Joint PhD projects
We are in the process of setting up joint PhD projects between the members of tthe Biomolecular spectroscopy & dynamics Cluster (BioC).
Solvation dynamics and structure around proteins and peptides (Wynne & Lapthorn)
Chemistry enabled by proteins relies on the fluctuations and flexibility of the protein scaffold. This flexibility is largely determined by water while at the same time the protein is known to affect the structure and dynamics of the surrounding water. A number of recent studies using very different techniques have come to the conclusion that a protein ties many water layers (7 to 10) to itself in an intimate embrace that has been termed the “protein dance”. However, other studies such as femtosecond infrared pump-probe studies on smaller solutes have clearly shown no effect on water structure and dynamics beyond the first solvation shell. Thus, we are in the highly unsatisfactory position where state-of-the-art studies by reputable groups completely disagree on the interaction of biomolecules with the surrounding aqueous medium. Here we propose that this conflict can be resolved through the application of a very high dynamic range time-domain version of Raman spectroscopy covering the spectral range <125 MHz to ~30 THz combined with broadband dielectric spectroscopy covering the spectral range 100 MHz to 200 THz. These complementary techniques will be used to solve the controversies relating to the interaction of proteins, peptides, and other molecules of biological significance with the surrounding water as well as to characterise low-frequency modes in the biomolecules themselves.
New tools, old ticks: uncovering the transmission biology of disease vectors through emerging technologies
A project in Parasitology in collaboration with the UCP group.
Summary
This project will combine chemical physics, proteomics and disease ecology to gain novel insights into the transmission and feeding ecology of an important disease vector, the tick species Ixodes ricinus. In harnessing the power of novel technologies, including spectroscopy and proteomics, and applying them to a significant disease problem, this project will be breaking new ground at the interface of molecular, environmental, and health sciences.
Background and Aims
Vector-borne diseases account for much of the world’s health problems. In the northern hemisphere, ticks in the genus Ixodes are the principal vectors for emerging diseases including Lyme borreliosis (LB) and tick-borne encephalitis.
A striking knowledge gap with respect to tick-borne diseases is the lack of quantitative information about how ticks interact with their biotic and abiotic environment. Ixodes ticks are considered host generalists that acquire their blood meal, of which they take several throughout their life, from a wide range of vertebrate species. In the case of LB, only some species (small mammals, certain birds) are competent reservoirs, whereas others (e.g., deer) are non-competent and do not transmit. The frequency at which ticks feed on different host species within a particular environment will therefore have a profound effect on local pathogen prevalence in ticks. However, there is currently no established technology for determining retrospectively which host species a tick collected in the field has taken its blood meal from. Likewise, there is a lack of methods for determining whether a tick acquired its last blood meal one month or one year ago and thus how quickly ticks are progressing to their next life stage. These technology gaps continue to limit our mechanistic understanding of how the local environmental conditions ticks are exposed to (e.g. vertebrate host communities, climate) can drive human disease risk.
The project has three major aims:
1) To establish the use of near-infrared spectroscopy (NIRS) to age-grade free-living ticks1
2) To apply tandem mass spectral libraries to discriminate the sources of tick blood meals in European ticks2
3) To dissect transmission dynamics in high and low risk sites for Lyme borreliosis using the approaches developed in aims 1) and 3)
1 Reeves WK, Peiri KHS, Scholte E-J, Wirtz RA, and Dowell FE. 2010. Age-grading the biting midgeCulicoides sonorensis using near-infrared spectroscopy. Medical And Veterinary Entomology, 24(1), 32–37. Med Vet Entomol, 2010 vol. 24 (1) pp. 32-37.
2 Özlem Önder, Wenguang Shao, Brian D Kemps, Henry Lam, and D. Brisson. 2013. Identifying sources of tick blood meals using unidentified tandem mass spectral libraries. Nature Communications, 4, 1746–10.
Training and Environment
The project will provide exceptional opportunities for training in state-of-the-art technologies in infectious disease research. At the same time, these technologies have much broader applicability, giving the scholar useful transferable skills for a variety of career choices in biomedical sciences.
The Wynne lab will provide training in spectroscopic techniques. Experiments will be based around a new (2014) state-of-the-art Fourier-transform infrared (FTIR) spectrometer from Bruker with detection capabilities from far- to near-IR. New statistical analysis methods will be implemented such as neural network analysis of the age-dependent spectra.
The Burchmore lab will offer in-depth training in the use of mass spectrometry for host blood meal identification based on proteomic signatures. This will include the potential to develop novel approaches such as the use of MALDI – TOF/TOF mass spectrometers for high throughput acquisition of spectral libraries.
Biek and Ferguson will provide guidance and training in field and lab-based ecological techniques as well as epidemiological concepts and models and their applications in the context of disease control. Due to the nature of the project the scholar will also be developing important general skills in experimental design as well as statistical and computational analyses.
The scholar will be joining a vibrant community of students and postdocs working on interdisciplinary approaches in infectious disease and life sciences, providing opportunities to develop broader scientific perspectives.
Requirements
Applicants should have a first or upper second class degree in a relevant science discipline (e.g. molecular biology, zoology, biochemistry, bioinformatics), be highly motivated and have excellent English communication skills. The successful candidate will need to be enthusiastic about acquiring new skills in an interdisciplinary setting and have a strong interest in biological processes as well as new technologies such as mass spec and infrared spectroscopy. Research experience, laboratory skills, knowledge about ecological fieldwork, and demonstrated ability to work independently will be considered an advantage.
*For MVLS applications we advise that any application is made via the online application system, this can be foundhere. Applicants should select "MVLS - Lord Kelvin Adam Smith Scholarship" for the programme of study and give the title of the project and supervisors name. *
Lead Supervisor: Dr Roman Biek Institute of Biodiversity Animal Health and Comparative Medicine |
Supervisor 2: Professor Klaas Wynne Chemistry |
Supervisor 3: Dr Richard Burchmore Parasitology |
Supervisor 4: Dr Heather Ferguson Institute of Biodiversity Animal Health and Comparative Medicine |
For more information, see Shortlisted Kelvin Smith PhD Projects 2015/16 or contact Dr Roman Biek.
Mapping and controlling nucleation
Applications are invited for a 3.5 to 4 year PhD studentship to study the chemical physics of (crystal) nucleation in the Ultrafast Chemical Physics (UCP) group under the supervision of Prof Klaas Wynne and possibly in association with the Centre for Continuous Manufacturing and Crystallisation. The UCP group has 18 years of experience in femtosecond laser spectroscopy and ultrafast dynamics. In the past few years, we have expanded into ultraslow dynamics using microscopy and in particular fluorescence lifetime imaging (FLIM). See references 1 and 2. This project will investigate the physics of crystal nucleation using various forms of microscopy.
The chemical physics of crystal nucleation is of great fundamental and practical importance but is yet poorly understood. It is therefore one of the grand challenges on the border between physics, chemistry, and chemical engineering. Our group focuses on nucleation of new phases under highly non-equilibrium conditions and in the neighbourhood of a liquid-liquid demixing critical point. This allows for a high degree of control that has not been explored previously. Nucleation of new phases will be studied with “normal” microscopy (bright field, phase contrast, polarisation), confocal Raman microscopy, and fluorescence microscopy including FLIM.
We are now looking for a PhD student who is interested in developing new imaging techniques including the use of spatial light modulators and interfacing a microscope with a high power pulsed laser. The ideal candidate for this position is a chemical physicist, physical chemist, or somebody with knowledge of optics or microscopy. The student will be working alongside a team of researchers with experience in ultrafast techniques, chemical physics, and microscopy.
Informal enquiries can be made to: Prof Klaas Wynne, School of Chemistry, University of Glasgow, G12 8QQ, t: (0141) 330-8522, e: Klaas.Wynne@glasgow.ac.uk, u: http://www.wijnne.com/
Requirements
Applicants should have a first or upper second-class degree in a relevant science discipline (e.g., physical chemistry, physics), be highly motivated and have excellent English communication skills. The successful candidate will need to be enthusiastic about acquiring new skills in an interdisciplinary setting and have a strong interest in microscopy and the development of new laser-based microscopy techniques. Research experience, laboratory skills, and demonstrated ability to work independently will be considered an advantage. The position is available to UK and EU residents from October 2015 onwards.
References
- J. Mosses, C.D. Syme, and K. Wynne, ‘The order parameter of liquid-liquid phase transitions’, J. Phys. Chem. Lett., 6, 38-43 (2015). (http://dx.doi.org/10.1021/jz5022763)
- J. Mosses, D.A. Turton, L. Lue, J. Sefcik, and K. Wynne, “Crystal templating through liquid–liquid phase separation”, Chem. Commun. 51, 1139-1142 (2014). (http://dx.doi.org/10.1039/c4cc07880b) See also The role of liquid-liquid demixing in crystallisation: icy fluff balls
