Dr Jarema Malicki
Reader in Developmental Genetics
Room: D18 Firth Court
Eukaryotic cilia are fascinating highly polarized cell surface features that frequently detect and/or process extracellular signals, including small molecules, light, and polypeptides. We aim to understand how signal transduction mechanisms are assembled in cilia and how they function is processes as diverse as embryonic patterning, vision, and metabolism.
The laboratory has also some interest in other aspects of cell polarity, such as membrane subcompartmentalization and organelle positioning in cell’s cytoplasm.
Ciliogenesis and Cell Polarity
We use several types of microscopy to visualize cilia: conventional confocal microscopy, selective plane illumination microscopy (SPIM), and stochastic optical reconstruction microscopy (STORM).
To identify binding partners of ciliary proteins, we use tandem affinity purification (TAP) followed by mass spectrometry and yeast two-hybrid screens. We also use mass spectrometry to identify post-translational modifications, such as acetylation, on ciliary proteins.
Undergraduate and postgraduate taught modules
Postgraduate PhD Opportunity
FROM MOLECULES TO VISION
Funding status: This project is funded by Fight For Sight, an eye research charity. Funding includes a stipend of 17,000 GBP/year for three years and a travel allowance. Applicants are expected to have excellent record of academic performance, and research experience in biochemistry and molecular genetics. Interested individuals are encouraged to contact Dr. Jarema Malicki for further details. Review of applications is in progress.
Photoreceptors of the vertebrate eye are exquisite biological sensors capable of detecting single photons. Light sensitivity of photoreceptors is mediated by hundreds of millions of opsin molecules tightly packed into hundreds of membrane folds that form the so-called outer segment.
As the outer segment is constantly renewed throughout the lifetime of the organism, it is estimated that 100-1000 opsin molecules are transported to the outer segment every second. The molecular mechanism that mediates opsin transport is one of the central unsolved puzzles of photoreceptor biology. This transport mechanism is also of paramount medical importance as its defects lead to photoreceptor death and blindness in a range of human genetic disorders, including retinitis pigmentosa, cone-rod dystrophies, Bardet-Biedl Syndrome and others.
The goal of this project is to identify molecular mechanisms that mediate opsin transport. This will be accomplished using biochemical and imaging approaches. Biochemistry experiments will include tandem affinity purification (TAP), a two-step protocol designed to recover intact protein complexes from cells and tissues. In parallel, transport mechanism components will be localized at high resolution using advanced imaging super-resolution microscopy techniques, stochastic optical reconstruction microscopy (STORM) in particular.
The Malicki lab has long experience with studies of the visual system in general and photoreceptor cells in particular.
IMAGING LIFE BEYOND THE DIFFRACTION LIMIT OF LIGHT
Funding status: Awaiting funding decision/Possible external funding
Ever since its invention centuries ago, light microscopy has been hampered by the diffractive properties of light, which limit resolution to ca. 200 nm. This resolution limit precludes the visualization of many subcellular structures and has been a major obstacle in the imaging of biological processes. Recent advances in fluorophore excitation methods and image processing algorithms have overcome this limitation, increasing image resolution by as much as 10 times to about 20 nm. This new form of imaging is termed super-resolution microscopy.
Super-resolution microscopy opens unprecedented opportunities. We take advantage of this approach to image subcellular structures that regulate intracellular traffic. We focus on barrier mechanisms that regulate protein movement between the cell’s cytoplasm and the cilium, a tiny subcellular compartment involved in signal detection on cell surface. The cilium is just 250 nm across and so conventional light microscopy is not suitable visualize its inner architecture. The inner components of cilia are, however, essential for the function of many cells, tissues, and organs, including sensory neurons.
As the initial step, we applied super-resolution microscopy to image cilia of a simple unicellular organism, Tetrahymena. By localizing over 30 protein epitopes, we generated a 3D model of the cilia base. As the next step, we will extend these imaging studies to vertebrate tissues, focusing on the nervous system. We will use transgenic lines that express specialized fluorescent proteins suitable for super-resolution imaging in sensory neurons of zebrafish. This will make it possible to image vital structures, such as cilia or synaptic termini, in unprecedented detail and thereby gain insight into their function.
Keywords: Cell Biology / Development, Genetics
For informal enquiries about any of these projects or application process, please feel free to contact me.
For further information about this project, and how to apply, see our PhD Opportunities page:
- Hazime K & Malicki JJ (2017) Apico-basal Polarity Determinants Encoded by crumbs Genes Affect Ciliary Shaft Protein Composition, IFT Movement Dynamics, and Cilia Length. Genetics, 207(3), 1041-1051. View this article in WRRO
- Malicki JJ & Johnson CA (2017) The Cilium: Cellular Antenna and Central Processing Unit. Trends in Cell Biology, 27(2), 126-140. View this article in WRRO
- Pooranachandran N & Malicki JJ (2016) Unexpected Roles for Ciliary Kinesins and Intraflagellar Transport Proteins. Genetics, 203(2), 771-785.
- Jin D, Ni TT, Sun J, Wan H, Amack JD, Yu G, Fleming J, Chiang C, Li W, Papierniak A, Cheepala S, Conseil G, Cole SPC, Zhou B, Drummond IA, Schuetz JD, Malicki J & Zhong TP (2014) Prostaglandin signalling regulates ciliogenesis by modulating intraflagellar transport. Nature Cell Biology, 16(9), 841-851. View this article in WRRO
- Malicki J (2012) Who drives the ciliary highway?. Bioarchitecture, 2(4), 111-117. View this article in WRRO
- Zhao C, Omori Y, Brodowska K, Kovach P & Malicki J (2012) Kinesin-2 family in vertebrate ciliogenesis.. Proc Natl Acad Sci U S A, 109(7), 2388-2393.
- Zhao C & Malicki J (2011) Nephrocystins and MKS proteins interact with IFT particle and facilitate transport of selected ciliary cargos.. EMBO J, 30(13), 2532-2544.