Genome-wide co-expression analysis in multiple tissues

Expression quantitative trait loci (eQTLs) represent genetic control points of gene expression, and can be categorized as cis- and trans-acting, reflecting local and distant regulation of gene expression respectively. Although there is evidence of co-regulation within clusters of trans-eQTLs, the extent of co-expression patterns and their relationship with the genotypes at eQTLs are not fully understood. We have mapped thousands of cis- and trans-eQTLs in four tissues (fat, kidney, adrenal and left ventricle) in a large panel of rat recombinant inbred (RI) strains. Here we investigate the genome-wide correlation structure in expression levels of eQTL transcripts and underlying genotypes to elucidate the nature of co-regulation within cis- and trans-eQTL datasets. Across the four tissues, we consistently found statistically significant correlations of cis-regulated gene expression to be rare (<0.9% of all pairs tested). Most (>80%) of the observed significant correlations of cis-regulated gene expression are explained by correlation of the underlying genotypes. In comparison, co-expression of trans-regulated gene expression is more common, with significant correlation ranging from 2.9%-14.9% of all pairs of trans-eQTL transcripts. We observed a total of 81 trans-eQTL clusters (hot-spots), defined as consisting of > or =10 eQTLs linked to a common region, with very high levels of correlation between trans-regulated transcripts (77.2-90.2%). Moreover, functional analysis of large trans-eQTL clusters (> or =30 eQTLs) revealed significant functional enrichment among genes comprising 80% of the large clusters. The results of this genome-wide co-expression study show the effects of the eQTL genotypes on the observed patterns of correlation, and suggest that functional relatedness between genes underlying trans-eQTLs is reflected in the degree of co-expression observed in trans-eQTL clusters. Our results demonstrate the power of an integrative, systematic approach to the analysis of a large gene expression dataset to uncover underlying structure, and inform future eQTL studies

Spectroscopic biomedical imaging with the Medipix2 detector

This study confirms that the Medipix2 x-ray detector enables spectroscopic bio-medical plain radiography. We show that the detector has the potential to provide new, useful information beyond the limited spectroscopic information of modern dual-energy computed tomography (CT) scanners. Full spectroscopic 3D-imaging is likely to be the next major technological advance in computed tomography, moving the modality towards molecular imaging applications. This paper focuses on the enabling technology which allows spectroscopic data collection and why this information is useful. In this preliminary study we acquired the first spectroscopic images of human tissue and other biological samples obtained using the Medipix2 detector. The images presented here include the clear resolution of the 1.4mm long distal phalanx of a 20 week old miscarried foetus, showing clear energy-dependent variations. The opportunities for further research using the forthcoming Medipix3 detector are discussed and a prototype spectroscopic CT scanner (MARS, Medipix All Resolution System) is briefly described

Numerical modeling of REE fractionation patterns in fluorapatite from the olympic dam deposit (South Australia)

Trace element signatures in apatite are used to study hydrothermal processes due to the ability of this mineral to chemically record and preserve the impact of individual hydrothermal events. Interpretation of rare earth element (REE)-signatures in hydrothermal apatite can be complex due to not only evolving fO2, fS2 and fluid composition, but also to variety of different REE-complexes (Cl-, F-, P-, SO4, CO3, oxide, OH− etc.) in hydrothermal fluid, and the significant differences in solubility and stability that these complexes exhibit. This contribution applies numerical modeling to evolving REE-signatures in apatite within the Olympic Dam iron-oxide-copper-gold deposit, South Australia with the aim of constraining fluid evolution. The REE-signatures of three unique types of apatite from hydrothermal assemblages that crystallized under partially constrained conditions have been numerically modeled, and the partitioning coefficients between apatite and fluid calculated in each case. Results of these calculations replicate the measured data well and show a transition from early light rare earth element (LREE)- to later middle rare earth element (MREE)-enriched apatite, which can be achieved by an evolution in the proportions of different REE-complexes. Modeling also efficiently explains the switch from REE-signatures with negative to positive Eu-anomalies. REE transport in hydrothermal fluids at Olympic Dam is attributed to REE–chloride complexes, thus explaining both the LREE-enriched character of the deposit and the relatively LREE-depleted nature of later generations of apatite. REE deposition may, however, have been induced by a weakening of REE–Cl activity and subsequent REE complexation with fluoride species. The conspicuous positive Eu-anomalies displayed by later apatite with are attributed to crystallization from high pH fluids characterized by the presence of Eu3+ species.Sasha Krneta, Cristiana L. Ciobanu, Nigel J. Cook and Kathy J. Ehri

Detection of trace elements/isotopes in Olympic Dam copper concentrates by nanoSIMS

Many analytical techniques for trace element analysis are available to the geochemist and geometallurgist to understand and, ideally, quantify the distribution of trace and minor components in a mineral deposit. Bulk trace element data are useful, but do not provide information regarding specific host minerals—or lack thereof, in cases of surface adherence or fracture fill—for each element. The CAMECA nanoscale secondary ion mass spectrometer (nanoSIMS) 50 and 50L instruments feature ultra-low minimum detection limits (to parts-per-billion) and sub-micron spatial resolution, a combination not found in any other analytical platform. Using ore and copper concentrate samples from the Olympic Dam mining-processing operation, South Australia, we demonstrate the application of nanoSIMS to understand the mineralogical distribution of potential by-product and detrimental elements. Results show previously undetected mineral host assemblages and elemental associations, providing geochemists with insight into mineral formation and elemental remobilization—and metallurgists with critical information necessary for optimizing ore processing techniques. Gold and Te may be seen associated with brannerite, and Ag prefers chalcocite over bornite. Rare earth elements may be found in trace quantities in fluorapatite and fluorite, which may report to final concentrates as entrained liberated or gangue-sulfide composite particles. Selenium, As, and Te reside in sulfides, commonly in association with Pb, Bi, Ag, and Au. Radionuclide daughters of the 238U decay chain may be located using nanoSIMS, providing critical information on these trace components that is unavailable using other microanalytical techniques. These radionuclides are observed in many minerals but seem particularly enriched in uranium minerals, some phosphates and sulfates, and within high surface area minerals. The nanoSIMS has proven a valuable tool in determining the spatial distribution of trace elements and isotopes in fine-grained copper ore, providing researchers with crucial evidence needed to answer questions of ore formation, ore alteration, and ore processing.Mark Rollog, Nigel J. Cook, Paul Guagliardo, Kathy Ehrig, Cristiana L. Ciobanu and Matt Kilbur

Nanoscale study of titanomagnetite from the Panzhihua Layered Intrusion, southwest China: multistage exsolutions record ore formation

Titanomagnetite from Fe-Ti-V ores of the Lanjiahuoshan deposit, Panzhihua layered intrusion, Southwest China, was investigated at the nanoscale. The objectives were to establish the composition of exsolution phases and their mutual relationships in order to evaluate the sequence of exsolution among oxide phases, and assess mechanisms of ore formation during magma emplacement. At the micron-scale, titanomagnetite shows crosscutting sets of exsolutions with ilmenite and Al-Mg-Fe-spinel (pleonaste), as well as overprint, both in terms of phase re-equilibration and remobilization of trace elements. Most complex textures were found in titanomagnetite surrounded by ilmenite and this was selected for high-angle annular dark field scanning transmission electron microscopy (HAADF STEM) imaging and STEM energy-dispersive X-ray spectrometry (EDS) spot analysis and mapping on a thin foil prepared in situ on a focused ion beam scanning electron microscope platform. Titanomagnetite revealed two sequential sets of exsolutions, {111} crosscutting {100}, which are associated with changes in phase speciation and trace element distribution patterns. Qandilite is the dominant spinel phase inside titanomagnetite; magnesioferrite is also identified. In contrast, Fe-poor, Al-rich, Mg-bearing spinel is present within ilmenite outside the grain. Vanadium enrichment in newly-formed magnetite lamellae is clear evidence for trace element remobilization. This V-rich magnetite shows epitaxial relationships with ilmenite at the contact with titanomagnetite. Two-fold super-structuring in ilmenite is evidence for non-redox re-equilibration between titanomagnetite and ilmenite, supporting published experimental data. In contrast, the transformation of cubic Ti-rich spinel into rhombohedral ilmenite imaged at the nanoscale represents the “oxy-exsolution” model of titanomagnetite–ilmenite re-equilibration via formation of a transient ulvöspinel species. Nanoscale disorder is encountered as vacancy layers in Ti-rich spinel, and lower symmetry in the Fe-poor, Al-Mg phase, suggesting that slow cooling rates can preserve small-scale phase equilibration. The cooling history of titanomagnetite ore can be reconstructed as three distinct stages, concordant with published models for the magma plumbing system: equilibrium crystallization of Al-rich, Mg-bearing titanomagnetite from cumulus melts at ~55 km, with initial exsolutions occurring above 800 °C at moderate fO2 conditions (Stage 1); crosscutting {111} exsolutions resulting in formation of qandilite, attributable to temperature increase due to emplacement of another batch of melt affecting the interstitial cumulus during uplift. Formation of 2-fold superstructure ilmenite + V-rich magnetite exsolution pairs representing non-redox equilibration indicates resetting of the cooling path at this stage (Stage 2); and ilmenite formation from pre-existing Ti-rich spinel and ulvöspinel, illustrative of redox-driven cooling paths at <10 km (Stage 3). HAADF STEM provides direct imaging of atomic arrangements, allowing recognition of processes not recognizable at the micron-scale, and can thus be used to constrain exsolution models during ore formation.Wenyuan Gao, Cristiana L. Ciobanu, Nigel J. Cook, Ashley Slattery, Fei Huang and Dan Son

Intermobility of barium, strontium, and lead in chloride and sulfate leach solutions

Production of radionuclide-free copper concentrates is dependent on understanding and controlling the deportment of daughter radionuclides (RNs) produced from 238U decay, specifically 226Ra, 210Pb, and 210Po. Sulfuric acid leaching is currently employed in the Olympic Dam processing plant (South Australia) to remove U and fluorine from copper concentrates prior to smelting but does not adequately remove the aforementioned RN. Due to chemical similarities between lead and alkaline earth metals (including Ra), two sets of experiments were designed to understand solution interactions between Sr, Ba, and Pb at various conditions. Nanoscale secondary ion mass spectrometry (NanoSIMS) isotopic spatial distribution maps and laser ablation inductively coupled-plasma mass spectrometry transects were performed on laboratory-grown crystals of baryte, celestite, and anglesite which had been exposed to different solutions under different pH and reaction time conditions. Analysis of experimental products reveals three uptake mechanisms: overgrowth of nearly pure SrSO4 and PbSO4 on baryte; incorporation of minor of Pb and Ba into celestite due to diffusion; and extensive replacement of Pb by Sr (and less extensive replacement of Pb by Ba) in anglesite via coupled dissolution-reprecipitation reactions. The presence of H2SO4 either enhanced or inhibited these reactions. Kinetic modelling supports the experimental results, showing potential for extrapolating the (Sr, Ba, Pb)SO4 system to encompass RaSO4. Direct observation of grain-scale element distributions by nanoSIMS aids understanding of the controlling conditions and mechanisms of replacement that may be critical steps for Pb and Ra removal from concentrates by allowing construction of a cationic replacement scenario targeting Pb or Ra, or ideally all insoluble sulfates. Experimental results provide a foundation for further investigation of RN uptake during minerals processing, especially during acid leaching. The new evidence enhances understanding of micro- to nanoscale chemical interactions and not only aids determination of where radionuclides reside during each processing stage but also guides development of flowsheets targeting their removal.Mark Rollog, Nigel J. Cook, Paul Guagliardo, Kathy Ehrig, Sarah E. Gilbert and Matt Kilbur

Polytypism and polysomatism in mixed-layer chalcogenides: characterization of PbBi(4)Te(4)S(3) and inferences for ordered phases in the aleksite series

Bi-Pb-chalcogenides of the aleksite series represent homologous mixed-layer compounds derived from tetradymite (Bi₂Te₂S). Considering tetradymite as composed of five-atom (Bi₂Te₂S) layers, the named minerals of the aleksite homologous series, aleksite (PbBi₂Te₂S₂) and saddlebackite, (Pb₂Bi₂Te₂S₃) have been considered as phases formed by regular stacking of longer seven- and nine-atom layers. High-angle annular dark-field scanning transmission electron microscope (HAADF-STEM) imaging of thinned foils prepared in-situ on domains deemed homogeneous from electron probe microanalysis, STEM energy-dispersive X-ray spectrometry (EDS) element mapping and fast Fourier transforms (FFTs) from the images offer new insights into these structures. The hitherto-unnamed phase, PbBi₄Te₄S₃, previously interpreted as regular intergrowths of five- and seven-atom layers, is characterized in terms of regular repeats of five- and seven-atom layers over distances of at least 350 nm, defining the (57), or 24H polytype. Imaging of other domains in the same lamella with identical composition at the electron microprobe scale reveals the presence of two additional polytypes: (5559), or 48H; and (557.559) or 72H. Unit cell dimensions for all three polytypes of PbBi₄Te₄S₃ can be both measured and predicted from the HAADF STEM imaging and FFTs. STEM EDS mapping of each polytype confirm the internal structure of each layer. Lead and S occur within the centre of the layers, i.e., Te–Bi–S–Pb–S–Bi–Te in the seven-atom layer, Te–Bi–S–Pb–S–Pb–S–Bi–Te in the nine-atom layer, and so on. Polytypism is an intrinsic feature of the aleksite series, with each named mineral or unnamed phase, except the simple five-atom layer, defined by several alternative stacking sequences of different length, readily explaining the differing c values given in previous work. Homology is defined in terms of layer width and the stacking arrangement of those layers. Coherent structures of the same composition need not only be built of layers of adjacent size (i.e., five- and seven-atom layers) but, as exemplified by the (5559) polytype, may also contain non-adjacent layers, a finding not anticipated in previous work. New polysomes remain to be discovered in nature and each potentially exists as multiple polytypes. The present study further emphasizes the utility of HAADF STEM imaging and atomic-scale STEM EDS element mapping as an optimal tool for tracking stacking sequences and characterising structures in mixed-layer compounds.Nigel J. Cook, Cristiana L. Ciobanu, Wenyuan Liu, Ashley Slattery, Benjamin P. Wade, Stuart J. Mills, and Christopher J. Stanle

Mineralogy of zirconium in iron‐oxides: a micron‐ to nanoscale study of hematite ore from peculiar Knob, South Australia

Zirconium is an element of considerable petrogenetic significance but is rarely found in hematite at concentrations higher than a few parts-per-million (ppm). Coarse-grained hematite ore from the metamorphosed Peculiar Knob iron deposit, South Australia, contains anomalous concentrations of Zr and has been investigated using microanalytical techniques that can bridge the micron- to nanoscales to understand the distribution of Zr in the ore. Hematite displays textures attributable to annealing under conditions of high-grade metamorphism, deformation twins (r~85° to hematite elongation), relict magnetite and fields of sub-micron-wide inclusions of baddeleyite as conjugate needles with orientation at ~110°/70°. Skeletal and granoblastic zircon, containing only a few ppm U, are both present interstitial to hematite. Using laser-ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) spot analysis and mapping, the concentration of Zr in hematite is determined to be ~260 ppm on average (up to 680 ppm). The Zr content is, however, directly attributable to nm-scale inclusions of baddeleyite pervasively distributed throughout the hematite rather than Zr in solid solution. Distinction between nm-scale inclusions and lattice-bound trace element substitutions cannot be made from LA-ICP-MS data alone and requires nanoscale characterization. Scandium-rich (up to 0.18 wt. % Sc2O3) cores in zircon are documented by microprobe analysis and mapping. Using high-angle annular dark field scanning transmission electron microscopy imaging (HAADF-STEM) and energy-dispersive spectrometry STEM mapping of foils prepared in-situ by focused ion beam methods, we identify [ 01¯1 ]baddeleyite epitaxially intergrown with [ 22¯.1 ]hematite. Lattice vectors at 84–86° underpinning the epitaxial intergrowth orientation correspond to directions of r-twins but not to the orientation of the needles, which display a ~15° misfit. This is attributable to directions of trellis exsolutions in a precursor titanomagnetite. U–Pb dating of zircon gives a 206Pb/238U weighted mean age of 1741 ± 49 Ma (sensitive high-resolution ion microprobe U–Pb method). Based on the findings presented here, detrital titanomagnetite from erosion of mafic rocks is considered the most likely source for Zr, Ti, Cr and Sc. Whether such detrital horizons accumulated in a basin with chemical precipitation of Fe-minerals (banded iron formation) is debatable, but such Fe-rich sediments clearly included detrital horizons. Martitization during the diagenesis-supergene enrichment cycle was followed by high-grade metamorphism during the ~1.73–1.69 Ga Kimban Orogeny during which martite recrystallized as granoblastic hematite. Later interaction with hydrothermal fluids associated with ~1.6 Ga Hiltaba-granitoids led to W, Sn and Sb enrichment in the hematite. By reconstructing the evolution of the massive orebody at Peculiar Knob, we show how application of complimentary advanced microanalytical techniques, in-situ and on the same material but at different scales, provides critical constraints on ore-forming processes.William Keyser, Cristiana L. Ciobanu, Nigel J. Cook, Holly Feltus, Geoff Johnson, Ashley Slattery, Benjamin P. Wade and Kathy Ehri

Silician Magnetite: Si–Fe-nanoprecipitates and other mineral inclusions in magnetite from the Olympic Dam deposit, South Australia

A comprehensive nanoscale study on magnetite from samples from the outer, weakly mineralized shell at Olympic Dam, South Australia, has been undertaken using atom-scale resolution High Angle Annular Dark Field Scanning Transmission Electron Microscopy (HAADF STEM) imaging and STEM energy-dispersive X-ray spectrometry mapping and spot analysis, supported by STEM simulations. Silician magnetite within these samples is characterized and the significance of nanoscale inclusions in hydrothermal and magmatic magnetite addressed. Silician magnetite, here containing Si–Fe-nanoprecipitates and a diverse range of nanomineral inclusions [(ferro)actinolite, diopside and epidote but also U-, W-(Mo), Y-As- and As-S-nanoparticles] appears typical for these samples. We observe both silician magnetite nanoprecipitates with spinel-type structures and a γ-Fe₁.₅SiO₄ phase with maghemite structure. These are distinct from one another and occur as bleb-like and nm-wide strips along d₁₁₁ in magnetite, respectively. Overprinting of silician magnetite during transition from K-feldspar to sericite is also expressed as abundant lattice-scale defects (twinning, faults) associated with the transformation of nanoprecipitates with spinel structure into maghemite via Fe-vacancy ordering. Such mineral associations are characteristic of early, alkali-calcic alteration in the iron-oxide copper gold (IOCG) system at Olympic Dam. Magmatic magnetite from granite hosting the deposit is quite distinct from silician magnetite and features nanomineral associations of hercynite-ulvöspinel-ilmenite. Silician magnetite has petrogenetic value in defining stages of ore deposit evolution at Olympic Dam and for IOCG systems elsewhere. The new data also add new perspectives into the definition of silician magnetite and its occurrence in ore deposits.Cristiana L. Ciobanu, Max R. Verdugo-Ihl, Ashley Slattery, Nigel J. Cook, Kathy Ehrig, Liam Courtney-Davies, and Benjamin P. Wad