Model-Independent 3D Descriptors of Vertebral Cancellous Bone Architecture

High-resolution micro computed tomography has enabled measurement of bone architecture derived from 3D representations of cancellous bone. Twenty-eight vertebral bodies were obtained from four embalmed male cadavers. From 3D anaglyphs, trabecular rod thickness and length were measured and the trabecular rod Buckling index was calculated. From 3D voxel-based datasets, bone volume density, trabecular thickness, and trabecular separation were measured. Also, trabecular bone pattern factor, structural model index, connectivity density, and degree of anisotropy were calculated. Bone volume density alone explains 59% of the variability in trabecular rod Buckling index. The addition of connectivity density, trabecular separation, and structural model index, in a multiple regression statistical model, improves the explanatory power to 77%. The relationships between measures of cancellous bone architecture and a derived measure of trabecular rod strength were investigated. Morphological descriptors of cancellous bone provide a composite explanatory model of trabecular rod strength

Application of in vivo micro-computed tomography in the temporal characterisation of subchondral bone architecture in a rat model of low-dose monosodium iodoacetate-induced osteoarthritis

The electronic version of this article is the complete one and can be found online at: http://arthritis-research.com/content/13/6/R210Introduction: Osteoarthritis (OA) is a complex, multifactorial joint disease affecting both the cartilage and the subchondral bone. Animal models of OA aid in the understanding of the pathogenesis of OA and testing suitable drugs for OA treatment. In this study we characterized the temporal changes in the tibial subchondral bone architecture in a rat model of low-dose monosodium iodoacetate (MIA)-induced OA using in vivo micro-computed tomography (CT). Methods: Male Wistar rats received a single intra-articular injection of low-dose MIA (0.2 mg) in the right knee joint and sterile saline in the left knee joint. The animals were scanned in vivo by micro-CT at two, six, and ten weeks post-injection, analogous to early, intermediate, and advanced stages of OA, to assess architectural changes in the tibial subchondral bone. The articular cartilage changes in the tibiae were assessed macroscopically and histologically at ten weeks post-injection. Results: Interestingly, tibiae of the MIA-injected knees showed significant bone loss at two weeks, followed by increased trabecular thickness and separation at six and ten weeks. The trabecular number was decreased at all time points compared to control tibiae. The tibial subchondral plate thickness of the MIA-injected knee was increased at two and six weeks and the plate porosity was increased at all time points compared to control. At ten weeks, histology revealed loss of proteoglycans, chondrocyte necrosis, chondrocyte clusters, cartilage fibrillation, and delamination in the MIA-injected tibiae, whereas the control tibiae showed no changes. Micro-CT images and histology showed the presence of subchondral bone sclerosis, cysts, and osteophytes. Conclusions: These findings demonstrate that the low-dose MIA rat model closely mimics the pathological features of progressive human OA. The low-dose MIA rat model is therefore suitable to study the effect of therapeutic drugs on cartilage and bone in a non-trauma model of OA. In vivo micro-CT is a non-destructive imaging technique that can track structural changes in the tibial subchondral bone in this animal model, and could also be used to track changes in bone in preclinical drug intervention studies for OA treatments.Geetha Mohan, Egon Perilli, Julia S Kuliwaba, Julia M Humphries, Ian H Parkinson and Nicola L Fazzalar

Investigating ocean deoxygenation during the PETM through the Cr isotopic signature of foraminifera

Over the past several decades, oxygen minimum zones have rapidly expanded due to rising temperatures raising concerns about the impacts of future climate change. One way to better understand the drivers behind this expansion is to evaluate the links between climate and seawater deoxygenation in the past especially in times of geologically abrupt climate change such as the Palaeocene-Eocene Thermal Maximum (PETM), a well characterised period of rapid warming ~56 million years ago. We have developed and applied the novel redox proxies of foraminiferal Cr isotopes(δ53Cr) and Ce anomalies (Ce/Ce*) to assess changes in paleo-redox conditions arising from changes in oxygen availability. Both δ53Cr and Cr concentrations decrease notably over the PETM at intermediate to upper abyssal water depths,indicative of widespread reductions in dissolved oxygen concentrations. An apparent correlation between the sizes of δ53Cr and benthic δ18O excursions during the PETM suggests temperature is one of the main controlling factors of deoxygenation in the open ocean. ODP Sites 1210 in the Pacific and 1263 in the Southeast Atlantic suggest that deoxygenation is associated with warming and circulation changes, as supported by Ce/Ce* data. Our geochemical data are supported by simulations from an intermediate complexity climate model (cGENIE), which show that during the PETM anoxia was mostly restricted to the Tethys Sea, while hypoxia was more widespread as a result of increasing atmospheric CO2 (from 1 to 6 times pre-industrial values)

Understanding Far-Infrared Absorption in the S=1 Antiferromagnetic Chain Compound NENP

Infrared transmission measurements on the $S=1$ antiferromagnetic chain compound NENP in applied magnetic fields show a sharp absorption line at the field-shifted Haldane gap. This violates a wave-vector selection rule of the Hamiltonian normally used for NENP, as the gap excitations occur at the Brillouin zone boundary. We argue that the crystal structure admits terms which can explain the absorption lines. In addition, in an applied field, staggered orientations of the g-tensors produce a staggered magnetic field. This can explain the observation of a finite gap at all applied fields.Comment: 12 pages, revtex, preprint HU-CMT-93H9

Isotopic signature of dissolved iron delivered to the Southern Ocean from hydrothermal vents in the East Scotia Sea

It has recently been demonstrated that hydrothermal vents are an important source of dissolved Fe (dFe) to the Southern Ocean. The isotopic composition (?56Fe) of dFe in vent fluids appears to be distinct from other sources of dFe to the deep ocean, but the evolution of ?56Fe during mixing between vent fluids and seawater is poorly constrained. Here we present the evolution of ?56Fe for dFe in hydrothermal fluids and dispersing plumes from two sites in the East Scotia Sea. We show that ?56Fe values in the buoyant plume are distinctly lower (as low as ?1.19 ‰) than the hydrothermal fluids (?0.29 ‰), attributed to (i) precipitation of Fe-sulfides in the early stages of mixing, and (ii) partial oxidation of Fe(II) to Fe(III), > 55 % of which subsequently precipitates as Fe-oxyhydroxides. By contrast, the ?56Fe signature of stabilized dFe in the neutrally buoyant plume is ?0.3 to ?0.5 ‰. This cannot be explained by continued dilution of the buoyant plume with background seawater; rather, we suggest that isotope fractionation of dFe occurs during plume dilution due to Fe ligand complexation and exchange with labile particulate Fe. The ?56Fe signature of stabilized hydrothermal dFe in the East Scotia Sea is distinct from background seawater and may be used to quantify the hydrothermal dFe input to the ocean interior

Subregional DXA-derived vertebral bone mineral measures are stronger predictors of failure load in specimens with lower areal bone mineral density, compared to those with higher areal bone mineral density

Measurement of areal bone mineral density (aBMD) in intravertebral subregions may increase the diagnostic sensitivity of dual-energy X-ray absorptiometry (DXA)-derived parameters for vertebral fragility. This study investigated whether DXA-derived bone parameters in vertebral subregions were better predictors of vertebral bone strength in specimens with low aBMD, compared to those with higher aBMD. Twenty-five lumbar vertebrae (15 embalmed and 10 fresh-frozen) were scanned with posteroanterior- (PA) and lateral-projection DXA, and then mechanically tested in compression to ultimate failure. Whole-vertebral aBMD and bone mineral content (BMC) were measured from the PA- and lateral-projection scans and within 6 intravertebral subregions. Multivariate regression was used to predict ultimate failure load by BMC, adjusted for vertebral size and specimen fixation status across the whole specimen set, and when subgrouped into specimens with low aBMD and high aBMD. Adjusted BMC explained a substantial proportion of variance in ultimate vertebral load, when measured over the whole vertebral area in lateral projection (adjusted R2 0.84) and across the six subregions (ROIs 2–7) (adjusted R2 range 0.58–0.78). The association between adjusted BMC, either measured subregionally or across the whole vertebral area, and vertebral failure load, was increased for the subgroup of specimens with identified ‘low aBMD’, compared to those with ‘high aBMD’, particularly in the anterior subregion where the adjusted R2 differed by 0.44. The relative contribution of BMC measured in vertebral subregions to ultimate failure load is greater among specimens with lower aBMD, compared to those with higher aBMD, particularly in the anterior subregion of the vertebral body

Toward interoperable bioscience data

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Genetics 44 (2012): 121-126, doi:10.1038/ng.1054.To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.The authors also acknowledge the following funding sources in particular: UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/I000771/1 to S.-A.S. and A.T.; UK BBSRC BB/I025840/1 to S.-A.S.; UK BBSRC BB/I000917/1 to D.F.; EU CarcinoGENOMICS (PL037712) to J.K.; US National Institutes of Health (NIH) 1RC2CA148222-01 to W.H. and the HSCI; US MIRADA LTERS DEB-0717390 and Alfred P. Sloan Foundation (ICoMM) to L.A.-Z.; Swiss Federal Government through the Federal Office of Education and Science (FOES) to L.B. and I.X.; EU Innovative Medicines Initiative (IMI) Open PHACTS 115191 to C.T.E.; US Department of Energy (DOE) DE-AC02- 06CH11357 and Arthur P. Sloan Foundation (2011- 6-05) to J.G.; UK BBSRC SysMO-DB2 BB/I004637/1 and BBG0102181 to C.G.; UK BBSRC BB/I000933/1 to C.S. and J.L.G.; UK MRC UD99999906 to J.L.G.; US NIH R21 MH087336 (National Institute of Mental Health) and R00 GM079953 (National Institute of General Medical Science) to A.L.; NIH U54 HG006097 to J.C. and C.E.S.; Australian government through the National Collaborative Research Infrastructure Strategy (NCRIS); BIRN U24-RR025736 and BioScholar RO1-GM083871 to G.B. and the 2009 Super Science initiative to C.A.S

Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology

The mitotic spindle is an essential molecular machine involved in cell division, whose composition has been studied extensively by detailed cellular biology, high-throughput proteomics, and RNA interference experiments. However, because of its dynamic organization and complex regulation it is difficult to obtain a complete description of its molecular composition. We have implemented an integrated computational approach to characterize novel human spindle components and have analysed in detail the individual candidates predicted to be spindle proteins, as well as the network of predicted relations connecting known and putative spindle proteins. The subsequent experimental validation of a number of predicted novel proteins confirmed not only their association with the spindle apparatus but also their role in mitosis. We found that 75% of our tested proteins are localizing to the spindle apparatus compared to a success rate of 35% when expert knowledge alone was used. We compare our results to the previously published MitoCheck study and see that our approach does validate some findings by this consortium. Further, we predict so-called “hidden spindle hub”, proteins whose network of interactions is still poorly characterised by experimental means and which are thought to influence the functionality of the mitotic spindle on a large scale. Our analyses suggest that we are still far from knowing the complete repertoire of functionally important components of the human spindle network. Combining integrated bio-computational approaches and single gene experimental follow-ups could be key to exploring the still hidden regions of the human spindle system

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits