Intergranular diffusion rates from the analysis of garnet surfaces: implications for metamorphic equilibration

Novel approaches to garnet analysis have been used to assess rates of intergranular diffusion between different matrix phases and garnet porphyroblasts in a regionally metamorphosed staurolite-mica-schist from the Barrovian-type area in Scotland. X-ray maps and chemical traverses of planar porphyroblast surfaces reveal chemical heterogeneity of the garnet grain boundary linked to the nature of the adjacent matrix phase. The garnet preserves evidence of low temperature retrograde exchange with matrix minerals and diffusion profiles documenting cation movement along the garnet boundaries. Garnet–quartz and garnet–plagioclase boundaries preserve evidence of sluggish Mg, Mn and Fe diffusion at comparable rates to volume diffusion in garnet, whereas diffusion along garnet–biotite interfaces is much more effective. Evidence of particularly slow Al transport, probably coupled to Fe3+ exchange, is locally preserved on garnet surfaces adjacent to Fe-oxide phases. The Ca distribution on the garnet surface shows the most complex behaviour, with long-wavelength heterogeneities apparently unrelated to the matrix grain boundaries. This implies that the Ca content of garnet is controlled by local availability and is thought likely to reflect disequilibrium established during garnet growth. Geochemical anomalies on the garnet surfaces are also linked to the location of triple junctions between the porphyroblasts and the matrix phases, and imply enhanced transport along these channels. The slow rates of intergranular diffusion and the characteristics of different boundary types may explain many features associated with the prograde growth of garnet porphyroblasts. Thus, minerals such as quartz, Fe-oxides and plagioclase whose boundaries with garnet are characterized by slow intergranular diffusion rates appear to be preferentially trapped as inclusions within porphyroblasts. As such grain boundary diffusion rates may be a significant kinetic impediment to metamorphic equilibrium and garnet may struggle to maintain chemical and textural equilibrium during growth in pelites

Effective crustal permeability controls fault evolution: An integrated structural, mineralogical and isotopic study in granitic gneiss, Monte Rosa, Northern Italy

Two dextral faults within granitic gneiss in the Monte Rosa nappe, northern Italy reveal key differences in their evolution controlled by evolving permeability and water/rock reactions. The comparison reveals that identical host rock lithologies develop radically different mineralogies within the fault zones, resulting in fundamentally different deformation histories. Oxygen and hydrogen isotope analyses coupled to microstructural characterisation show that infiltration of meteoric water occurred into both fault zones. The smaller Virgin Fault shows evidence of periodic closed system behaviour, which promoted the growth of hydrothermal K-feldspar, whilst the more open system behaviour of the adjacent Ciao Ciao Fault generated a weaker muscovite-rich fault core, which promoted a step change in fault evolution. Effective crustal permeability is a vital control on fault evolution and, coupled to the temperature (i.e. depth) at which key mineral transformations occur, is probably a more significant factor than host rock strength in controlling fault development. The study suggests that whether a fault in granitic basement grows into a large structure may be largely controlled by the initial hydrological properties of the host rocks. Small faults exposed at the surface may therefore be evolutionary “dead-ends” that typically do not represent the early stages in the development of larger faults

Structural controls on the interaction between basin fluids and a rift flank fault: constraints from the Bwamba Fault, East African Rift

We present petrographic and structural analyses of a basement-hosted border fault in the East African Rift. Understanding the mechanical evolution and fluid-rock interaction of rift-flank faults is integral to developing models of fluid flow in the crust, where hydraulic connections may occur between basement faults and basin sediments. The Bwamba Fault forms the flank of the Rwenzori Mountains Horst in western Uganda, and has locally reactivated older mylonitic fabrics in the basement gneisses. The fault core features discrete mineralised and veined units. Shear fabrics and fault scarp striations indicate predominately normal kinematics, with minor strike-slip faulting and fabrics. Transient brittle failure was accompanied by two phases of fluid ingress, associated with veining and mineralisation. The first was localised and strongly influenced by host lithology. The second involved widespread Fe-oxide and jarosite mineralisation. The latter signals the onset of a hydraulic connection between Fe- and S-rich sedimentary rocks in the adjacent Semliki Rift Basin and the Bwamba Fault, involving co-seismic and or post-seismic fluid injection into the fault at ca. 150–200 °C, and 2.5–3 km depth. Such evolving permeability connections between basin sediments and basement faults are important for local hydrocarbon and geothermal systems, and may be typical of active rifts

Deformation-induced and reaction-enhanced permeability in metabasic gneisses, Iona, Scotland: controls and scales of retrograde fluid movement

The spatial distribution of greenschist-facies retrograde reaction products in metabasic gneisses from Iona, western Scotland, has been investigated. The retrograde products may be broadly accounted for by a single reaction, but their different spatial and temporal development indicates that a series of reactions occur with significantly different scales of metasomatic transfer. After initial fluid influx linked to deformation-induced high permeability, reaction-enhanced permeability, coupled to cycling of fluid pressure during faulting, strongly controls the pervasive retrogression. Ca-plagioclase and pyroxene in the gneisses are replaced by albite and chlorite in pseudomorphic textures, and this is followed by localized epidotization of the albite. Two main generations of epidote are formed in the gneisses. Epidosite formation is associated with prominent zones of cataclasite indicating a strong link between faulting and fluid influx. In contrast, complete alteration of albite to epidote in the host metabasic gneisses is spatially complex, and areas of pervasive alteration may be constrained by both epidote-rich veins and cataclasites. In other instances, reaction fronts are unrelated to structural features. Volume changes associated with individual stages of the reaction history strongly control the localized distribution of epidote and the earlier more widespread development of chlorite and albite. Such behaviour contrasts with adjacent granitic gneisses where epidotization is restricted to local structural conduits. Many small-scale mineralized fractures with evidence of having previously contained fluids do not enhance the pervasive retrogression of the metabasic gneisses and represent conduits of fluid removal. Retrogression of these basement gneisses is dominated by a complex combination of reaction-enhanced and reaction-restricted permeability, kinetic controls on the nucleation of reaction products, changes in fluid composition buffered by the reactions, and periodic local migration of fluids associated with fault movements. This combination generates spatially complex patterns of epidotization that are limited by cation supply rather than fluid availability and alternations between focused and pervasive types of retrogression

Proxy Measures of Fitness Suggest Coastal Fish Farms Can Act as Population Sources and Not Ecological Traps for Wild Gadoid Fish

Background: Ecological traps form when artificial structures are added to natural habitats and induce mismatches between habitat preferences and fitness consequences. Their existence in terrestrial systems has been documented, yet little evidence suggests they occur in marine environments. Coastal fish farms are widespread artificial structures in coastal ecosystems and are highly attractive to wild fish. Methodology/Principal Findings: To investigate if coastal salmon farms act as ecological traps for wild Atlantic cod (Gadus morhua) and saithe (Pollachius virens), we compared proxy measures of fitness between farm-associated fish and control fish caught distant from farms in nine locations throughout coastal Norway, the largest coastal fish farming industry in the world. Farms modified wild fish diets in both quality and quantity, thereby providing farm-associated wild fish with a strong trophic subsidy. This translated to greater somatic (saithe: 1.06–1.12 times; cod: 1.06–1.11 times) and liver condition indices (saithe: 1.4–1.8 times; cod: 2.0–2.8 times) than control fish caught distant from farms. Parasite loads of farm-associated wild fish were modified from control fish, with increased external and decreased internal parasites, however the strong effect of the trophic subsidy overrode any effects of altered loads upon condition. Conclusions and Significance: Proxy measures of fitness provided no evidence that salmon farms function as ecological traps for wild fish. We suggest fish farms may act as population sources for wild fish, provided they are protected from fishing while resident at farms to allow their increased condition to manifest as greater reproductive output.Funding was provided by the Norwegian Research Council Havet og kysten program to the CoastACE project (no: 173384)

Growth zoning of garnet porphyroblasts: grain boundary and microtopographic controls

Chemical zoning in the outer few 10s of microns of garnet porphyroblasts has been investigated to assess the scale of chemical equilibrium with matrix minerals in a pelitic schist. Garnet porphyroblasts from the Late Proterozoic amphibolite‐facies regional metamorphic mica schists from Glen Roy in the Scottish Highlands contain typical prograde growth zoning patterns. Edge compositions have been measured via a combination of analysis of traverses across the planar edges of porphyroblast surfaces coupled to X‐ray mapping of small areas within polished thin sections at the immediate edge of the porphyroblasts. These approaches reveal local variation in garnet composition, especially of grossular (Ca) and almandine (Fe) components, with a range at the edge from <7 mol% grs to >16 mol% grs, across distances of less then 50 mm. This small‐scale patchy compositional zoning is as much variation as the core‐rim compositional zoning across the whole of a 3 mm porphyroblast. Ca and Fe heterogeneity occurs on a scale suggesting a combination of inefficient diffusive exchange across grain boundaries during prograde growth and the evolving microtopography of the porphyroblast surface control garnet composition. The latter creates haloes of compositional zoning adjacent to some inclusions, which typically extend from the inclusion towards the porphyroblast edge during further growth. The lack of a consistent equilibrium composition at the garnet edge is also apparent in the internal zoning of the porphyroblast and so processes occurring during entrapment of some mineral inclusions have a profound influence on the overall chemical zoning. Garnet compositions and associated zoning patterns are widely used by petrologists to reconstruct P‐T‐t paths for crustal rocks. The evidence of extremely localized (10‐50 mm scale) equilibrium during growth further undermines these approaches

Large scale statistical inference of signaling pathways from RNAi and microarray data

<p>Abstract</p> <p>Background</p> <p>The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain insights into signaling pathways by observing downstream effects of individual knock-downs on gene expression. These secondary effects can be used to computationally reverse engineer features of the upstream signaling pathway.</p> <p>Results</p> <p>In this paper we address this challenging problem by extending previous work by Markowetz <it>et al</it>., who proposed a statistical framework to score networks hypotheses in a Bayesian manner. Our extensions go in three directions: First, we introduce a way to omit the data discretization step needed in the original framework via a calculation based on <it>p</it>-values instead. Second, we show how prior assumptions on the network structure can be incorporated into the scoring scheme using regularization techniques. Third and most important, we propose methods to scale up the original approach, which is limited to around 5 genes, to large scale networks.</p> <p>Conclusion</p> <p>Comparisons of these methods on artificial data are conducted. Our proposed module network is employed to infer the signaling network between 13 genes in the ER-<it>α </it>pathway in human MCF-7 breast cancer cells. Using a bootstrapping approach this reconstruction can be found with good statistical stability.</p> <p>The code for the module network inference method is available in the latest version of the <it>R</it>-package <it>nem</it>, which can be obtained from the Bioconductor homepage.</p

Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions

<p>Abstract</p> <p>Background</p> <p>Modern gene perturbation techniques, like RNA interference (RNAi), enable us to study effects of targeted interventions in cells efficiently. In combination with mRNA or protein expression data this allows to gain insights into the behavior of complex biological systems.</p> <p>Results</p> <p>In this paper, we propose Deterministic Effects Propagation Networks (DEPNs) as a special Bayesian Network approach to reverse engineer signaling networks from a combination of protein expression and perturbation data. DEPNs allow to reconstruct protein networks based on combinatorial intervention effects, which are monitored via changes of the protein expression or activation over one or a few time points. Our implementation of DEPNs allows for latent network nodes (i.e. proteins without measurements) and has a built in mechanism to impute missing data. The robustness of our approach was tested on simulated data. We applied DEPNs to reconstruct the <it>ERBB </it>signaling network in <it>de novo </it>trastuzumab resistant human breast cancer cells, where protein expression was monitored on Reverse Phase Protein Arrays (RPPAs) after knockdown of network proteins using RNAi.</p> <p>Conclusion</p> <p>DEPNs offer a robust, efficient and simple approach to infer protein signaling networks from multiple interventions. The method as well as the data have been made part of the latest version of the R package "nem" available as a supplement to this paper and via the Bioconductor repository.</p

Early life vitamin D depletion alters the postnatal response to skeletal loading in growing and mature bone

There is increasing evidence of persistent effects of early life vitamin D exposure on later skeletal health; linking low levels in early life to smaller bone size in childhood as well as increased fracture risk later in adulthood, independently of later vitamin D status. A major determinant of bone mass acquisition across all ages is mechanical loading. We tested the hypothesis in an animal model system that early life vitamin D depletion results in abrogation of the response to mechanical loading, with consequent reduction in bone size, mass and strength during both childhood and adulthood. A murine model was created in which pregnant dams were either vitamin D deficient or replete, and their offspring moved to a vitamin D replete diet at weaning. Tibias of the offspring were mechanically loaded and bone structure, extrinsic strength and growth measured both during growth and after skeletal maturity. Offspring of vitamin D deplete mice demonstrated lower bone mass in the non loaded limb and reduced bone mass accrual in response to loading in both the growing skeleton and after skeletal maturity. Early life vitamin D depletion led to reduced bone strength and altered bone biomechanical properties. These findings suggest early life vitamin D status may, in part, determine the propensity to osteoporosis and fracture that blights later life in many individuals

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies—sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/ parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.publishedVersio