Undergraduate summer studentships

Dr Emily Caseley

Please note that the deadline for applications for this project is noon on Monday 12^th February 2024

Identification of novel potassium channel inhibitors for the development of treatments for KCNT1-related epilepsy

For more details about the placement and how to apply please see the job description

Gain of function mutations in the human KCNT1 gene, which encodes the KNa1.1 potassium ion channel subunit, cause severe drug-resistant childhood epilepsies. Many of the affected children develop seizures within the first few months of life, which can cause other debilitating disabilities, yet none of the existing anti-epilepsy medications are effective in treating this form of epilepsy. Our research therefore focuses on identifying and characterising novel inhibitors of the KNa1.1 channel, with the aim of developing them as potential therapeutic treatments. We have previously published a paper describing the use of computational tools and protein structural data to identify new inhibitors of this potassium channel (Cole et al, 2020, iScience), and in our current work we have used this structure-based methodology to identify a series of novel, structurally diverse small molecule inhibitors.

Objectives

In this project we aim to expand on our previous work identifying novel inhibitors by investigating the potential that natural products have to act as KNa1.1 potassium ion channel inhibitors. Using our established workflow, an in silico screen will be carried out against the recently published human cryo-electron microscopy structure of the human KNa1.1 protein to identify natural products of interest. The products with the highest docking scores will then be tested in vitro using a HEK293 KCNT1 stable cell line and a fluorescence assay to determine whether they modulate KNa1.1 activity.
 

Dr Miriam Hurley

Remodelling of structure-function relationships underlying cardiac dysfunction in ageing: A multi-scale systems approach

For more details about the placement and how to apply please see the job description

Piezo-1 is a mechanically sensitive ion channel. Notably, Piezo-1 activation contributes to an increased reactive oxygen species (ROS) production and subsequent elevated calcium signalling due to the modulation of calcium handling proteins.  

With age, Piezo-1 expression within the heart increases. Piezo-1 is known to modulate the functional calcium release and re-uptake channels, namely the ryanodine receptor and sarcoendoplasmic reticulum calcium ATPase respectively. Cardiac remodelling with age can occur in response to pressure overload. This is of interest due to Piezo-1’s responsiveness to stretch, a response that we have previously characterised within the heart’s cardiac conduction system upon the initiation of mechanical stimulation. However, the global heterogeneity of Piezo-1’s distribution across the heart is unknown. 

The aim of this project is to characterise the distribution of Piezo-1 from the level of the whole heart to the nanoscale level of the calcium release unit within 6-, 12- and 24-month male Wistar rats. In turn, understanding structural heterogeneity of Piezo-1 across age will provide a mechanistic insight into our understanding of the heart’s local and global structure-function relationship by allowing us to study Piezo-1 expression and orientation in regard to tissue remodelling, calcium dynamics and ROS production. 
 

Objectives

The primary objective of this project is to characterise the local and global orientation of the Piezo-1 channel within the rat aging heart in relation to the cardiac conduction system and calcium handling proteins. 

A secondary objective is to identify suitable antibodies to investigate Piezo-1 distribution which will enable the future investigation of Piezo-1 within the wider research group. A final objective is to learn and apply image analysis techniques to quantify the structural heterogeneity of Piezo-1 across age.  

To achieve all three objectives, isolated hearts from 6-, 12- and 24-month male Wistar rats that have been previously collected and cryoprotected will undergo tissue sectioning and immunofluorescence investigation. Confocal microscopy will be undertaken to visualise Piezo-1 across the heart with a spatial resolution of 250 nm. The subsequent application of super-resolution expansion microscopy will involve learning a novel microscopy technique to gain an 8-fold improvement in spatial resolution that is typically gained from the ‘gold-standard’ confocal microscopy approach. This will provide an unprecedented understanding of Piezo-1’s location within the heart at a nanoscale level in relation to crucial calcium handling proteins. 
 

Dr Dongbo Li

Multigenerational Trophic Responses to Coupled Short- and Long-term Environmental Change 

For more details about the placement and how to apply please see the job description

Recent climate change has modified biological processes from genes to ecosystems, across all biomes, but a fundamental challenge is to understand and predict species’ responses to future change. In particular, there is a major gap in knowledge concerning how interactions between species will be affected by future environmental change. This project, funded by the Natural Environmental Research Council, is investigating how long-term temperature increases impact insect host-parasitoid interactions, and whether they can adapt across multiple generations. We are carrying out laboratory microcosm experiments in which insect populations are exposed to continuous 2 or 4 ℃ temperature increases over 2 years (≥18 generations). Furthermore, we are investigating how temperature extremes ability to track climate change. This will improve our understanding of ecosystem responses to environmental change, and our ability to predict future pest and disease outbreaks, threats from invasive species, and extinction risk.

Objectives

The successful applicant will undertake a laboratory experiment to investigate how multiple environmental stressors (i.e. temperature and humidity) affect the life-history traits of moth hosts and their parasitoids through acclimation, under the supervision of Dr. Dongbo Li and other lab members. The applicant will be trained in general lab skills, specific techniques to measure traits, and in the design and conduct of scientific experiments. The applicant will collect their own dataset from this experiment, and be encouraged to build on their statistical skills using the programming language R when analysing their data. The applicant will join the research group, and be involved in our general lab work, including population monitoring, and insect stock maintenance.

LAZY but effective: Deciphering the role of LAZY genes in regulating plant architecture

For more details about the placement and how to apply please see the job description

Overall plant architecture (consisting of the number, spacing and angle of secondary root and shoot branches) determines the efficiency of crops to capture essential resources such as water and nutrients below-ground, and light above-ground. Plant architecture is critically regulated by gravitropic growth, and recently, members of the highly conserved LAZY gene family have been demonstrated to play crucial roles in regulation of branching angle, a key determinant of plant architecture. How these genes regulate branching angle in secondary organs remains to be elucidated. Previous work in the Kepinski lab has identified a novel dominant point mutation in LAZY4, (described as lazy4D) through an EMS mutagenesis screen in the model plant, Arabidopsis. Lateral roots in the lazy4D mutant demonstrate steeper rooting, a highly desirable trait, that maximises nitrogen uptake and drought tolerance in cereal species. This makes LAZY4 (and related LAZY genes) attractive targets for genetic modification to engineer deeper rooting in crop plants. This project aims to elucidate the molecular mechanisms that underpin the lazy4D (and more broadly, LAZY genes) dependent regulation of root and shoot branching angle, to identify new tools for the targeted manipulation of plant architecture in the quest for sustainable food production.

Objectives

1.    To investigate the effect of the ‘D’ mutation on protein stability: To do this, WT and mutated GFP tagged LAZY4 proteins will be transiently expressed in N. benthamiana, and protein levels assessed through a well established western blotting protocol.  Soluble GFP will be used as a control. 
2.    To investigate the effect of the ‘D’ mutation on subcellular protein targeting: Preliminary data has suggested that LAZY proteins may be targeted to the cellular cytoskeleton during transient expression analysis in N. benthamiana, and that the ‘D’ mutation may enhance this targeting. The UG will confirm this, using live cell confocal microscopy in transgenic Arabidopsis plants co-expressing LAZY4/4D-mCherry as well as LifeAct:GFP or MT:GFP. Further, using chemical inhibitor treatments such as oryzalin, we will assess the effect disruption of cytoskeletal targeting on LAZY4/4D targeting and function.
3.    To identify new binding partners of lazy4D: If time permits, we will compare the interactome of the lazy4d mutant protein with that of the wild type version using yeast one hybrid assays and mass spectrometry. This work will be done in collaboration with the Morita group in Japan. 

Contribution of muscle stem cells to diaphragm weakness in sepsis

For more details about the placement and how to apply please see the job description

The diaphragm generates contractions that allow breathing, which is vital for human survival. Acute inflammatory clinical conditions such as sepsis can cause severe and rapid-onset diaphragm weakness. Additionally, patients with Covid-19 can develop diaphragm weakness, and sepsis and Covid-19 have been found to interact and cause poor clinical outcomes. Diaphragm weakness can cause problems with breathing, coughing or swallowing, and consequently, this contributes to worse symptoms in patients as well as higher hospitalisations and mortality rates. Recently, the BBC reported “Sepsis failings still causing too many deaths”, highlighting the need for sepsis to become a “key priority” for healthcare. There is no treatment for sepsis-induced diaphragm weakness, and the underlying mechanisms remain unclear. Skeletal muscle health is maintained by quiescent muscle stem cells (MuSCs), but their role in sepsis-induced diaphragm weakness is yet to be explored. Mechanisms of sepsis-induced diaphragm weakness will be investigated in a mouse model of sepsis. To assess whether impaired muscle regeneration is involved in sepsis-induced diaphragm weakness, MuSCs will be isolated from mouse diaphragm using fluorescent activated cell sorting (FACS). MuSC properties can then be compared in mice with sepsis-induced diaphragm weakness to control mice, to identify differences which may contribute to disease pathology.

Objectives

The successful candidate will be directly supervised by Dr Emily Storey to investigate the role of MuSCs in sepsis-induced diaphragm weakness. MuSCs will be isolated from diaphragms from mice with sepsis-induced diaphragm weakness, as well as control mice, by mechanical and enzymatic digestion of the tissue followed by FACS. The properties of the MuSCs will then be compared using data output from the FACS analysis, and the expression of myogenic markers will be explored in the MuSC cell populations.

The successful candidate will learn laboratory skills including primary cell isolation, flow cytometry and polymerase chain reaction (PCR). The candidate will attend weekly tutorials and laboratory meetings, in addition to being asked to regularly present findings in scientific discussions as part of a multidisciplinary team including collaboration with clinicians working in the intensive care unit (ICU) department at St James’ Hospital. The work will take place in the School of Biomedical Sciences, Faculty of Biological Science.

Applicants should be motivated, collaborative and interested in muscle biology and clinical disease. Necessary training will be provided to ensure successful delivery of the project, but previous experience of cell-based techniques would be an advantage.