What are we researching?

Our research group focuses on two areas: first, using 3D image data to answer interesting biological questions; and second, developing novel software to reduce the difficulty of analyzing the 3D image data we're interested in. Most of our team is from Diamond Light Source, the UK's national synchrotron. As our research incorporates different scientific disciplines, the background of our team is split between biology, imaging, and computer science.

We work with many different types of 3D imaging data. Right now, we're working with data from a technique called Cryo soft X-ray tomography (see below for more information) to answer questions about how organelles inside the cells may change in Huntington disease.

Aerial view of Diamond Light Source on the Harwell Science and Innovation Campus in South Oxfordshire, UK.

What are we studying?

Protein Misfolding Disorders

Protein misfolding disorders are a class of diseases associated with unchecked protein misfolding and aggregation. Some examples we are focusing on are Huntington's Disease and Alzheimer's Disease. In each case, a protein or a protein fragment takes a nonstandard structure due to a genetic mutation or abnormal cellular processing. It's common that the nonstandard structure is prone to self-aggregation, or clumping together. By aggregating, the normal cellular function of the protein is lost and sometimes, the aggregated form can take on a new cellular function or interactions. In these ways, the structural changes at the protein level lead to structural changes at the cellular level and finally to the manifestations of the disease.

Huntington's Disease Overview

Huntington's Disease mainly affects the brain and gets worse over time. It's caused by a genetic mutation in the Huntington gene. Early symptoms of the disease are subtle mood changes and cognitive difficulties. These are usually followed by a lack of coordination and unsteady gait which can then progress to uncoordinated, jerky body movements and cognitive decline. In the brain, Huntington's Disease is characterized by loss of a specific type of neuron (striatal) and a progressive pattern of brain atrophy. Currently, diagnosis of Huntington's is through psychiatric examinations, neuroimaging and a genetic test. However, since no treatment or cure currently exists, and the knowledge can affect many people in a family because of the genetic nature of the mutation, many patients choose not to be tested early in life.

At the molecular level, the mutation occurs in a specific stretch of the Huntington gene. The mutation is an expansion; extra DNA bases are added in where they shouldn't be which leads to extra amino acids in the protein once it's been translated. These extra amino acids lead to atypical processing of the protein, creating a small fragment that includes the expanded area. This fragment is what then aggregates leading to the disease. Localisation studies have shown that this fragment can be found both in the nucleus and in the cytoplasm of brain cells. And that mitochondrial function is lowered in Huntington's Disease.

We are testing the hypothesis that the presence of Huntington aggregates leads to structural changes in the cell - perhaps through reorganisation of the structures already present, an increase or decrease in the number of a specific type of structure, or changes in size and shape of a structure. To answer this biology question, we use a technique called Cryo soft X-ray Tomography (see below for more information) that can capture the detailed structure of intracellular components. Below is the image of a Huntington cell under Cryo soft X-ray Tomography, showing the nucleus (N) and cytoplasm (C) that consists of numerous organelles.

Cryo Soft X-ray Tomography

Cryo Soft X-ray Tomography (cryoSXT) is a technique that bridges the gap between light microscopy and electron microscopy. This means we can image whole cells with good contrast giving us the ability to visualize cellular compartments, organelles and some cytoskeletal elements. All of this is done at very cold temperatures and without chemically fixing or staining the cells to achieve contrast. However, this technique only provides a limited resolution, which means we cannot see individual proteins or protein complexes.

Soft X-ray Microscope at Diamond Light Source.

Workflow Overview

In our previous workflow on this project (https://www.zooniverse.org/projects/msbrhonclif/science-scribbler), the citizen scientists have helped annotate the organelles inside the cell. Annotation is the process of labelling and representing objects (organelles) in the imaging data. It is a complicated and difficult task since there are different types of organelles with various intensities, sizes and shapes. In addition, differentiating the subcellular structure (organelle) from the background (non-organelle) is particularly difficult in gray scale images due to a low signal-to-noise ratio. Because of this, there is a lot of variabilty and subjectivity in the original annotation data we collected. Before analysing this data, we would like to clean it up so that we can answer the biological questions more accurately and correctly.

This is where we need your help! In order to overcome the variability associated with the original annotations, we need your help to ensure a consensus emerges!