Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas.

Glioma is recognized to be a highly heterogeneous CNS malignancy, whose diverse cellular composition and cellular interactions have not been well characterized. To gain new clinical- and biological-insights into the genetically-bifurcated IDH1 mutant (mt) vs wildtype (wt) forms of glioma, we integrated data from protein, genomic and MR imaging from 20 treatment-naïve glioma cases and 16 recurrent GBM cases. Multiplexed immunofluorescence (MxIF) was used to generate single cell data for 43 protein markers representing all cancer hallmarks, Genomic sequencing (exome and RNA (normal and tumor) and magnetic resonance imaging (MRI) quantitative features (protocols were T1-post, FLAIR and ADC) from whole tumor, peritumoral edema and enhancing core vs equivalent normal region were also collected from patients. Based on MxIF analysis, 85,767 cells (glioma cases) and 56,304 cells (GBM cases) were used to generate cell-level data for 24 biomarkers. K-means clustering was used to generate 7 distinct groups of cells with divergent biomarker profiles and deconvolution was used to assign RNA data into three classes. Spatial and molecular heterogeneity metrics were generated for the cell data. All features were compared between IDH mt and IDHwt patients and were finally combined to provide a holistic/integrated comparison. Protein expression by hallmark was generally lower in the IDHmt vs wt patients. Molecular and spatial heterogeneity scores for angiogenesis and cell invasion also differed between IDHmt and wt gliomas irrespective of prior treatment and tumor grade; these differences also persisted in the MR imaging features of peritumoral edema and contrast enhancement volumes. A coherent picture of enhanced angiogenesis in IDHwt tumors was derived from multiple platforms (genomic, proteomic and imaging) and scales from individual proteins to cell clusters and heterogeneity, as well as bulk tumor RNA and imaging features. Longer overall survival for IDH1mt glioma patients may reflect mutation-driven alterations in cellular, molecular, and spatial heterogeneity which manifest in discernable radiological manifestations

Revised Thickness of the Lunar Crust from GRAIL Data: Implications for Lunar Bulk Composition

High-resolution gravity data from GRAIL have yielded new estimates of the bulk density and thickness of the lunar crust. The bulk density of the highlands crust is 2550 kg m-3. From a comparison with crustal composition measured remotely, this density implies a mean porosity of 12%. With this bulk density and constraints from the Apollo seismic experiment, the average global crustal thickness is found to lie between 34 and 43 km, a value 10 to 20 km less than several previous estimates. Crustal thickness is a central parameter in estimating bulk lunar composition. Estimates of the concentrations of refractory elements in the Moon from heat flow, remote sensing and sample data, and geophysical data fall into two categories: those with refractory element abundances enriched by 50% or more relative to Earth, and those with abundances the same as Earth. Settling this issue has implications for processes operating during lunar formation. The crustal thickness resulting from analysis of GRAIL data is less than several previous estimates. We show here that a refractory-enriched Moon is not require

Structure and Evolution of the Lunar Procellarum Region as Revealed by GRAIL Gravity Data

The Procellarum region is a broad area on the nearside of the Moon that is characterized by low elevations, thin crust, and high surface concentrations of the heat-producing elements uranium, thorium, and potassium. The Procellarum region has been interpreted as an ancient impact basin approximately 3200 km in diameter, though supporting evidence at the surface would have been largely obscured as a result of the great antiquity and poor preservation of any diagnostic features. Here we use data from the Gravity Recovery and Interior Laboratory (GRAIL) mission to examine the subsurface structure of Procellarum. The Bouguer gravity anomalies and gravity gradients reveal a pattern of narrow linear anomalies that border the Procellarum region and are interpreted to be the frozen remnants of lava-filled rifts and the underlying feeder dikes that served as the magma plumbing system for much of the nearside mare volcanism. The discontinuous surface structures that were earlier interpreted as remnants of an impact basin rim are shown in GRAIL data to be a part of this continuous set of quasi-rectangular border structures with angular intersections, contrary to the expected circular or elliptical shape of an impact basin. The spatial pattern of magmatic-tectonic structures bounding Procellarum is consistent with their formation in response to thermal stresses produced by the differential cooling of the province relative to its surroundings, coupled with magmatic activity driven by the elevated heat flux in the region

Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing

Pancreatic adenocarcinoma (PAC) is among the most lethal malignancies. While research has implicated multiple genes in disease pathogenesis, identification of therapeutic leads has been difficult and the majority of currently available therapies provide only marginal benefit. To address this issue, our goal was to genomically characterize individual PAC patients to understand the range of aberrations that are occurring in each tumor. Because our understanding of PAC tumorigenesis is limited, evaluation of separate cases may reveal aberrations, that are less common but may provide relevant information on the disease, or that may represent viable therapeutic targets for the patient. We used next generation sequencing to assess global somatic events across 3 PAC patients to characterize each patient and to identify potential targets. This study is the first to report whole genome sequencing (WGS) findings in paired tumor/normal samples collected from 3 separate PAC patients. We generated on average 132 billion mappable bases across all patients using WGS, and identified 142 somatic coding events including point mutations, insertion/deletions, and chromosomal copy number variants. We did not identify any significant somatic translocation events. We also performed RNA sequencing on 2 of these patients' tumors for which tumor RNA was available to evaluate expression changes that may be associated with somatic events, and generated over 100 million mapped reads for each patient. We further performed pathway analysis of all sequencing data to identify processes that may be the most heavily impacted from somatic and expression alterations. As expected, the KRAS signaling pathway was the most heavily impacted pathway (P<0.05), along with tumor-stroma interactions and tumor suppressive pathways. While sequencing of more patients is needed, the high resolution genomic and transcriptomic information we have acquired here provides valuable information on the molecular composition of PAC and helps to establish a foundation for improved therapeutic selection

Viscoelastic properties of bovine articular cartilage attached to subchondral bone at high frequencies

<p>Abstract</p> <p>Background</p> <p>Articular cartilage is a viscoelastic material, but its exact behaviour under the full range of physiological loading frequencies is unknown. The objective of this study was to measure the viscoelastic properties of bovine articular cartilage at loading frequencies of up to 92 Hz.</p> <p>Methods</p> <p>Intact tibial plateau cartilage, attached to subchondral bone, was investigated by dynamic mechanical analysis (DMA). A sinusoidally varying compressive force of between 16 N and 36 N, at frequencies from 1 Hz to 92 Hz, was applied to the cartilage surface by a flat indenter. The storage modulus, loss modulus and phase angle (between the applied force and the deformation induced) were determined.</p> <p>Results</p> <p>The storage modulus, <it>E'</it>, increased with increasing frequency, but at higher frequencies it tended towards a constant value. Its dependence on frequency, <it>f</it>, could be represented by, <it>E' </it>= <it>Alog</it>_{<it>e </it>}(<it>f</it>) + <it>B </it>where <it>A </it>= 2.5 ± 0.6 MPa and <it>B </it>= 50.1 ± 12.5 MPa (mean ± standard error). The values of the loss modulus (4.8 ± 1.0 MPa mean ± standard deviation) were much less than the values of storage modulus and showed no dependence on frequency. The phase angle was found to be non-zero for all frequencies tested (4.9 ± 0.6°).</p> <p>Conclusion</p> <p>Articular cartilage is viscoelastic throughout the full range of frequencies investigated. The behaviour has implications for mechanical damage to articular cartilage and the onset of osteoarthritis. Storage modulus increases with frequency, until the plateau region is reached, and has a higher value than loss modulus. Furthermore, loss modulus does not increase with loading frequency. This means that more energy is stored by the tissue than is dissipated and that this effect is greater at higher frequencies. The main mechanism for this excess energy to be dissipated is by the formation of cracks.</p

MolProbity: all-atom structure validation for macromolecular crystallography

MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction

Gravity Recovery and Interior Laboratory (GRAIL): Extended Mission and End-Game Status

The Gravity Recovery and Interior Laboratory (GRAIL) [1], NASA s eleventh Discovery mission, successfully executed its Primary Mission (PM) in lunar orbit between March 1, 2012 and May 29, 2012. GRAIL s Extended Mission (XM) initiated on August 30, 2012 and was successfully completed on December 14, 2012. The XM provided an additional three months of gravity mapping at half the altitude (23 km) of the PM (55 km), and is providing higherresolution gravity models that are being used to map the upper crust of the Moon in unprecedented detail

Three Pseudomonas putida FNR Family Proteins with Different Sensitivities to O-2

The Escherichia coli fumarate-nitrate reduction regulator (FNR) protein is the paradigm for bacterial O2-sensing transcription factors. However, unlike E. coli, some bacterial species possess multiple FNR proteins that presumably have evolved to fulfill distinct roles. Here, three FNR proteins (ANR, PP_3233, and PP_3287) from a single bacterial species, Pseudomonas putida KT2440, have been analyzed. Under anaerobic conditions, all three proteins had spectral properties resembling those of [4Fe-4S] proteins. The reactivity of the ANR [4Fe-4S] cluster with O2 was similar to that of E. coli FNR, and during conversion to the apo-protein, via a [2Fe-2S] intermediate, cluster sulfur was retained. Like ANR, reconstituted PP_3233 and PP_3287 were converted to [2Fe-2S] forms when exposed to O2, but their [4Fe-4S] clusters reacted more slowly. Transcription from an FNR-dependent promoter with a consensus FNR-binding site in P. putida and E. coli strains expressing only one FNR protein was consistent with the in vitro responses to O2. Taken together, the experimental results suggest that the local environments of the iron-sulfur clusters in the different P. putida FNR proteins influence their reactivity with O2, such that ANR resembles E. coli FNR and is highly responsive to low concentrations of O2, whereas PP_3233 and PP_3287 have evolved to be less sensitive to O2