The Australian Breast Cancer Tissue Bank (ABCTB)

The ABCTB was established in 2006 as an open access, not for profit resource dedicated to providing biospecimens and/or data to both national and international research projects in the field of breast cancer. Donors are consented according to standard ethical principles for use of their material for unspecified future research. ABCTB collects fully annotated clinical samples and associated clinical and longitudinal data from donors. Material and data is supplied to research projects.</p

Probing the Gas Content of Late-stage Protoplanetary Disks with N_2H^+

The lifetime of gas in circumstellar disks is a fundamental quantity that informs our understanding of planet formation. Studying disk gas evolution requires measurements of disk masses around stars of various ages. Because H_2 gas is unobservable under most disk conditions, total disk masses are based on indirect tracers such as sub-mm dust and CO emission. The uncertainty in the relation between these tracers and the disk mass increases as the disk evolves. In a few well-studied disks, CO exhibits depletions of up to 100× below the assumed interstellar value. Thus, additional tracers are required to accurately determine the total gas mass. The relative lack of nitrogen found in solid solar system bodies may indicate that it persists in volatile form, making nitrogen-bearing species more robust tracers of gas in more evolved disks. Here we present Atacama Large Millimeter/submillimeter Array detections of N_2H^+ in two mature, ~5–11 Myr old disks in the Upper Scorpius OB Association. Such detections imply the presence of H_2-rich gas and sources of ionization, both required for N_2H^+ formation. The Upper Sco disks also show elevated N_2H^+/CO flux ratios when compared to previously observed disks with ≳10× higher CO fluxes. Based on line ratio predictions from a grid of thermochemical disk models, a significantly reduced CO/H_2 abundance of <10^(−6) for a gas-to-dust ratio of ≳100 is required to produce the observed N_2H^+ fluxes. These systems appear to maintain H_2 gas reservoirs and indicate that carbon- and nitrogen-bearing species follow distinct physical or chemical pathways as disks evolve

Coenzyme Q10 Prevents Insulin Signaling Dysregulation and Inflammation Prior to Development of Insulin Resistance in Male Offspring of a Rat Model of Poor Maternal Nutrition and Accelerated Postnatal Growth.

Low birth weight and rapid postnatal growth increases the risk of developing insulin resistance and type 2 diabetes in later life. However, underlying mechanisms and potential intervention strategies are poorly defined. Here we demonstrate that male Wistar rats exposed to a low-protein diet in utero that had a low birth weight but then underwent postnatal catch-up growth (recuperated offspring) had reductions in the insulin signaling proteins p110-β (13% ± 6% of controls [P < .001]) and insulin receptor substrate-1 (39% ± 10% of controls [P < .05]) in adipose tissue. These changes were not accompanied by any change in expression of the corresponding mRNAs, suggesting posttranscriptional regulation. Recuperated animals displayed evidence of a proinflammatory phenotype of their adipose tissue with increased IL-6 (139% ± 8% [P < .05]) and IL1-β (154% ± 16% [P < .05]) that may contribute to the insulin signaling protein dysregulation. Postweaning dietary supplementation of recuperated animals with coenzyme Q (CoQ10) (1 mg/kg of body weight per day) prevented the programmed reduction in insulin receptor substrate-1 and p110-β and the programmed increased in IL-6. These findings suggest that postweaning CoQ10 supplementation has antiinflammatory properties and can prevent programmed changes in insulin-signaling protein expression. We conclude that CoQ10 supplementation represents an attractive intervention strategy to prevent the development of insulin resistance that results from suboptimal in utero nutrition.This work was supported by The British Heart Foundation [PG/09/037/27387, FS/09/029/27902]; Medical Research Council [MC UU 12012/4] and Diabetes UK [12/0004508]. SEO is a member of the MRC Metabolic Diseases Unit. IPH is supported by the Department of Health’s NIHR Biomedical Research Centres funding scheme at UCLH/UCL.This is the author accepted manuscript. The final version is available from the Endocrine Society via http://dx.doi.org/10.1210/en.2015-142

The RNA binding protein Larp1 regulates cell division, apoptosis and cell migration.

The RNA binding protein Larp1 was originally shown to be involved in spermatogenesis, embryogenesis and cell-cycle progression in Drosophila. Our data show that mammalian Larp1 is found in a complex with poly A binding protein and eukaryote initiation factor 4E and is associated with 60S and 80S ribosomal subunits. A reduction in Larp1 expression by siRNA inhibits global protein synthesis rates and results in mitotic arrest and delayed cell migration. Consistent with these data we show that Larp1 protein is present at the leading edge of migrating cells and interacts directly with cytoskeletal components. Taken together, these data suggest a role for Larp1 in facilitating the synthesis of proteins required for cellular remodelling and migration

Formation and Evolution of Planetary Systems: Cold Outer Disks Associated with Sun-like stars

We present the discovery of debris systems around three solar mass stars based upon observations performed with the Spitzer Space Telescope as part of a Legacy Science Program, ``the Formation and Evolution of Planetary Systems'' (FEPS). We also confirm the presence of debris around two other stars. All the stars exhibit infrared emission in excess of the expected photospheres in the 70 micron band, but are consistent with photospheric emission at <= 33 micron. This restricts the maximum temperature of debris in equilibrium with the stellar radiation to T < 70 K. We find that these sources are relatively old in the FEPS sample, in the age range 0.7 - 3 Gyr. Based on models of the spectral energy distributions, we suggest that these debris systems represent materials generated by collisions of planetesimal belts. We speculate on the nature of these systems through comparisons to our own Kuiper Belt, and on the likely planet(s) responsible for stirring the system and ultimately releasing dust through collisions. We further report observations of a nearby star HD 13974 (d =11 pc) that is indistinguishable from a bare photosphere at both 24 micron and 70 micron. The observations place strong upper limits on the presence of any cold dust in this nearby system (L_IR/L_* < 10^{-5.2}).Comment: 31 pages, 9 figures, accepted for publication in Ap

Offspring sex ratio of a woodland songbird is unrelated to habitat fragmentation

We assessed whether the sex ratio of nestling Marsh Tits (Poecile palustris) varied with habitat fragmentation by sampling broods from two British woodland areas with contrasting patch size, and comparing the data with published results from an extensive forest in Poland. We found no evidence for manipulation of offspring sex ratios, supporting findings from Poland, and suggesting that this trait may be typical of the species. The results are important in helping to understand the origin of biased sex ratios observed among adult Marsh Tits in the declining population in Britain

A self-consistent, multi-variate method for the determination of gas phase rate coefficients, applied to reactions of atmospheric VOCs and the hydroxyl radical

Gas-phase rate coefficients are fundamental to understanding atmospheric chemistry, yet experimental data are not available for the oxidation reactions of many of the thousands of volatile organic compounds (VOCs) observed in the troposphere. Here a new experimental method is reported for the simultaneous study of reactions between multiple different VOCs and OH, the most important daytime atmospheric radical oxidant. This technique is based upon established relative rate concepts but has the advantage of a much higher throughput of target VOCs. By evaluating multiple VOCs in each experiment, and through measurement of the depletion in each VOC after reaction with OH, the OH + VOC reaction rate coefficients can be derived. Results from experiments conducted under controlled laboratory conditions were in good agreement with the available literature for the reaction of nineteen VOCs, prepared in synthetic gas mixtures, with OH. This approach was used to determine a rate coefficient for the reaction of OH with 2,3-dimethylpent-1-ene for the first time; k = 5.7 (±0.3) × 10–11–cm3 molecule−1 s−1. In addition, a further seven VOCs had only two, or fewer, individual OH rate coefficient measurements available in the literature. The results from this work were in good agreement with those measurements. A similar dataset, at an elevated temperature of 323 (±10) K, was used to determine new OH rate coefficients for twelve aromatic, five alkane, five alkene and three monoterpene VOC + OH reactions. In OH relative reactivity experiments that used ambient air at the University of York, a large number of different VOCs were observed, of which 23 were positively identified. 19 OH rate coefficients were derived from these ambient air samples, including ten reactions for which data was previously unavailable at the elevated reaction temperature of T = 323 (±10) K

Keras R-CNN: library for cell detection in biological images using deep neural networks

Background: A common yet still manual task in basic biology research, high-throughput drug screening and digital pathology is identifying the number, location, and type of individual cells in images. Object detection methods can be useful for identifying individual cells as well as their phenotype in one step. State-of-the-art deep learning for object detection is poised to improve the accuracy and efficiency of biological image analysis. Results: We created Keras R-CNN to bring leading computational research to the everyday practice of bioimage analysts. Keras R-CNN implements deep learning object detection techniques using Keras and Tensorflow (https://github.com/broadinstitute/keras-rcnn). We demonstrate the command line tool’s simplified Application Programming Interface on two important biological problems, nucleus detection and malaria stage classification, and show its potential for identifying and classifying a large number of cells. For malaria stage classification, we compare results with expert human annotators and find comparable performance. Conclusions: Keras R-CNN is a Python package that performs automated cell identification for both brightfield and fluorescence images and can process large image sets. Both the package and image datasets are freely available on GitHub and the Broad Bioimage Benchmark Collection