Leigh syndrome: One disorder, more than 75 monogenic causes

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137543/1/ana24551_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137543/2/ana24551.pd

Paddock scale modelling to assess effectiveness of agricultural management practice in improving water quality in the Great Barrier Reef Catchments

Agriculture in the catchment areas adjacent to the World Heritage listed Great Barrier Reef (GBR) Marine Park generates pollutants that are a concern for the health of the Reef. Under the Paddock to Reef Integrated Monitoring, Modelling and Reporting program (P2R) of the Reef Plan, the impacts of improved agricultural management practices on water quality entering the GBR are modelled to evaluate the effectiveness of Government water quality improvement policies. The Source Catchments modelling framework estimates loads of pollutants entering the GBR lagoon from rivers. However, Source Catchments does not have the capacity to represent the collection of management practices available to farmers that affect water quality in runoff and drainage at a paddock scale. Therefore, paddock scale agricultural systems models were used to demonstrate the effects of management practice adoption and to provide input to the catchment scale models. Paddock scale models were used because they represent a level of process detail compatible with the management practice investments and implementation on-ground. A fit-for-purpose modelling approach was used, where the paddock model most suited to a given land use and/or water quality pollutant was applied. Three one-dimensional agricultural systems models were employed; HowLeaky in grains, APSIM in sugarcane with HowLeaky post-processing for herbicides and phosphorous and GRASP in grazing lands. These models share similar soil water balance, ground cover and runoff sub-models. However, they vary in the level of detail, particularly in terms of representing crop growth and in the processes considered, such as pesticide degradation and export. In grains and sugarcane cropping, the pollutant time-series (e.g. load per day per unit area) in the Source Catchments models was replaced with an output time-series from HowLeaky or APSIM for each soil-climate spatial combination. Management practices were grouped into systems classed as A, B, C or D. The proportion of each of these management systems contributing to the modelled loads was adjusted to reflect data on the prevalence of adoption of improved management practices in the GBR catchment. In grazing lands, GRASP pasture utilisation and ground cover time-series outputs were interrogated to derive relationships between changes in grazing system management and changes in the USLE C-factors. The USLE is used to predict hillslope erosion in the Source Catchments model. Scaling indices derived from GRASP outputs were used to adjust the USLE C-factors applied in Source Catchments where management practices had changed. The P2R program has demonstrated the effectiveness of linking paddock scale models or emergent models derived from them with catchment scale models. This has enabled detailed management options to be simulated to investigate broad scale water quality impacts of the adoption of improved agricultural practices

Chalk cliff retreat in East Sussex and Kent 1870s to 2001

The retreat of chalk cliffs fringing the eastern English Channel contributes shingle to the beaches which helps to protect the cliffs and slow down erosion. Conversely, cliff retreat endangers settlements and infrastructure on the clifftop. Rates of retreat have been calculated by a variety of methods over the past century, but no attempt has been made to provide a complete coverage that allows for a true comparison of retreat rates over the entire coastline. Using historic maps and recent orthophotos, cliff retreat rates have been calculated for consecutive 50 m sections of chalk cliff along the English side of the entire eastern English Channel for a period of 125 years. The chalk cliffs of East Sussex erode at an average rate of 0.25 - 0.3 m y−1 while those in Kent at a rate of 0.1 m y−1

Development and Evaluation of Methods for Surveying Fish Populations in Nearshore Waters

Nearshore areas provide critical habitat for a range of fish species targeted by commercial and recreational fisheries, both of which make an important contribution to local economies in rural areas. However, established trawl survey methods are not suited to many nearshore areas, owing to shallow depths, obstructions on the sea bed or vulnerable habitats, so there is a lack of information on fish abundance in these areas. The aim of the present project was to develop and test survey methods applicable to Scottish inshore waters, focussing on baited underwater cameras, fish traps, systematic rod-and-line surveys and observations of fish bycatch in crustacean trap fisheries, and to carry out associated studies of fish movements. A lightweight baited underwater camera system was developed that could be deployed by two persons from inshore fishing vessels and small boats. The system consisted of a digital camera and strobes in underwater housings, mounted on a frame of aluminium alloy tubing, suspended above the seabed by sub-surface floats on one leg of a J-shaped mooring. The camera was baited with oily fish and a standardized 1 hour deployment period was used, to minimize variability in results due to changing tidal currents and bait degradation. Photographs were taken at 30 second intervals throughout the deployment period. On retrieval, the photographs were examined to derive indices of fish abundance, such as the time to first arrival of particular species (TFA) and the maximum number of individuals seen in the field of view at any time during the deployment (MaxN). The BUC system was developed and tested in the Firth of Clyde and then deployed at a range of other locations in Lamlash Bay, Arran, the Firth of Lorn, the Sound of Mull, Loch Sunart, Loch Etive, around Skye, Galloway and in Orkney. The BUC system was successfully deployed from a range of types of vessel in depths down to 40 m. Over thirty species of fish were recorded in total, including species of commercial interest, with lesser spotted dogfish, Scyliorhinus canicula, being the most commonly recorded. The number of species and indices of abundance were highest at sites on the Galloway peninsula. When compared within a single area, BUC detected more species than angling or fish traps, but less than in visual transects by SCUBA divers. BUC shows great potential as a cost-effective survey method, able to show relative differences in abundance between areas. It is likely that it would also be effective in detecting temporal trends, though this was outside the scope of the present project. A Norwegian design of collapsible cod trap, Roscoff traps designed for common prawns and Norway lobster creels were investigated as fish traps. There were differences in catch rates and species composition related to the trap design. Roscoff traps appeared to be suitable for sampling juvenile cod (Gadus morhua) in complex habitat in shallow water, whereas collapsible cod traps are suitable for larger fish, but need to be fished in greater numbers to obtain sufficient data. Creel fisheries were surveyed by questionnaire and by on-board catch sampling. A range of fish species is taken as bycatch in creels, with some obvious differences in species composition between crab fishing and Norway lobster fishing in relation to the depths and ground types fished. The present results suggest that the catch rates of commercial fish species may be too low for creeling to be a useful way of monitoring fish stocks, but sampling throughout the year in different areas would be desirable to assess this more fully. A small-scale pilot study in Galloway indicated some potential for rod-and-line surveys to generate useful information on the abundance of certain fishes. The Scottish Sea Angling Conservation Network and the Scottish Shark Tagging Project already collect information on catches of angling target species and on tagging and recaptures of tagged fish. This would be augmented by encouraging anglers to submit returns with an indication of fishing duration even when they have not caught anything. However, we were unsuccessful in recruiting volunteers to participate in a randomized angling survey. Further work is required to develop statistically robust angling surveys in which volunteer anglers would be willing to participate. Experience indicates that payment of expenses would be required for volunteers to agree to fish according to a survey protocol. To study movements of a species of interest to recreational sea anglers, spurdog (Squalus acanthias), ten specimens in Loch Etive were tagged with data storage tags designed to record water temperature and depth. To date, one tag has been recovered and the downloaded data shows an interesting pattern of nocturnal movements into shallow water. More information should become available when more of the tagged spurdog are recaptured. The following recommendations arise from the present study: To improve our understanding of baited methods of surveying fish and to develop improved estimates of abundance, modelling studies of bait odour dispersal and fish responses are required, building on previous work in this area. Further trials of baited underwater cameras at different sites and under different conditions are required to assess the degree of variability in the different types of abundance index that can be derived. Further work to compare different survey methods is required at sites with greater fish abundance, e.g. at sites around the Galloway peninsula. A BUC system with greater depth limit (e.g. 200 m) should be developed to extend the range of habitats in which it can be used to include other species of interest. Further work is required to assess the size and species selectivity of different designs of fish trap. An intensive pilot survey of an area of interest, such as an actual or proposed marine protected area, by BUC and fish traps would provide a good test of the ability of these methods to generate data of use to inshore fishery managers and conservation interests. Seasonal sampling of fish bycatch in Norway lobster and crab creel fisheries is desirable to further assess the potential for creel fisheries to be used to monitor fish populations. Ongoing analysis of recreational sea-angling catch and tagging records should be encouraged and supported by Marine Scotland. There should be continued engagement between recreational sea-anglers and fishery scientists in Marine Scotland and universities

Biochemical and molecular diagnosis of mitochondrial respiratory chain disorders

AbstractBiochemical diagnosis of mitochondrial respiratory chain disorders requires caution to avoid misdiagnosis of secondary enzyme defects, and can be improved by the use of conservative diagnostic criteria. Pathogenic mutations causing mitochondrial disorders have now been identified in more than 30 mitochondrial DNA (mtDNA) genes encoding respiratory chain subunits, ribosomal- and t-RNAs. mtDNA mutations appear to be responsible for most adult patients with mitochondrial disease and approximately a quarter of paediatric patients. A family history suggesting maternal inheritance is the exception rather than the norm for children with mtDNA mutations, many of whom have de novo mutations. Prenatal diagnosis and pre-implantation genetic diagnosis can be offered to some women at risk of transmitting a mtDNA mutation, particularly those at lower recurrence risk. Mutations in more than 30 nuclear genes, including those encoding for respiratory chain subunits and assembly factors, have now been shown to cause mitochondrial disorders, creating difficulties in prioritising which genes should be studied by mutation analysis in individual patients. A number of approaches offer promise to guide the choice of candidate genes, including Blue Native-PAGE immunoblotting and microarray expression analysis

Converting oak woodland or savanna to vineyards may stress groundwater supply in summer

Water resources are important to land-use planning, especially in regions where converting native oak woodlands or savannas to wine grape vineyards may affect the amount of water available for restoring salmon runs. Research has shown that woodland conversion to grasslands (for possible rangeland grazing) leads to greater and more sustained stream flow and groundwater recharge; however, little information is available about woodland conversion to vineyards. To inform resource managers and planners, we developed a water balance model for soil and applied it to vineyards, native oak woodlands and annual grasslands to evaluate their relative use of groundwater. We applied the model to Sonoma County, using climate data from 1999 to 2011, and determined that oak tree canopy coverage of 40% to 60% results in annual groundwater extraction equivalent to that of an established irrigated vineyard. However, vineyard groundwater use far exceeded that of oak woodlands in late summer to early fall, which could further stress already affected groundwater resources. We also evaluated the prediction sensitivity of the model to key parameters associated with rain levels, soil water-holding capacity and irrigation management

Recruitment of a critically endangered sawfish into a riverine nursery depends on natural flow regimes

The freshwater sawfish (Pristis pristis) was recently listed as the most Evolutionarily Distinct and Globally Endangered (EDGE) animal. The Fitzroy River in the remote Kimberley region of north-western Australia represents a significant stronghold for the species, which uses the freshwater reaches of the river as a nursery. There is also mounting pressure to develop the water resources of the region for agriculture that may substantially affect life history dynamics of sawfish in this system. However, the relationship between hydrology and population dynamics of freshwater sawfish was unknown. We used standardized catch data collected over 17 years to determine how wet season volume influences recruitment of freshwater sawfish into their riverine nursery. Negligible recruitment occurred in years with few days of high flood levels (above 98th percentile of cease-to-flow stage height), and relatively high recruitment occurred in years with 14 or more days of high flood levels. This relationship is indicative of a distinct boom-or-bust cycle, whereby freshwater sawfish rely almost entirely on the few years with large wet season floods, and the brief periods of highest water levels within these years, to replenish juvenile populations in the Fitzroy River nursery. This has direct implications for sustainable water resource management for the Fitzroy River basin in order to preserve one of the last known intact nursery habitats for this globally threatened species

Scallop swimming kinematics and muscle performance: modelling the effects of "within-animal" variation in temperature sensitivity

Escape behaviour was investigated in Queen scallops (Aequipecten opercularis) acclimated to 5, 10 or 15 degrees C and tested at their acclimation temperature. Scallops are active molluscs, able to escape from predators by jet-propelled swimming using a striated muscle working in opposition to an elastic hinge ligament. The first cycle of the escape response was recorded using high-speed video ( 250 Hz) and whole-animal velocity and acceleration determined. Muscle shortening velocity, force and power output were calculated using measurements of valve movement and jet area, and a simple biomechanical model. The average shortening speed of the adductor muscle had a Q(10) of 2.04, significantly reducing the duration of the jetting phase of the cycle with increased temperature. Muscle lengthening velocity and the overall duration of the clap cycle were changed little over the range 5 - 15 degrees C, as these parameters were controlled by the relatively temperature-insensitive, hinge ligament. Improvements in the average power output of the adductor muscle over the first clap cycle ( 222 vs. 139 W kg(-1) wet mass at 15 and 5 degrees C respectively) were not translated into proportional increases in overall swimming velocity, which was only 32% higher at 15 degrees C ( 0.37m s(-1)) than 5 degrees C (0.28 m s(-1))

Ontogenetic Variation in Movements and Depth Use, and Evidence of Partial Migration in a Benthopelagic Elasmobranch

Tope (Galeorhinus galeus) is a highly mobile elasmobranch in the temperate to subtropical northeast Atlantic. It is highly migratory and has been shown to display complex movement patterns, such as partial migration, in the southern hemisphere. In the northeast Atlantic, previous mark-recapture studies have struggled to identify movement patterns and the species behavior is poorly described, yet identification of migratory behaviors and habitats of importance for the species is of paramount importance for effective management. Here, we combined fisheries independent survey data with mark-recapture (MR) data to investigate the distribution of different age classes of tope across the northeast Atlantic. We further investigated depth use in detail with archival electronic tags and a pop-up satellite archival tag (PSAT). We suggest previous studies struggling to find consistent movement patterns using MR data were confounded by a combination of site fidelity, partial migration by females, and increasing depth and home range of juveniles. Survey and MR data showed immature tope <40 cm were caught exclusively in continental shelf waters <45 m deep, showing a significant relationship between habitat depth and total length. Immature individuals seemed to remain on the continental shelf, while mature tope of both genders were caught in both shelf and offshore waters. This use of deeper water habitats by mature tope was further supported by archival tags, which indicated individuals use both shallow (<200 m depth) and deep-water habitats, diving to depths of 826 m; the deepest record for this species. The PSAT tag tracked the horizontal movements of an adult male, which confirmed utilization of both shallow inshore and deep offshore habitats. Most tope remained within 500 km of their tagging site, although some mature females had a larger, more southerly range, including connectivity with the Mediterranean. This study clearly demonstrates the highly migratory habits of tope, and suggests larger individuals divide their time between shallow and deep-water habitats. It shows the northeast Atlantic tope population should benefit from consistent management throughout its range