Time resolved amplified FRET identifies protein kinase B activation state as a marker for poor prognosis in clear cell renal cell carcinoma

Purpose Clear cell Renal Cell Carcinomas (ccRCC), the largest group of renal tumours, are resistant to classical therapies. The determination of the functional state of actionable biomarkers for the assessment of these adenocarcinomas is essential. The dysregulation of the oncoprotein, PKB/Akt has been linked with poor prognoses in human cancers. Material & methods We analysed the status of the PKB/Akt pathway in a representative tumour tissue microarray obtained from the primary tumours and their metastases in 60 ccRCC with long term follow up. We sought to define the evolution of this pathway from the primary tumour to the metastatic event and to know the impact of its functional state in tumour aggressiveness and patient survival. Two-site time resolved amplified FRET (A-FRET) was utilised for assessing the activation state of PKB/Akt and this was compared to conventional immunohistochemistry measurements. Results Activation state of PKB/Akt in primary tumours defined by A-FRET correlated with poorer overall survival (hazard ratio 0.228; p = 0.002). Whereas, increased protein expression of phosphoPKB/Akt, identified using classical immunohistochemistry, yielded no significant difference (hazard ratio 1.390; p = 0.548). Conclusions Quantitative determination of PKB/Akt activation in ccRCC primary tumours alongside other diagnostics tools could prove key in taking oncologists closer to an efficient personalised therapy in ccRCC patients. General significance The quantitative imaging technology based on Amplified-FRET can rapidly analyse protein activation states and molecular interactions. It could be used for prognosis and assess drug function during the early cycles of chemotherapy. It enables evaluation of clinical efficiency of personalised cancer treatment

Directly interrogating single quantum dot labelled UvrA2 molecules on DNA tightropes using an optically trapped nanoprobe

AbstractIn this study we describe a new methodology to physically probe individual complexes formed between proteins and DNA. By combining nanoscale, high speed physical force measurement with sensitive fluorescence imaging we investigate the complex formed between the prokaryotic DNA repair protein UvrA2 and DNA. This approach uses a triangular, optically-trapped “nanoprobe” with a nanometer scale tip protruding from one vertex. By scanning this tip along a single DNA strand suspended between surface-bound micron-scale beads, quantum-dot tagged UvrA2 molecules bound to these ‘”DNA tightropes” can be mechanically interrogated. Encounters with UvrA2 led to deflections of the whole nanoprobe structure, which were converted to resistive force. A force histogram from all 144 detected interactions generated a bimodal distribution centered on 2.6 and 8.1 pN, possibly reflecting the asymmetry of UvrA2’s binding to DNA. These observations successfully demonstrate the use of a highly controllable purpose-designed and built synthetic nanoprobe combined with fluorescence imaging to study protein-DNA interactions at the single molecule level.</jats:p

Reassessing the origin of Triton

Agnor & Hamilton (2006) demonstrated that the disruption of a binary was an effective mechanism to capture Triton. The subsequent evolution of Triton's post-capture orbit could have proceeded through gravitational tides. The study by Agnor & Hamilton (2006) is repeated in the framework of the Nice model to determine the post-capture orbit of Triton. After capture it is then subjected to tidal evolution. The perturbations from the Sun and the figure of Neptune are included. The perturbations from the Sun acting on Triton cause it to spend a long time in its high-eccentricity phase, usually of the order of 10 Myr, while the typical time to circularise to its current orbit is some 200 Myr. The current orbit of Triton is consistent with an origin through binary capture and tidal evolution, even though the model prefers Triton to be closer to Neptune than it is today. The probability of capturing Triton in this manner is approximately 0.7%. Since the capture of Triton was at most a 50% event -- since only Neptune has one, but Uranus does not -- we deduce that in the primordial trans-Neptunian disc there were 100 binaries with at least one Triton-sized member. Morbidelli et al. (2009) concludes there were some 1000 Triton-sized bodies in the trans-Neptunian proto-planetary disc, so the primordial binary fraction with at least one Triton-sized member is 10%. This value is consistent with theoretical predictions, but at the low end. If Triton was captured at the same time as Neptune's irregular satellites, the far majority of these, including Nereid, would be lost. This suggests either that Triton was captured on an orbit with a small semi-major axis a < 50 R_N (a rare event), or that it was captured before the dynamical instability of the Nice model, or that some other mechanism was at play. The issue of keeping the irregular satellites remains unresolved.Comment: Accepted in Icarus 201

Cosmologies with a time dependent vacuum

The idea that the cosmological term, Lambda, should be a time dependent quantity in cosmology is a most natural one. It is difficult to conceive an expanding universe with a strictly constant vacuum energy density, namely one that has remained immutable since the origin of time. A smoothly evolving vacuum energy density that inherits its time-dependence from cosmological functions, such as the Hubble rate or the scale factor, is not only a qualitatively more plausible and intuitive idea, but is also suggested by fundamental physics, in particular by quantum field theory (QFT) in curved space-time. To implement this notion, is not strictly necessary to resort to ad hoc scalar fields, as usually done in the literature (e.g. in quintessence formulations and the like). A "running" Lambda term can be expected on very similar grounds as one expects (and observes) the running of couplings and masses with a physical energy scale in QFT. Furthermore, the experimental evidence that the equation of state of the dark energy could be evolving with time/redshift (including the possibility that it might currently behave phantom-like) suggests that a time-variable Lambda term (possibly accompanied by a variable Newton's gravitational coupling G=G(t)) could account in a natural way for all these features. Remarkably enough, a class of these models (the "new cosmon") could even be the clue for solving the old cosmological constant problem, including the coincidence problem.Comment: LaTeX, 15 pages, 4 figure

Sperm design and variation in the New World blackbirds (Icteridae)

Post-copulatory sexual selection (PCSS) is thought to be one of the evolutionary forces responsible for the rapid and divergent evolution of sperm design. However, whereas in some taxa particular sperm traits are positively associated with PCSS, in other taxa, these relationships are negative, and the causes of these different patterns across taxa are poorly understood. In a comparative study using New World blackbirds (Icteridae), we tested whether sperm design was influenced by the level of PCSS and found significant positive associations with the level of PCSS for all sperm components but head length. Additionally, whereas the absolute length of sperm components increased, their variation declined with the intensity of PCSS, indicating stabilizing selection around an optimal sperm design. Given the diversity of, and strong selection on, sperm design, it seems likely that sperm phenotype may influence sperm velocity within species. However, in contrast to other recent studies of passerine birds, but consistent with several other studies, we found no significant link between sperm design and velocity, using four different species that vary both in sperm design and PCSS. Potential reasons for this discrepancy between studies are discussed

The normalisation of drug supply: The social<i>supply</i>of drugs as the “other side” of the history of normalisation

Aims: Describes how the relative normalisation of recreational drug use in the UK has been productive of, and fused with, the relatively normalised and non-commercial social supply of recreational drugs. Methods: Semi-structured interviews with 60 social suppliers of recreational drugs in two studies (involving a student population n = 30 and general population sample n = 30). Respondents were recruited via purposive snowball sampling and local advertising. Findings: Both samples provided strong evidence of the normalised supply of recreational drugs in micro-sites of friendship and close social networks. Many social suppliers described “drift” into social supply and normalised use was suggested to be productive of supply relationships that both suppliers and consumers regard as something less than “real” dealing in order to reinforce their preconceptions of themselves as relatively non-deviant. Some evidence for a broader acceptance of social supply is also presented. Conclusions: The fairly recent context of relative normalisation of recreational drug use has coalesced with the social supply of recreational drugs in micro-sites of use and exchange whereby a range of “social” supply acts (sometimes even involving large amounts of drugs/money) have become accepted as something closer to gift-giving or friendship exchange dynamics within social networks rather than dealing proper. To some degree, there is increasing sensitivity to this within the criminal justice system

Postcopulatory sexual selection

The female reproductive tract is where competition between the sperm of different males takes place, aided and abetted by the female herself. Intense postcopulatory sexual selection fosters inter-sexual conflict and drives rapid evolutionary change to generate a startling diversity of morphological, behavioural and physiological adaptations. We identify three main issues that should be resolved to advance our understanding of postcopulatory sexual selection. We need to determine the genetic basis of different male fertility traits and female traits that mediate sperm selection; identify the genes or genomic regions that control these traits; and establish the coevolutionary trajectory of sexes