14.12. 2017, Biologie tukové tkáně

PhD project: Complex screening of gene expression using RNA sequencing analysis with the focus on the early human development

Early postnatal period is critical with respect to development of the key physiological functions and homeostatic mechanisms of the newborn, as well as for imprinting the metabolic features that could be manifested during the adolescence and adulthood. At the Institute of Physiology of the Czech Academy of Sciences, a unique biobank of the autopsy samples of various tissues is available that had been collected from human newborns, mostly very premature newborn, at several maternity hospitals in Prague more than 15 years ago. These rare materials were already used to characterize various aspects of early human development using analysis of expression of individual genes at the transcript and protein level. The goal of the project is to extend these studies by applying the RNA sequencing analysis (RNA-seq) for the complex characterization of gene expression in the human newborn tissues. Over the last years, RNA-seq has become a standard method for global gene expression profiling. However, pipelines to perform RNA-seq data processing remain challenging due to the large size of the raw data files and the hardware requirements. The project will focus on RNA-seq data acquisition as well as the development and application of computational methods for RNA-seq analysis, functional interpretation, and visualization in order to reveal various aspects of early human development and its control, also with regards to various pathologies.

The project will proceed in a close collaboration between the Department of Adipose Tissue Biology and the Department of Metabolomics of the Institute of Physiology of the Czech Academy of Sciences, and the Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University (http://udmp.lf1.cuni.cz/en/genomics-and-bioinformatics-laboratory) in Prague. This multidisciplinary environment will be key for the appropriate training of the student and successful work on the project.The basic salary provided by the Institute may be increased from another budget.

 

Candidate’s profile (requirements):

MSc degree in cellular and molecular biology with a strong interest to work in the biomedical research and bioinformatics. Experience of working in a laboratory is preferred.

 

Relevant Publications:

1. Mele M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, et al. Human genomics. The human transcriptome across tissues and individuals. Science. 2015;348(6235):660-5.

2. Brauner P, Kopecky P, Flachs P, Kuda O, Vorlicek J, Planickova L, Vitkova I, Andreelli F, Foretz M, Viollet B, et al. Expression of Uncoupling Protein 3 and GLUT4 Gene in Skeletal Muscle of Preterm Newborns: Possible Control by AMP-Activated Protein Kinase. PediatrRes. 2006;60(5):569-75.

 

Supervisor:

Jan Kopecký, MD, PhD, jan.kopecky@fgu.cas.cz