish those used in Berlin. We recently published a method to sort specific stages of C.elegans embryogenesis (Stoeckius et al, 2009) as a part of my BIMSB-NYU PhD project.
Marlon successfully defended his thesis with the grade summa cum laude from Humboldt-Universität-zu Berlin on 20 June 2011.
Stoeckius M; Maaskola J; Colombo T; Rahn HP; Friedlaender MR; Li N; Chen W; Piano F; Rajewsky N Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression Nature Methods 6 (10): 745-751 (2009-10)
Martina Weigt (2010): Genome wide DNA CpG methylation profiling using massive parallel bisulfite sequencing
Supervisory team: Wei Chen and Fei Li
Contact: martina.weigt@mdc-berlin.de
DNA methylation is, besides histone modyfication, the key feature of epigenetic modification. It holds multiple functions in plants and higher animal phylia. In mammals, CpG methylation is generally regarded as a regulator of transcription and is essential for processes such as development, parental allele-specific imprinting and dosage compensation by X inactivation in females. It has been also implicated in many human pathologies including cancer. During my study to investigate the CpG methylation profile on a genome wide scale, I will first set up the technique of reduced representation bisulfite sequencing (RRBS) and then apply it in different biological systems.