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

A Multi-Scale Agent Based Model of Colon Carcinogenesis

Colorectal cancer (CRC) is a major cause of cancer mortality and there remain aspects of its formation which are not understood. The colon contains an epithelium punctuated by flask shaped invaginations called the crypts of Lieberkühn. These crypts are monoclonal in nature while adenomas are thought to be polyclonal, suggesting that multiple crypts are involved in carcinogenesis. It has been reported that fields of mutated tissue surround adenomas but the causes and growth of these fields are not well understood. There are two competing hypotheses regarding growth, the first being that mutated cells from one crypt invade neighbouring crypts, and the second that mutated crypts replicate themselves more often than wild-type crypts. To investigate these processes two agent based models were developed. The first model represents cells as agents and is similar to previous models in the field, but is novel in including the geometry of the crypt mouth. This is necessary to model multiple interacting crypts. This model is the first in the literature to be used to represent multiple crypts and is used to investigate invasion of neighbour crypts by mutated cells. The second model represents whole crypts as agents, which allows the entire colon to be simulated for multiple decades of biological time, as far as we are aware this is the first such model. The cell scale model predicts that crypt invasion does not occur, but that mutated cells can invade the flat mucosa above neighbouring crypts. Analysis of in-vivo data is consistent with this prediction. The crypt as agent model predicts fields of ~41,000 crypts, in agreement with data in the literature, this corresponds to a field ~23mm in diameter. This project models pre-cancerous fields for the first time over a variety of scales, making specific novel predictions which are in agreement with in-vivo data where such data exist. Two agent based models were created to study the development of precancerous fields, one a model with cells as agents to study cell scale phenomena and the other with crypts as agents to allow processes to be studied on larger spatial and temporal scales. These models could potentially be used to refine clinic practice by predicting the required frequency of post-intervention monitoring of patients or the necessity of further intervention

Ikaite pseudomorphs in Neoproterozoic Dalradian slates record Earth’s coldest metamorphism

Calcite pseudomorphs have replaced euhedral ikaite (CaCO3.6H2O)porphyroblasts in Dalradian calcareous slates and metadolostones of western Scotland, with a volume decrease of at least 47%. Porphyroblast-fabric relationships indicate that the initial growth of ikaite post-dates a penetrative tectonic fabric developed during upright folding. This is the first reported occurrence of metamorphic ikaite porphyroblasts and points towards growth within the slates during an ultra-low temperature metamorphism with an exceptionally low geothermal gradient. This event is associated with the penetration of long-lived and extreme permafrost deep into sub aerially exposed bedrock during Neoproterozoic glaciation. The presence of the well preserved pseudomorphs within the Easdale slates of the Argyll group implies that a Neoproterozoic orogenic unconformity exists above the stratigraphic position of theserocks

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

Demographic and Phenotypic Effects of Human Mediated Trophic Subsidy on a Large Australian Lizard (Varanus varius): Meal Ticket or Last Supper?

Humans are increasingly subsidizing and altering natural food webs via changes to nutrient cycling and productivity. Where human trophic subsidies are concentrated and persistent within natural environments, their consumption could have complex consequences for wild animals through altering habitat preferences, phenotypes and fitness attributes that influence population dynamics. Human trophic subsidies conceptually create both costs and benefits for animals that receive increased calorific and altered nutritional inputs. Here, we evaluated the effects of a common terrestrial human trophic subsidies, human food refuse, on population and phenotypic (comprising morphological and physiological health indices) parameters of a large predatory lizard (∼2 m length), the lace monitor (Varanus varius), in southern Australia by comparison with individuals not receiving human trophic subsidies. At human trophic subsidies sites, lizards were significantly more abundant and their sex ratio highly male biased compared to control sites in natural forest. Human trophic subsidies recipient lizards were significantly longer, heavier and in much greater body condition. Blood parasites were significantly lower in human trophic subsidies lizards. Collectively, our results imply that human trophic subsidized sites were especially attractive to adult male lace monitors and had large phenotypic effects. However, we cannot rule out that the male-biased aggregations of large monitors at human trophic subsidized sites could lead to reductions in reproductive fitness, through mate competition and offspring survival, and through greater exposure of eggs and juveniles to predation. These possibilities could have negative population consequences. Aggregations of these large predators may also have flow on effects to surrounding food web dynamics through elevated predation levels. Given that flux of energy and nutrients into food webs is central to the regulation of populations and their communities, we advocate further studies of human trophic subsidies be undertaken to evaluate the potentially large ecological implications of this significant human environmental alteration

Prevention not cure: a review of methods to avoid sea lice infestations in salmon 1 aquaculture

The Atlantic salmon aquaculture industry still struggles with ectoparasitic sea lice despite decades of research and development invested into louse removal methods. In contrast, methods to prevent infestations before they occur have received relatively little research effort, yet may offer key benefits over treatment‐focused methods. Here, we summarise the range of potential and existing preventative methods, conduct a meta‐analysis of studies trialling the efficacy of existing preventative methods and discuss the rationale for a shift to the prevention‐focused louse management paradigm. Barrier technologies that minimise host–parasite encounter rates provide the greatest protection against lice, with a weighted median 76% reduction in infestation density in cages with plankton mesh ‘snorkels’ or ‘skirts’, and up to a 100% reduction for fully enclosed cages. Other methods such as geographic spatiotemporal management, manipulation of swimming depth, functional feeds, repellents and host cue masking can drive smaller reductions that may be additive when used in combination with barrier technologies. Finally, ongoing development of louse‐resistant salmon lineages may lead to long‐term improvements if genetic gain is maintained, while the development of an effective vaccine remains a key target. Preventative methods emphasise host resistance traits while simultaneously reducing host–parasite encounters. Effective implementation has the potential to dramatically reduce the need for delousing and thus improve fish welfare, productivity and sustainability in louse‐prone salmon farming regions.submittedVersio

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

In situ sea lice egg sterilization with UVC light

Sea-cage salmon farming creates ideal conditions for population growth of the salmon louse Lepeophtheirus salmonis, potentially leading to poor welfare and mortality in farmed salmon and nearby wild salmonids. Frequent delousing treatments are necessary, but current treatments have drawbacks in terms of financial cost, stress to stock, and/or environmental impacts. We tested whether 254 nm ultraviolet-C light (UVC) could function as a new treatment to reduce production of infective copepodids in infested sea-cages. In Experiment 1, we removed mature egg strings from female lice and exposed the egg strings to precise doses of UVC light. A total dose of 0.008 J cm-2 reduced copepodid production by 5 %, while a 95 % reduction occurred at 0.09 J cm-2. In Experiment 2, we exposed salmon with attached adult lice to UVC light while they swam freely in tanks over a 6 day period, achieving a dose of ~0.1 J cm-2. The treatment resulted in a 99 % reduction in copepodid production relative to control groups. However, UVC negatively impacted fish welfare, causing higher rates of cataracts and skin irritation. In Experiment 3, we tested the sensitivity of fish (without lice) to increasing doses of UVC light, and found that minor skin injuries occurred at >60 % effective doses, while cataracts began to develop at very low doses. We conclude that UVC should only be used with caution, either for treatment of waste water to prevent louse eggs and larvae entering the environment (e.g. after delousing), or for short periods of time in-cage to suppress lice reproduction until fish are harvested.publishedVersio

Changes in demersal wild fish aggregations beneath a sea-cage fish farm after the cessation of farming

Demersal, non-cryptic, wild fish were counted in replicate 100 m2 transects beneath a floating sea-cage fish farm and two nearby sandy locations at Gran Canaria (Canary Islands, eastern Atlantic) four times before and after the cessation of farming. Cessation of farming involved the removal of farmed fish and ceasing of the daily feeding, although farm structures (cages and moorings) remained. A “beyond-BACI” sampling design provided the framework to detect the effect of the cessation of farming, which produced qualitative and quantitative changes in the composition and structure of the fish assemblages beneath the sea-cage fish farm compared with two nearby controls. The aggregative effect on wild fish due to the existence of the farm decreased from approximately 50 times compared to nearby controls when the farm was in full operation to (large-sized mugilids), large benthic chondrichthyid rays and Pagellus spp. declined markedly at the fish farm after the cessation of farming, suggesting that the removal of daily feeding was responsible for their disappearance. In contrast, abundances of herbivores, benthic macro- and meso-carnivores were similar beneath the fish farm both before and after the cessation of farming. Benthic macro-carnivores, however, were more abundant beneath the sea-cages compared to control locations, supporting the hypothesis that the increase in the physical structure beneath farms plays a role in aggregating these species. Sparids occurred beneath the sea-cages only after the cessation of farming, while the two natural control locations did not show differences from before to after the cessation of farming. Overall, the results show that the wild fish assemblage beneath the farm partially changed after the cessation of farming to a more natural state, approaching the assemblages observed at the control sites

Sentinels in Salmon Aquaculture: Heart Rates Across Seasons and During Crowding Events

Advances in tag technology now make it possible to monitor the behavior of small groups of individual fish as bioindicators of population wellbeing in commercial aquaculture settings. For example, tags may detect unusual patterns in fish heart rate, which could serve as an early indicator of whether fish health or welfare is becoming compromised. Here, we investigated the use of commercially available heart rate biologgers implanted into 24 Atlantic salmon weighing 3.6 ± 0.8 kg (mean ± SD) to monitor fish over 5 months in a standard 12 m × 12 m square sea cage containing ∼6,000 conspecifics. Post tagging, fish established a diurnal heart rate rhythm within 24 h, which stabilized after 4 days. Whilst the registered tagged fish mortality over the trial period was 0%, only 75% of tagged fish were recaptured at harvest, resulting in an unexplained tag loss rate of 25%. After 5 months, tagged fish were approximately 20% lighter and 8% shorter, but of the similar condition when compared to untagged fish. Distinct diurnal heart rate patterns were observed and changed with seasonal day length of natural illumination. Fish exhibited lower heart rates at night [winter 39 ± 0.2 beats per min (bpm), spring 37 ± 0.2 bpm, summer 43 ± 0.3 bpm, mean ± SE] than during the day (winter 50 ± 0.3 bpm, spring 48 ± 0.2 bpm, summer 49 ± 0.2 bpm) with the difference between night and day heart rates near half during the summer (6 bpm) compared to winter and spring (both 11 bpm). When fish experienced moderate and severe crowding events in early summer, the highest hourly heart rates reached 60 ± 2.5 bpm and 72 ± 2.4 bpm, respectively, on the day of crowding. Here, if the negative sublethal effects on fish that carry tags (e.g., growth rate) can be substantially reduced, the ability to monitor diurnal heart rate patterns across seasons and detect changes during crowding events, and using heart rate biologgers could be a useful warning mechanism for detecting sudden changes in fish behavior in sea cages.publishedVersio