Novel nucleosomal particles containing core histones and linker DNA but no histone H1

Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ∼147 bp of DNA wrapped ∼1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ∼160 bp, and then converts it to a core particle, containing ∼147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these \u27proto-chromatosomes\u27 are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1

Droplet digital PCR based detection of EGFR mutations in advanced lung cancer patient liquid biopsies : a comparison of circulating tumour DNA extraction kits

Background: Mutations in the epidermal growth factor receptor gene, EGFR, predict response or resistance to first generation tyrosine kinase inhibitors in non-small cell lung cancer. These biomarkers can now be conveniently detected from liquid biopsies, however technical details of these assays are still being refined. Objective: To compare detection of four different non-small cell lung cancer (NSCLC) associated EGFR mutations from patient ctDNA isolated with five different ctDNA isolation kit. Methods: Droplet digital PCR (ddPCR) assays detecting four EGFR mutations were developed. ctDNA was isolated with five kits from plasma samples, one pleural and one ascites fluid from nine NSCLC patients with known EGFR mutations. ctDNA fragment sizes and concentrations were also assessed. Results: Each kit isolated DNA from all samples which contained an expected dominant DNA fragment of ~ 170 base pairs. Normalised for plasma input, one kit produced ctDNA extracts which consistently enabled the highest cop n umber detection for all EGFR variants, and importantly was able to validate mutations in all patient samples. Other kits stood out in regards to cost economy as well as ease and speed of processing but were less efficient and one kit was found to be incompatible with ddPCR. Conclusion: This study demonstrated successful ctDNA isolation from plasma, pleural fluid and ascites by four of five ctDNA isolation kits. The QIAmp circulating nucleic acid kit produced consistently the most sensitive detection of EGFR variants. While other kits allow for lower volume plasma input down to 0.1 ml, are faster, more economical and simpler to use, they are challenged by very low ctDNA concentrations in plasma

Experience-Dependent Effects of Muscimol-Induced Hippocampal Excitation on Mnemonic Discrimination

Memory requires similar episodes with overlapping features to be represented distinctly, a process that is disrupted in many clinical conditions as well as normal aging. Data from humans have linked this ability to activity in hippocampal CA3 and dentate gyrus (DG). While animal models have shown the perirhinal cortex is critical for disambiguating similar stimuli, hippocampal activity has not been causally linked to discrimination abilities. The goal of the current study was to determine how disrupting CA3/DG activity would impact performance on a rodent mnemonic discrimination task. Rats were surgically implanted with bilateral guide cannulae targeting dorsal CA3/DG. In Experiment 1, the effect of intra-hippocampal muscimol on target-lure discrimination was assessed within subjects in randomized blocks. Muscimol initially impaired discrimination across all levels of target-lure similarity, but performance improved on subsequent test blocks irrespective of stimulus similarity and infusion condition. To clarify these results, Experiment 2 examined whether prior experience with objects influenced the effect of muscimol on target-lure discrimination. Rats that received vehicle infusions in a first test block, followed by muscimol in a second block, did not show discrimination impairments for target-lure pairs of any similarity. In contrast, rats that received muscimol infusions in the first test block were impaired across all levels of target-lure similarity. Following discrimination tests, rats from Experiment 2 were trained on a spatial alternation task. Muscimol infusions increased the number of spatial errors made, relative to vehicle infusions, confirming that muscimol remained effective in disrupting behavioral performance. At the conclusion of behavioral experiments, fluorescence in situ hybridization for the immediate-early genes Arc and Homer1a was used to determine the proportion of neurons active following muscimol infusion. Contrary to expectations, muscimol increased neural activity in DG. An additional experiment was carried out to quantify neural activity in naïve rats that received an intra-hippocampal infusion of vehicle or muscimol. Results confirmed that muscimol led to DG excitation, likely through its actions on interneuron populations in hilar and molecular layers of DG and consequent disinhibition of principal cells. Taken together, our results suggest disruption of coordinated neural activity across the hippocampus impairs mnemonic discrimination when lure stimuli are novel

VAST: An ASKAP Survey for Variables and Slow Transients

The Australian Square Kilometre Array Pathfinder (ASKAP) will give us an unprecedented opportunity to investigate the transient sky at radio wavelengths. In this paper we present VAST, an ASKAP survey for Variables and Slow Transients. VAST will exploit the wide-field survey capabilities of ASKAP to enable the discovery and investigation of variable and transient phenomena from the local to the cosmological, including flare stars, intermittent pulsars, X-ray binaries, magnetars, extreme scattering events, interstellar scintillation, radio supernovae and orphan afterglows of gamma ray bursts. In addition, it will allow us to probe unexplored regions of parameter space where new classes of transient sources may be detected. In this paper we review the known radio transient and variable populations and the current results from blind radio surveys. We outline a comprehensive program based on a multi-tiered survey strategy to characterise the radio transient sky through detection and monitoring of transient and variable sources on the ASKAP imaging timescales of five seconds and greater. We also present an analysis of the expected source populations that we will be able to detect with VAST.Comment: 29 pages, 8 figures. Submitted for publication in Pub. Astron. Soc. Australi

Exploring the Atmospheric Dynamics of the Extreme Ultrahot Jupiter KELT-9b Using TESS Photometry

We carry out a phase-curve analysis of the KELT-9 system using photometric observations from NASA's Transiting Exoplanet Survey Satellite (TESS). The measured secondary eclipse depth and peak-to-peak atmospheric brightness modulation are 650⁺¹⁴₋₁₅ and 566 ± 16 ppm, respectively. The planet's brightness variation reaches maximum 31 ± 5 minutes before the midpoint of the secondary eclipse, indicating a 5.°2 ± 0.°9 eastward shift in the dayside hot spot from the substellar point. We also detect stellar pulsations on KELT-9 with a period of 7.58695 ± 0.00091 hr. The dayside emission of KELT-9b in the TESS bandpass is consistent with a blackbody brightness temperature of 4600 ± 100 K. The corresponding nightside brightness temperature is 3040 ± 100 K, comparable to the dayside temperatures of the hottest known exoplanets. In addition, we detect a significant phase-curve signal at the first harmonic of the orbital frequency and a marginal signal at the second harmonic. While the amplitude of the first harmonic component is consistent with the predicted ellipsoidal distortion modulation assuming equilibrium tides, the phase of this photometric variation is shifted relative to the expectation. Placing KELT-9b in the context of other exoplanets with phase-curve observations, we find that the elevated nightside temperature and relatively low day–night temperature contrast agree with the predictions of atmospheric models that include H₂ dissociation and recombination. The nightside temperature of KELT-9b implies an atmospheric composition containing about 50% molecular and 50% atomic hydrogen at 0.1 bar, a nightside emission spectrum that deviates significantly from a blackbody, and a 0.5–2.0 μm transmission spectrum that is featureless at low resolution

Peeling the astronomical onion

Water ice is the most abundant solid in the Universe. Understanding the formation, structure and multiplicity of physicochemical roles for water ice in the cold, dense interstellar environments in which it is predominantly observed is a crucial quest for astrochemistry as these are regions active in star and planet formation. Intuitively, we would expect the mobility of water molecules deposited or synthesised on dust grain surfaces at temperatures below 50 K to be very limited. This work delves into the thermally-activated mobility of H2O molecules on model interstellar grain surfaces. The energy required to initiate this process is studied by reflection-absorption infrared spectroscopy of small quantities of water on amorphous silica and highly oriented pyrolytic graphite surfaces as the surface is annealed. Strongly non-Arrhenius behaviour is observed with an activation energy of 2 kJ mol-1 on the silica surface below 25 K and 0 kJ mol-1 on both surfaces between 25 and 100 K. The astrophysical implication of these results is that on timescales shorter than that estimated for the formation of a complete monolayer of water ice on a grain, aggregation of water ice will result in a non-uniform coating of water, hence leaving bare grain surface exposed. Other molecules can thus be formed or adsorbed on this bare surface

Exploring the atmospheric dynamics of the extreme ultra-hot Jupiter KELT-9b using TESS photometry

We carry out a phase-curve analysis of the KELT-9 system using photometric observations from NASA's Transiting Exoplanet Survey Satellite (TESS). The measured secondary eclipse depth and peak-to-peak atmospheric brightness modulation are $650^{+14}_{-15}$ ppm and $566\pm16$ ppm, respectively. The planet's brightness variation reaches maximum $31\pm5$ minutes before the midpoint of the secondary eclipse, indicating a $5\overset{\circ}{.}2\pm0\overset{\circ}{.}9$ eastward shift in the dayside hot spot from the substellar point. We also detect stellar pulsations on KELT-9 with a period of $7.58695\pm0.00091$ hours. The dayside emission of KELT-9b in the TESS bandpass is consistent with a blackbody brightness temperature of $4600\pm100$ K. The corresponding nightside brightness temperature is $3040\pm100$ K, comparable to the dayside temperatures of the hottest known exoplanets. In addition, we detect a significant phase-curve signal at the first harmonic of the orbital frequency and a marginal signal at the second harmonic. While the amplitude of the first harmonic component is consistent with the predicted ellipsoidal distortion modulation assuming equilibrium tides, the phase of this photometric variation is shifted relative to the expectation. Placing KELT-9b in the context of other exoplanets with phase-curve observations, we find that the elevated nightside temperature and relatively low day-night temperature contrast agree with the predictions of atmospheric models that include H$_{2}$ dissociation and recombination. The nightside temperature of KELT-9b implies an atmospheric composition containing about 50% molecular and 50% atomic hydrogen at 0.1 bar, a nightside emission spectrum that deviates significantly from a blackbody, and a 0.5-2.0 $\mu$m transmission spectrum that is featureless at low resolution.Comment: Published in AJ, updated with proof corrections. 17 pages, 8 figure

A systematic review of tests for lymph node status in primary endometrial cancer

<p>Abstract</p> <p>Background</p> <p>The lymph node status of a patient is a key determinate in staging, prognosis and adjuvant treatment of endometrial cancer. Despite this, the potential additional morbidity associated with lymphadenectomy makes its role controversial. This study systematically reviews the accuracy literature on sentinel node biopsy; ultra sound scanning, magnetic resonance imaging (MRI) and computer tomography (CT) for determining lymph node status in endometrial cancer.</p> <p>Methods</p> <p>Relevant articles were identified form MEDLINE (1966–2006), EMBASE (1980–2006), MEDION, the Cochrane library, hand searching of reference lists from primary articles and reviews, conference abstracts and contact with experts in the field. The review included 18 relevant primary studies (693 women). Data was extracted for study characteristics and quality. Bivariate random-effect model meta-analysis was used to estimate diagnostic accuracy of the various index tests.</p> <p>Results</p> <p>MRI (pooled positive LR 26.7, 95% CI 10.6 – 67.6 and negative LR 0.29 95% CI 0.17 – 0.49) and successful sentinel node biopsy (pooled positive LR 18.9 95% CI 6.7 – 53.2 and negative LR 0.22, 95% CI 0.1 – 0.48) were the most accurate tests. CT was not as accurate a test (pooled positive LR 3.8, 95% CI 2.0 – 7.3 and negative LR of 0.62, 95% CI 0.45 – 0.86. There was only one study that reported the use of ultrasound scanning.</p> <p>Conclusion</p> <p>MRI and sentinel node biopsy have shown similar diagnostic accuracy in confirming lymph node status among women with primary endometrial cancer than CT scanning, although the comparisons made are indirect and hence subject to bias. MRI should be used in preference, in light of the ASTEC trial, because of its non invasive nature.</p

Impaired spine stability underlies plaque-related spine loss in an Alzheimer's disease mouse model

Dendritic spines, the site of most excitatory synapses in the brain, are lost in Alzheimer’s disease and in related mouse models, undoubtedly contributing to cognitive dysfunction. We hypothesized that spine loss results from plaque-associated alterations of spine stability, causing an imbalance in spine forma-tion and elimination. To investigate effects of plaques on spine stability in vivo, we observed cortical neu-rons using multiphoton microscopy in a mouse model of amyloid pathology before and after extensive plaque deposition. We also observed age-matched non-transgenic mice to study normal effects of aging on spine plasticity. We found that spine density and struc-tural plasticity are maintained during normal aging. Tg2576 mice had normal spine density and plasticity before plaques appeared, but after amyloid pathology is established, severe disruptions were observed. In con-trol animals, spine formation and elimination were equivalent over 1 hour of observation (5 % of observed spines), resulting in stable spine density. However, in aged Tg2576 mice spine elimination increased, specifi-cally in the immediate vicinity of plaques. Spine forma-tion was unchanged, resulting in spine loss. These data show a small population of rapidly changing spines in adult and even elderly mouse cortex; further, in the vicinity of amyloid plaques, spine stability is markedly impaired leading to loss of synaptic structural in