Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists

<p>Abstract</p> <p>Background</p> <p>Numerous gene lists or "classifiers" have been derived from global gene expression data that assign breast cancers to good and poor prognosis groups. A remarkable feature of these molecular signatures is that they have few genes in common, prompting speculation that they may use distinct genes to measure the same pathophysiological process(es), such as proliferation. However, this supposition has not been rigorously tested. If gene-based classifiers function by measuring a minimal number of cellular processes, we hypothesized that the informative genes for these processes could be identified and the data sets could be adjusted for the predictive contributions of those genes. Such adjustment would then attenuate the predictive function of any signature measuring that same process.</p> <p>Results</p> <p>We tested this hypothesis directly using a novel iterative-subtractive approach. We evaluated five gene expression data sets that sample a broad range of breast cancer subtypes. In all data sets, the dominant cluster capable of predicting metastasis was heavily populated by genes that fluctuate in concert with the cell cycle. When six well-characterized classifiers were examined, all contained a higher than expected proportion of genes that correlate with this cluster. Furthermore, when the data sets were globally adjusted for the cell cycle cluster, each classifier lost its ability to assign tumors to appropriate high and low risk groups. In contrast, adjusting for other predictive gene clusters did not impact their performance.</p> <p>Conclusion</p> <p>These data indicate that the discriminative ability of breast cancer classifiers is dependent upon genes that correlate with cell cycle progression.</p

Hypoxia-inducible Gene Domain 1 Proteins in Yeast Mitochondria Protect Against Proton Leak Through Complex IV

Hypoxia-inducible gene domain 1 (HIGD1) proteins are small integral membrane proteins, conserved from bacteria to humans, that associate with oxidative phosphorylation supercomplexes. Using yeast as a model organism, we have shown previously that its two HIGD1 proteins, Rcf1 and Rcf2, are required for the generation and maintenance of a normal membrane potential (ΔΨ) across the inner mitochondrial membrane (IMM). We postulated that the lower ΔΨ observed in the absence of the HIGD1 proteins may be due to decreased proton pumping by complex IV (CIV) or enhanced leak of protons across the IMM. Here we measured the ΔΨ generated by complex III (CIII) to discriminate between these possibilities. First, we found that the decreased ΔΨ observed in the absence of the HIGD1 proteins cannot be due to decreased proton pumping by CIV because CIII, operating alone, also exhibited a decreased ΔΨ when HIGD1 proteins were absent. Because CIII can neither lower its pumping stoichiometry nor transfer protons completely across the IMM, this result indicates that HIGD1 protein ablation enhances proton leak across the IMM. Second, we demonstrate that this proton leak occurs through CIV because ΔΨ generation by CIII is restored when CIV is removed from the cell. Third, the proton leak appeared to take place through an inactive population of CIV that accumulates when HIGD1 proteins are absent. We conclude that HIGD1 proteins in yeast prevent CIV inactivation, likely by preventing the loss of lipids bound within the Cox3 protein of CIV

Passive, broadband and low-frequency suppression of laser amplitude noise to the shot-noise limit using hollow-core fibre

We use hollow-core fibre to preserve the spectrum and temporal profile of picosecond laser pulses in CBD to suppress 2.6 dB of amplitude noise at MHz noise frequencies, to within 0.01 dB of the shot-noise limit. We provide an enhanced version of the CBD scheme that concatenates circuits to suppress over multiple frequencies and over broad frequency ranges --- we perform a first demonstration that reduces total excess amplitude noise, between 2 - 6 MHz, by 85%. These demonstrations enable passive, broad-band, all-guided fibre laser technology operating at the shot-noise limit.Comment: 8 pages, 8 figure

Sustainability of the Built Environment [Written Evidence - SBE0060]

The following evidence gathered is of particular relevance to strategic pathway planning towards a decarbonised society where focus is placed on the design of environments rather than the design of buildings only. Building buildings is only one tool within a toolkit capable of improving and enhancing environments. The call for evidence suggests a narrow focus driven by potentially one-dimensional sustainable outcomes such as need for adaptation measures to building with little or no consideration for alternatives to building. Greater focus is needed on evidence that supports alternatives to building; new methods and new measures that account for social and cultural dimensions in evaluating sustainability in the built environment, and the embracing of multiplicity and diversity that allows for reskilling and knowledge-sharing in a meaningful way

Midlife and Late-Life Vascular Risk Factors and White Matter Microstructural Integrity: The Atherosclerosis Risk in Communities Neurocognitive Study.

BACKGROUND: Diffusion tensor imaging measures of white matter (WM) microstructural integrity appear to provide earlier indication of WM injury than WM hyperintensities; however, risk factors for poor WM microstructural integrity have not been established. Our study quantifies the association between vascular risk factors in midlife and late life with measures of late-life WM microstructural integrity. METHODS AND RESULTS: We used data from 1851 participants in ARIC (Atherosclerosis Risk in Communities Study) who completed 3-T magnetic resonance imaging, including diffusion tensor imaging, as part of the ARIC Neurocognitive Study (ARIC-NCS). We quantified the association among lipids, glucose, and blood pressure from the baseline ARIC visit (1987-1989, ages 44-65, midlife) and visit 5 of ARIC (2011-2013, ages 67-90, late life, concurrent with ARIC-NCS) with regional and overall WM mean diffusivity and fractional anisotropy obtained at ARIC visit 5 for ARIC participants. We also considered whether these associations were independent of or modified by WM hyperintensity volumes. We found that elevated blood pressure in midlife and late life and elevated glucose in midlife, but not late life, were associated with worse late-life WM microstructural integrity. These associations were independent of the degree of WM hyperintensity, and the association between glucose and WM microstructural integrity appeared stronger for those with the least WM hyperintensity. There was little support for an adverse association between lipids and WM microstructural integrity. CONCLUSIONS: Hypertension in both midlife and late life and elevated glucose in midlife are related to worse WM microstructural integrity in late life

Rod-shape theranostic nanoparticles facilitate antiretroviral drug biodistribution and activity in human immunodeficiency virus susceptible cells and tissues

Human immunodeficiency virus theranostics facilitates the development of long acting (LA) antiretroviral drugs (ARVs) by defining drug-particle cell depots. Optimal drug formulations are made possible based on precise particle composition, structure, shape and size. Through the creation of rod-shaped particles of defined sizes reflective of native LA drugs, theranostic probes can be deployed to measure particle-cell and tissue biodistribution, antiretroviral activities and drug retention. Methods: Herein, we created multimodal rilpivirine (RPV) 177lutetium labeled bismuth sulfide nanorods (177LuBSNRs) then evaluated their structure, morphology, configuration, chemical composition, biological responses and adverse reactions. Particle biodistribution was analyzed by single photon emission computed tomography (SPECT/CT) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) imaging. Results: Nanoformulated RPV and BSNRs-RPV particles showed comparable physicochemical and cell biological properties. Drug-particle pharmacokinetics (PK) and biodistribution in lymphoid tissue macrophages proved equivalent, one with the other. Rapid particle uptake and tissue distribution were observed, without adverse reactions, in primary blood-derived and tissue macrophages. The latter was seen within the marginal zones of spleen. Conclusions: These data, taken together, support the use of 177LuBSNRs as theranostic probes as a rapid assessment tool for PK LA ARV measurements