Openings

LSI Our laboratory is based at the Living Systems Institute at the University of Exeter. The new institute provides an exciting interdisciplinary environment bringing together leaders in Biology, Physics, Medicine and Mathematics.

Exciting upcoming PhD project on new super-resolution methods applied to RNA biology

A project with industrial partner Bio-Techne

Deadline: 30 Sep 2018
Title: Illuminating mechanisms of RNA transcription by novel optical super-resolution imaging approaches
Funding: Fees & Scholarship at RCUK levels, for eligible domestic and EU students
Start: January 2019 (earlier start in November 2018 negotiable)
Apply: Online

We have opened applications for this PhD project, interested candidates are highly encouraged to contact the supervisors, Christian Soeller or Steve West, to make enquiries and express their interest.

Pol II super-resolution imaging

We are inviting applications for a fully-funded PhD studentship to commence in January 2019 or as soon as possible thereafter, to be held at the Living Systems Institute at its Streatham Campus. For eligible students the studentship will cover UK/EU tuition fees plus an annual tax-free stipend.

Optical Super-Resolution Imaging and RNA Biology

Optical super-resolution imaging has come to the forefront of biological research because it combines two critical advantages, (1) the specificity and contrast of fluorescence markers which has revolutionized biological imaging and (2) access to the spatial resolution range of 5-200 nm over which bio-molecular interactions occur and that traditional imaging techniques cannot capture. In this project, we will translate methods previously used for optical super-resolution in fixed cells into live cell preparations, supported by the chemical biology expertise of Bio-Techne, our partner in an academia-industry collaboration.

In addition to the focus on method development, where we will exploit reversibly binding markers to implement high-resolution live-cell super-resolution imaging, we will use these new approaches to observe mechanisms of RNA transcription – one of the most fundamental processes in Cell Biology. Most transcription is carried out by RNA polymerase II (Pol II) but much of what we know about this comes from indirect experiments as we have been historically unable to directly observe the processes taking place. One of our major research interests is the mechanism by which transcription terminates in a process essential for genome punctuation. In utilizing our existing super-resolution expertise and developing new live cell capability, we aim to perform the first mechanistic dissection of the process by directly imaging it taking place. In particular, we aim to test the current model that transcriptional termination is caused by a 5’3’ exonuclease, Xrn2, pursuing a transcribing Pol II via the degradation of its associated nascent RNA. In addition to its fundamental importance, many of the processes and factors implicated in termination are mis-regulated in diseases including cancer and neurodegenerative disorders. This is an exciting opportunity at the interface of Biophysics and Molecular Biology underpinned by a strong commercial partner.

An Academia-Industry Collaborative Project

For this project we have partnered with Bio-Techne, a leading developer of high quality reagents and assay systems for biomedical researchers and clinical research laboratories. Bio-Techne Bristol is the home of the corporation’s chemical expertise and the manufacturing site for Tocris brand products. Bio-Techne will provide custom small molecule/peptide tools and fluorescent probes for this project, including development and synthesis of first-in-class compounds, which will enable the candidate to generate optical super-resolution data of outstanding quality. The candidate will have the opportunity to work closely with the industrial collaborator to gain additional commercial experience and transferable skills.

Living Systems Institute Hosting Laboratories

The project will be conducted in a collaboration between the Soeller and West laboratories which are based at the recently opened Living Systems Institute at the University of Exeter. The Living Systems Institute is a world-class, next generation, collaborative research community to revolutionise the diagnosis and treatment of diseases through basic research. The Living Systems Institute provides state-of-the-art facilities including optical imaging, molecular biology, mass-spectrometry and high performance computing.

Candidate Skills Sought

The ideal candidate has some experience in fluorescence imaging, quantitative analysis and basic biological techniques. The candidate will have a degree in Biophysics, Biology or a related area with a strong quantitative focus. We will provide training for all skills essential to this project including super-resolution imaging, molecular biology, data analysis and scientific writing. The successful candidate will have the opportunity to work in a highly interdisciplinary environment and interact with a highly motivated postgraduate cohort.

Pol II super-resolution detail

Figure. The figure shows the distribution of Pol II in the nucleus of a HCT116 cell. The diffraction limited data is shown in green and the super-resolution data obtained using the DNA-PAINT method that is fully established in our laboratories is shown in red-orange. The magnified inset demonstrates the small distances between adjacent Pol II sites which appear to form clusters within some areas of the nucleus. In this project we will extend this methodology from the fixed preparation shown here into live cells and also look simultaneously at Pol II and the exonuclease Xrn2.

References

  1. Jayasinghe, I., Clowsley, A. H., Lin, R., Lutz, T., Harrison, C., Green, E., Baddeley, D., Di Michele, L. & Soeller, C. True Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors. Cell Reports 22, 557–567 (2018).
  2. Lutz, T., Clowsley, A. H., Lin, R., Pagliara, S., Di Michele, L. & Soeller, C. Versatile multiplexed super-resolution imaging of nanostructures by Quencher-Exchange-PAINT. Nano Res. 78, 993 (2018).
  3. West, S., Proudfoot, N. J. & Dye, M. J. Molecular dissection of mammalian RNA polymerase II transcriptional termination. Mol Cell 29, 600–610 (2008).
  4. Eaton, J. D., Davidson, L., Bauer, D. L. V., Natsume, T., Kanemaki, M. T. & West, S. Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity. Genes & Development 32, 127–139 (2018).

The applications for the openings below have now closed !

PhD to work on new tricks that enable imaging in scattering samples

Deadline: 31st January 2018
Title: Microscopy in scattering media
Funding: EPSRC - Fees & Scholarship
Apply: Online

imaging around corners The scattering of light in imaging is often regarded as a problem, but has more recently been recognised to allow unexpected tricks, for example, seeing around corners, illustrated on the left. In microscopy, when one images through a scattering medium it seems on first sight that all detail has been lost in a "fog". This is illustrated below with an image taken on our microscope. No clear features are recognisable in the recorded image, everything appears to be a blur. However, there is information about the object encoded in the image.

The blurred image is not completely featureless, it contains information in the form of a speckle pattern, a fine granular pattern of light and dark regions. Such speckle patterns are very familiar to those who have previously worked with coherent light sources, such as lasers. By clever image processing, the speciality of our collaborator Jacopo Bertolotti, we can recover the image of the actual object, as if no scattering had taken place. This is illustrated in the reconstruction that was calculated from the recorded image. It clearly shows a pattern in the shape of an "F", matching the actual test pattern that we had used.

scattering imaging The PhD project will focus on extending this method into a practical way to take microscopy images in samples that are currently regarded as too scattering to allow any meaningful imaging. Since many biological samples, such as bone or the brain, are made of such strongly scattering materials, the new methodology has major relevance for bio-imaging.

The 4-year PhD project is run through the highly regarded MetaMaterials CDT in Physics, and will be co-supervised by Jacopo Bertolotti and Christian Soeller. Please feel free to contact us, we are happy to discuss all aspects of the project.

For further details, and to apply online, please consult the advert.

PhD to work on 3D super-resolution microscopy with deformable mirrors

Deadline: 10th January 2018
Title: Microscopy With a Deformable Mirror
Funding: EPSRC - Fees & Scholarship
Apply: Online

adaptive optics in astronomy In astronomy, adaptive optics using deformable mirrors has revolutionised ground based observation. Shown on the left, a telescope is shooting a laser into the sky to create a guide star, using deformable mirror technology.

In microscopy, we have only recently begun to use deformable mirrors for flexible and dynamic control of the optical properties. Deformable mirrors enable us to change the optical aberrations, either to compensate for aberrations in the system, or, as we intend here, to deliberately introduce aberrations that allow us to improve the ability to localise individual molecules in 3D.

mems deformable mirror In the project we will use a MEMS deformable mirror (see on the right) to dynamically control the properties of the microscope optics. This will allow us to build 3D super-resolution images of much improved quality, which is critical in the imaging of biological samples, such as animal and plant cells. The resolution improvement as compared to confocal microscopy is quite dramatic.

Phase Ramp
ImagingThe project builds on our very successful Phase Ramp Technology which is now used commercially in all Zeiss Elyra super-resolution microscopes.

The project will provide training in imaging, computing and optical design. Supervision is provided by Christian Soeller, Alex Corbett and Mike Deeks. Please feel free to contact us, we are happy to discuss all aspects of the project.

For further details, and to apply online, please consult the advert.