Methods and practice of detecting selection in human cancers

Cancer development and progression is an evolutionary process, understanding these evolutionary dynamics is important for treatment and diagnosis as how a cancer evolves determines its future prognosis. This thesis focuses on elucidating selective evolutionary pressures in cancers and somatic tissues using population genetics models and cancer genomics data. First a model for the expected diversity in the absence of selection was developed. This neutral model of evolution predicts that under neutrality the frequency of subclonal mutations is expected to follow a power law distribution. Surprisingly more than 30% of cancer across multiple cohorts fitted this model. The next part of the thesis develops models to explore the effects of selection given these should be observable as deviations from the neutral prediction. For this I developed two approaches. The first approach investigated selection at the level of individual samples and showed that a characteristic pattern of clusters of mutations is observed in deep sequencing experiments. Using a mathematical model, information encoded within these clusters can be used to measure the relative fitness of subclones and the time they emerge during tumour evolution. With this I observed strikingly high fitness advantages for subclones of above 20%. The second approach enables measuring recurrent patterns of selection in cohorts of sequenced cancers using dN/dS, the ratio of non-synonymous to synonymous mutations, a method originally developed for molecular species evolution. This approach demonstrates how selection coefficients can be extracted by combining measurements of dN/dS with the size of mutational lineages. With this approach selection coefficients were again observed to be strikingly high. Finally I looked at population dynamics in normal colonic tissue given that many mutations accumulate in physiologically normal tissue. I found that the current view of stem cell dynamics was unable to explain sequencing data from individual colonic crypts. Some new models were proposed that introduce a longer time scale evolution that suppresses the accumulation of mutations which appear consistent with the data

Structure of smectic defect cores: an X-ray study of 8CB liquid crystal ultra-thin films

We study the structure of very thin liquid crystal films frustrated by antagonistic anchorings in the smectic phase. In a cylindrical geometry, the structure is dominated by the defects for film thicknesses smaller than 150 nm and the detailed topology of the defects cores can be revealed by x-ray diffraction. They appear to be split in half tube-shaped Rotating Grain Boundaries (RGB). We determine the RGB spatial extension and evaluate its energy per unit line. Both are significantly larger than the ones usually proposed in the literatureComment: 4 page

A continuous information theoretic approach to the analysis of cutaneous receptor neurons

Information theoretic and statistical techniques for determining the number of discernible levels in cutaneous receptor neurons are reviewed. Reasons for the large variance in these results are discussed. A new continuous information theoretic analysis technique is presented that overcomes many of the problems in the other methods of analysis discussed. Comparison of this new method of analysis with a statistical technique developed by Schreiner et al. (1978) clearly shows some of the misconceptions that are associated with statistical analysis techniques, and why these problems cannot arise in the new information theoretic technique discussed here.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47432/1/422_2004_Article_BF00340064.pd

Collagen-induced arthritis in C57BL/6 mice is associated with a robust and sustained T-cell response to type II collagen

Many genetically modified mouse strains are now available on a C57BL/6 (H-2b) background, a strain that is relatively resistant to collagen-induced arthritis. To facilitate the molecular understanding of autoimmune arthritis, we characterised the induction of arthritis in C57BL/6 mice and then validated the disease as a relevant pre-clinical model for rheumatoid arthritis

Snap-Through of Unsymmetric Laminates Using Piezocomposite Actuators

The paper discusses the concept of using a piezoceramic actuator bonded to one side of a two-layer unsymmetric cross-ply [0/90]T laminate to provide the moments necessary to snap the laminate from one stable equilibrium shape to another. This concept could be applied to the morphing of structures. A model of this concept, which is based on the Rayleigh-Ritz technique and the use of energy and variational methods, is developed. The experimental phase of the study is discussed, including the measurement of the voltage level needed to snap the laminate. The voltage measurements and shapes are compared with predictions of the models and the agreement between measurements and the predictions are reasonable, both qualitatively and quantitatively. Suggestions for future activities are presented

A Primitive Based Generative Model to Infer Timing Information in Unpartitioned Handwriting Data

Biological movement control and planning is based upon motor primitives. In our approach, we presume that each motor primitive takes responsibility for controlling a small sub-block of motion, containing coherent muscle activation outputs. A central timing controller cues these subroutines of movement, creating complete movement strategies that are built up by overlaying primitives, thus creating synergies of muscle activation. This partitioning allows the movement to be defined by a sparse code representing the timing of primitive activations. This paper shows that it is possible to use a factorial hidden Markov model to infer primitives in handwriting data. The variation in the handwriting data can to a large extent be explained by timing variation in the triggering of the primitives. Once an appropriate set of primitives has been inferred, the characters can be represented as a set of timings of primitive activations, along with variances, giving a very compact representation of the character. The model is naturally partitioned into a low level primitive output stage, and a top-down primitive timing stage. This partitioning gives us an insight into behaviours such as scribbling, and what is learnt in order to write a new character.

Lamellipodium extension and membrane ruffling require different SNARE-mediated trafficking pathways

<p>Abstract</p> <p>Background</p> <p>Intracellular membrane traffic is an essential component of the membrane remodeling that supports lamellipodium extension during cell adhesion. The membrane trafficking pathways that contribute to cell adhesion have not been fully elucidated, but recent studies have implicated SNARE proteins. Here, the functions of several SNAREs (SNAP23, VAMP3, VAMP4 and syntaxin13) are characterized during the processes of cell spreading and membrane ruffling.</p> <p>Results</p> <p>We report the first description of a SNARE complex, containing SNAP23, syntaxin13 and cellubrevin/VAMP3, that is induced by cell adhesion to an extracellular matrix. Impairing the function of the SNAREs in the complex using inhibitory SNARE domains disrupted the recycling endosome, impeded delivery of integrins to the cell surface, and reduced haptotactic cell migration and spreading. Blocking SNAP23 also inhibited the formation of PMA-stimulated, F-actin-rich membrane ruffles; however, membrane ruffle formation was not significantly altered by inhibition of VAMP3 or syntaxin13. In contrast, membrane ruffling, and not cell spreading, was sensitive to inhibition of two SNAREs within the biosynthetic secretory pathway, GS15 and VAMP4. Consistent with this, formation of a complex containing VAMP4 and SNAP23 was enhanced by treatment of cells with PMA. The results reveal a requirement for the function of a SNAP23-syntaxin13-VAMP3 complex in the formation of lamellipodia during cell adhesion and of a VAMP4-SNAP23-containing complex during PMA-induced membrane ruffling.</p> <p>Conclusions</p> <p>Our findings suggest that different SNARE-mediated trafficking pathways support membrane remodeling during ECM-induced lamellipodium extension and PMA-induced ruffle formation, pointing to important mechanistic differences between these processes.</p

Selection of screw characteristics and operational boundary conditions to facilitate post-flush urine and faeces separation within single household sanitation systems

To ensure adequate access to sanitation in developing economies, off-grid single household sanitation has been proposed which obviates the need for significant infrastructure capital investment. Whilst treatment at this scale is most efficient when coupled to source separation (i.e. urine from faeces), existing source separation solutions have proved difficult to implement in this context. In this study, screw extrusion is therefore investigated to provide ‘post-flush’ source separation. Both screw characteristics and operational boundary conditions were evaluated. Preferential screw characteristics included tapering of the shaft and progressive pitch reduction, linked to a small extrusion aperture, the combination of which enhanced solids extrusion efficiency and promoted higher solids concentration in the extruded fraction. Whilst maximum extrusion efficiency was observed at high rotational speeds (over 400 rpm), this also promoted free water transport. Operating below 300 rpm instead introduced selectivity for transport of faecal sludge over urine, enabling phase separation. Constraining the volumetric ratio of urine to faeces also enhanced the extrusion rate of faecal sludge by increasing feed viscosity sufficient to overcome backpressure imposed by unmasticated food particles that would otherwise restrict separation. Importantly, this study demonstrates the feasibility of screw extrusion for ‘post flush’ separation of urine and faeces which constitutes a significant advancement towards realising sanitation at a single household scale