Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.

The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations.

Time-Resolved Fluorescence Anisotropy of a Molecular Rotor Resolves Microscopic Viscosity Parameters in Complex Environments.

Understanding viscosity in complex environments remains a largely unanswered question despite its importance in determining reaction rates in vivo. Here, time-resolved fluorescence anisotropy imaging (TR-FAIM) is combined with fluorescent molecular rotors (FMRs) to simultaneously determine two non-equivalent viscosity-related parameters in complex heterogeneous environments. The parameters, FMR rotational correlation time and lifetime, are extracted from fluorescence anisotropy decays, which in heterogeneous environments show dip-and-rise behavior due to multiple dye populations. Decays of this kind are found both in artificially constructed adiposomes and in live cell lipid droplet organelles. Molecular dynamics simulations are used to assign each population to nano-environments within the lipid systems. The less viscous population corresponds to the state showing an average 25° tilt to the lipid membrane normal, and the more viscous population to the state showing an average 55° tilt. This combined experimental and simulation approach enables a comprehensive description of the FMR probe behavior within viscous nano-environments in complex, biological systems.

Extracellular point mutations in FGFR2 elicit unexpected changes in intracellular signalling.

An understanding of cellular signalling from a systems-based approach has to be robust to assess the effects of point mutations in component proteins. Outcomes of these perturbations should be predictable in terms of downstream response, otherwise a holistic interpretation of biological processes or disease states cannot be obtained. Two single, proximal point mutations (S252W and P253R) in the extracellular region of FGFR2 (fibroblast growth factor receptor 2) prolong growth factor engagement resulting in dramatically different intracellular phenotypes. Following ligand stimulation, the wild-type receptor undergoes rapid endocytosis into lysosomes, whereas (SW)FGFR2 (the S252W FGFR2 point mutation) and (PR)FGFR2 (the P253R FGFR2 point mutation) remain on the cell membrane for an extended period of time, modifying protein recruitment and elevating downstream ERK (extracellular-signal-regulated kinase) phosphorylation. FLIM (fluorescent lifetime imaging microscopy) reveals that direct interaction of FRS2 (FGFR substrate 2) with wild-type receptor occurs primarily at the vesicular membrane, whereas the interaction with the P253R receptor occurs exclusively at the plasma membrane. These observations suggest that the altered FRS2 recruitment by the mutant receptors results in an abnormal cellular signalling mechanism. In the present study these profound intracellular phenotypes resulting from extracellular receptor modification reveal a new level of complexity which will challenge a systems biology interpretation.

Effect of refractive index on the fluorescence lifetime of green fluorescent protein.

The average fluorescence lifetime of the green fluorescent protein (GFP) in solution is a function of the refractive index of its environment. We report that this is also the case for GFP-tagged proteins in cells. Using time-correlated single-photon counting (TCSPC)-based fluorescence lifetime imaging (FLIM) with a confocal scanning microscope, images of GFP-tagged proteins in cells suspended in different refractive index media are obtained. It is found that the average fluorescence lifetime of GFP decreases on addition of glycerol or sucrose to the media in which the fixed cells are suspended. The inverse GFP lifetime is proportional to the refractive index squared. This is the case for GFP-tagged major histocompatibility complex (MHC) proteins with the GFP located inside the cytoplasm, and also for GPI-anchored GFP that is located outside the cell membrane. The implications of these findings are discussed with regard to total internal reflection fluorescence (TIRF) techniques where the change in refractive index is crucial in producing an evanescent wave to excite fluorophores near a glass interface. Our findings show that the GFP fluorescence lifetime is shortened in TIRF microscopy in comparison to confocal microscopy.

Diffusion in a sol-gel-derived medium with a view toward biosensor applications.

Time-resolved fluorescence anisotropy and fluorescence recovery after photobleaching were applied to study the diffusion of dyes and a fluorescence-labeled enzyme in a sol-gel-derived medium. This type of medium exhibits attractive properties such as robustness, low processing temperature, high porosity, large internal surface area, and can act as protective immobilization media for biologically active molecules. This makes it a suitable candidate for biosensor applications. The glasslike nature and good optical quality allows for light addressable entities to be incorporated and accessed using spectroscopy. This type of matrix, once formed, can be anything from an ordered gel to a robust glassy block depending on the aging process. In this work we apply confocal microscopy and time-resolved fluorescence techniques to study both rotational and lateral diffusion with aging time within a silica sol-gel derived monolith. An enzyme, horseradish peroxidase, was labeled with Alexa Fluor 488 and rotation related to both the enzyme and the probe monitored during the matrix aging process. Diffusion coefficients of between ca. 0.5 x 10(-7) and 4 x 10(-7) cm2 s(-1) were obtained from preliminary FRAP measurements of fluorescein and correlated to differences in the catalytic activity of HRP incorporated in the monolith.

Fluorescence probe techniques to monitor protein adsorption-induced conformation changes on biodegradable polymers.

The study of protein adsorption and any associated conformational changes on interaction with biomaterials is of great importance in the area of implants and tissue constructs. This study aimed to evaluate some fluorescent techniques to probe protein conformation on a selection of biodegradable polymers currently under investigation for biomedical applications. Because of the fluorescence emanating from the polymers, the use of monitoring intrinsic protein fluorescence was precluded. A highly solvatochromic fluorescent dye, Nile red, and a well-known protein label, fluorescein isothiocyanate, were employed to study the adsorption of serum albumin to polycaprolactone and to some extent also to two starch-containing polymer blends (SPCL and SEVA-C). A variety of fluorescence techniques, steady state, time resolved, and imaging were employed. Nile red was found to leach from the protein, while fluorescein isothiocyanate proved useful in elucidating a conformational change in the protein and the observation of protein aggregates adsorbed to the polymer surface. These effects were seen by making use of the phenomenon of energy migration between the fluorescent tags to monitor interprobe distance and the use of fluorescence lifetime imaging to ascertain the surface packing of the protein on polymer.

Determining a fluorophore's transition dipole moment from fluorescence lifetime measurements in solvents of varying refractive index.

The transition dipole moment of organic dyes PM546 and rhodamine 123 is calculated from fluorescence lifetime measurements in solutions of different refractive index. A model proposed by Toptygin et al (2002 J. Phys. Chem. B 106 3724-34) provides a relationship between the radiative rate constant and refractive index of the solvent, and allows the electronic transition dipole moments to be found: it is (7.1 ± 1.1) D for PM546 which matches that found in the literature, and (8.1 ± 0.1) D for rhodamine 123. Toptygin's model goes further in predicting the shape of the fluorescent dye and here we predict the shape of PM546 and rhodamine 123 to be ellipsoidal.

Molecular diffusion within sol-gel derived matrices viewed via fluorescence recovery after photobleaching.

A suitable matrix to host enzymes for biosensor applications should encage and retain the bioactive species, while allowing it to be accessed to exploit its catalytic properties. Sol-gel derived monoliths are promising in this aspect. Molecular diffusion was monitored using fluorescence labelled proteins and unbound fluorescence dye molecules (representative of enzyme substrates) and their interaction with and mobility within the host assessed using time-resolved fluorescence anisotropy and fluorescence recovery after photobleaching observed via confocal microscopy.