When people think of an atlas, they think of a world map, showing oceans, country borders, timelines, labelled with names of cities, rivers, etc. The atlas proposed here will show patterns of gene expression layered onto anatomical structures of the developing chick embryo, labelled with the names of structures, genes, etc. Just as a world atlas helps us to understand where we live, an atlas of the developing embryo will help us to comprehend how we form. We all develop from a single fertilized cell which multiplies into a mass of cells, this undergoes complex changes in shape, while growing to form the different organs and tissues that make up our bodies. By imaging chick embryos at different times during development, we will make a detailed map of anatomical structures as they form. The earliest stages are relatively simple as they are flat, but older embryos become increasingly more complicated and we will use a 3D imaging technique called 'Optical Projection Tomography' to image them. An atlas is not very useful without a systematic way to name its features so we will create a standard set of words, which will make it possible to query the atlas using tools based on computer science. But the overt structure of developing embryos hides a further level of anatomy, special groups of cells called 'organizers'. These organizers instruct cells around them so that the correct structures are made in the right place at the right time. Organizers are not always easy to identify; the 'polarizing region' responsible for patterning the digits of the limb for example looks just like the tissue all around it. About half a dozen organizers have been discovered, many through transplantation experiments in chick embryos, and we now know that they are best distinguished by specific genes that are active ('expressed) in their cells. In our project we plan to examine exactly which genes are expressed in four well defined organizers and produce a 3D map of their precise expression patterns in the whole embryo throughout development. Gene expression patterns of ~1000 genes will be mapped. This is a significant number of genes with which to begin to populate the chicken Atlas to be made publicly available to everyone over the internet. To determine what genes are expressed in these four different regions of early chick embryos (hypoblast, Hensen's node, floor plate of the neural tube and limb polarizing region) we will dissect out these tissues and use 'microarrays' to screen for all the genes they express and identify shared sets of genes. Genes expressed in the same place ('synexpression groups') are likely to be involved in the same biological process, so we hope to uncover sets of genes which work together to define an 'organizer'. But why focus on chicks rather than animals closer to humans? Amazingly, organizers and other signalling centres act in similar ways in different species as diverse as fish and man. Thus discoveries in the chick are relevant to human development and chicks are much easier to obtain and dissect than mouse embryos, so these two models are very complementary. The chick atlas however will be based on the same system developed for the mouse thus allowing comparisons. Conserved patterns of expression in chick and mouse will provide strong evidence for genes being functionally related while subtle differences can cast light on why a chick and mouse do not look the same. We will create a database to organize and manage this huge collection of data on gene expression patterns, anatomical structures, genes, etc. and develop new computer tools to query and analyse the data to discover new relationships and new functions for genes in development. This research will lead to a deeper understanding of the basic biological processes which will in turn help understanding of health issues such as congenital abnormalities, cancers and tissue repair.

Modern biology is becoming more and more multidisciplinary. This is especially the case for the area of 'Systems Biology', which aims to predict how the different biological processes interact to result in a functional organism. These processes include the transcription of DNA into RNA, which codes for amino acids that make up the proteins, as well as the levels of hormones and metabolites that affect the biological processes. In the proposed network, we address how variation at the DNA level affects the transcription of DNA into RNA and how this then affects the characteristics of the whole organism. The aim is to reconstruct the networks that describe how genes interact. While conceptually straightforward, the area of research requires integration between biology, computer science (bioinformatics) and mathematics. At present, there is already some level of integration between researchers in these areas, but a lot of work is done in isolation. In the proposed network we will bring together: 1) biological research in plants, animals and humans. 2) Bioinformatics research which covers databases that contain known information on gene networks but also translates novel statistical and mathematical models into user-friendly software. 3) Mathematical biology, focussed on the methods of reverse-engineering of gene regulatory network, from a variety of experiments. The network will achieve its goal of further integration by organising annual meetings. These meetings will consist of an interactive workshop followed by a scientific conference. The workshop will provide ample opportunity for training of young researchers, dissemination of 'best practise' and new software tools and initiation of new collaborative research. The Conference will disseminate the cutting edge of the research area to the wider community.

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

The Transmissible Spongiform Encephalopathy (TSE) diseases are a group of fatal neurodegenerative diseases which include scrapie in sheep, BSE in cattle and CJD in humans. TSE diseases (also known as prion diseases) differ from other neurodegenerative disorders such as Alzheimer's disease, due to their infectious nature. Instead of an conventional infectious agent such as a bacterium or virus the TSE infectious agent (the prion) is thought to be a misfolded form of a host protein (PrP). It has been hypothesised that the abnormally folded form of the protein (PrPSc) is able to bind to the normal protein which is found in brain tissue of all mammals, and convert it into the abnormal form. PrPSc accumulates as disease progresses, and may cause the death of neurons in the brain. PrPSc is usually found in infected tissue, and can be identified microscopically by the presence of abnormal protein aggregates in sections of brain tissue, or by its resistance to digestion with proteases on immunoblotting. PrPSc co-purifies with the TSE infectious agent, and correlates with the level of infectivity present. PrPSc was therefore thought to be the sole component of the 'prion', and is currently the only diagnostic marker used for TSE disease testing. PrPSc can exist as either diffuse deposits or large amyloid aggregates in tissue, but the role of each form in disease is unknown. Conflicting studies have suggested both an infectious and a protective role for PrP amyloid in TSE disease. In addition, other experiments have shown that PrPSc is not always present in infectious tissue. These findings raise serious questions about the suitability of PrPSc as the only available diagnostic marker, and it is important for both accurate disease diagnosis and the development of new therapies and treatments for these currently incurable diseases that we identify exactly which form of PrP is associated with infectivity. In this proposal, we aim study the amyloid form of PrPSc and its association with the infectious agent. In our laboratory we have observed that transgenic mice inoculated with brain material from a case of atypical human prion disease do not develop clinical or pathological signs of disease, but do produce large amyloid aggregates in the brain. We have been unable to transmit disease from brain tissue of mice possessing these aggregates, indicating the absence of TSE infectious agent in these tissues. Current diagnostic methods would have identified these mice as TSE infected, yet we have shown the mice lack both disease and infectious agent. Our results support the hypothesis that PrP amyloid is not infectious, and may be formed by seeding from amyloid in the inoculum, or may be a host protective mechanism by which smaller more infectious aggregates are sequestered into an inert form. We therefore aim to identify the role of amyloid in TSE disease by inoculating transgenic mice with oligomeric and amyloid forms of recombinant PrP to determine whether we can induce amyloid formation in transgenic mice in the absence of infected tissue inoculum, and whether such amyloid forms of PrP are infectious. We also aim to disrupt these amyloid deposits to determine whether smaller fragments from the amyloid are infectious. The results from these experiments will aid in our understanding of the role of PrP amyloid in TSE disease. If amyloid is a protective mechanism by which the host controls TSE infectivity, treatments which target the disruption of such aggregates may instead enhance disease, and would therefore be undesirable. These results will also help to identify specific forms of PrP associated with TSE infectivity, leading to the development of accurate diagnostic tests with low risk of both false negative and false positive results which is important ethically when developing diagnostic assays for human prion disease.