Etude génétique et fonctionnelle de l’ataxie spastique autosomique récessive de Charlevoix-Saguenay (ARSACS)

ARSACS is a recessive autosomal neurodegenerative condition characterized by cerebellar ataxia, spastic paraplegia and demyelinating sensitivo-motor polyneuropathy. ARSACS is caused by mutations in the SACS gene identified in 2000. Since then, cases have been reported worldwide. SACS encodes sacsin, a protein of still unknown function in spite of the description of numerous protein domains and of a recent focus on a potential implication in the regulation of mitochondrial physiology. Aims of this thesis were to identify new mutations in a large population of ataxic patients and then to functionally analyze their cellular effects in the mitochondrial compartment. We identified 2 variants in SACS in 10% of analyzed cases collected through the international SPATAX network. We also confirmed mutations in SACS in 5 patients identified using next-generation sequencing in the ATXAIC project, and studied a last case harbouring a large deletion encompassing the entire SACS gene identified by pangenomic CGH-array. For functional analyses, primary cultures of fibroblasts were obtained in 11 patients. A drastic and recurrent alteration of the mitochondrial network was observed in all patients except one. These anomalies seem very useful for the diagnosis of ARSACS when molecular results are difficult to interpret (missense variants). We therefore propose a grading diagnostic definition using clinical, genetic and cellular criteria for ARSACS. Finally, we started to study the mechanistic of the mitochondrial function of sacsin. Our preliminary data may suggest a potential role at the mitochondrial turn over level.ARSACS est une maladie neurodégénérative autosomique récessive caractérisée par une ataxie cérébelleuse, une paraplégie spastique et une polyneuropathie sensitivo-motrice démyélinisante. Le gène SACS, responsable de la maladie, a été identifié en 2000. Depuis, de nombreux cas ont été décrits dans le monde entier. Le gène SACS code pour la sacsine, dont la fonction reste inconnue malgré l’identification de nombreux domaines protéiques et surtout la description récente d’un rôle dans la physiologie mitochondriale. Les objectifs de ma thèse étaient d’identifier des mutations dans SACS au sein d’une large cohorte de patients atteints d’ataxie grâce à plusieurs collaborations puis d’étudier leurs effets au niveau du compartiment mitochondrial en utilisant essentiellement des cellules de malades. Nous avons pu identifier 2 variants de SACS dans 10% des cas analysés recrutés via le réseau international SPATAX. Nous avons parallèlement confirmé les mutations de SACS identifiées par séquençage haut-débit chez 5 autres patients via le PHRC ATAXIC et analysé un dernier cas porteur d’une délétion complète de SACS découverte par CGH-array pangénomique. Des cultures primaires de fibroblastes ont été obtenues chez 11 patients pour l’analyse fonctionnelle. Une altération de la morphologie des mitochondries a été observée chez tous les patients sauf un. Ces anomalies du réseau mitochondrial semblent très utiles pour cheminer vers le diagnostic d’ARSACS qui peut s’avérer complexe dans les situations non exceptionnelles où les résultats moléculaires sont délicats à interpréter (mutations faux-sens). Nous proposons une définition graduelle d’ARSACS reposant sur des critères cliniques, génétiques et cellulaires intégrant ces anomalies du réseau. Enfin, nous avons débuté l’exploration des mécanismes impliqués dans cette altération de la dynamique du réseau mitochondrial. Nos résultats préliminaires font évoquer une action potentielle de la sacsine au niveau du renouvellement des mitochondries

Corrigendum to ‘‘Distribution and environmental limitations of an amphibian pathogen in the Rocky Mountains, USA’’ [Biological Conservation 141 (2008) 1484–1492]

The author regrets that in the above published paper the following error occurred: In our recently published paper, ‘‘Distribution and environmental limitations of an amphibian pathogen in the Rocky Mountains, USA’’, we erroneously included the paper by J. Bosch et al. (2006), ‘‘Climate change and outbreaks of amphibian chytridiomycosis in a montane area of Central Spain: is there a link?’’ in a list of studies from the tropics. Clearly Dr. Bosch and colleagues worked in the temperate zone at a latitude very similar to that in our study suggesting that further investigation of additional similarities between the two sites might be useful

Where are Long-Toed Salamanders Found in a Game of Hide-And-Seek With Trout?

In many alpine lakes, trout have been introduced for recreational fishing and have replaced native amphibians as top predators. In these systems, trout are associated with reducing the abundance of amphibians and have extirpated populations of long-toed salamanders ( Ambystoma macrodactylum) from many lakes. Although rare, salamander coexistence with trout may occur in some lakes where habitat characteristics such as emergent vegetation and physical barriers are present, as these environments can provide refugia from predation. We sought to identify what key habitat features might allow this co-occurrence. We sampled seven lakes with salamanders and fish and seven with only salamanders in northwestern Montana between July and August 2012. We used minnow traps to capture salamander larvae and we quantified habitat characteristics (e.g., vegetation density, structural complexity) where salamanders were captured. We compared capture rates and habitat characteristics to determine whether lakes with and without fish differed. Preliminary results suggest that salamander capture rates were higher in lakes with fish (33%, 95% CI = 13-84%), but salamanders were smaller, as larvae had 68 percent shorter tails (51-91%) in lakes with fish. Despite these differences, we did not detect any differences in habitat characteristics. Unless minnow traps were used as refugia, our findings suggest that salamanders utilize similar habitat in these lakes regardless of the presence of fish. Future work will examine factors influencing salamander growth and tail length and determine whether adding habitat complexity is an effective strategy to facilitate coexistence of salamanders and fish

Characterizing the Distribution of an Endangered Salmonid Using Environmental DNA Analysis

Determining species distributions accurately is crucial to developing conservation and management strategies for imperiled species, but a challenging task for small populations. We evaluated the efficacy of environmental DNA (eDNA) analysis for improving detection and thus potentially refining the known distribution of Chinook salmon (Oncorhynchus tshawytscha) in the Methow and Okanogan Subbasins of the Upper Columbia River, which span the border between Washington, USA and British Columbia, Canada. We developed an assay to target a 90 base pair sequence of Chinook DNA and used quantitative polymerase chain reaction (qPCR) to quantify the amount of Chinook eDNA in triplicate 1-L water samples collected at 48 stream locations in June and again in August 2012. The overall probability of detecting Chinook with our eDNA method in areas within the known distribution was 0.77 (±0.05 SE). Detection probability was lower in June (0.62, ±0.08 SE) during high flows and at the beginning of spring Chinook migration than during base flows in August (0.93, ±0.04 SE). In the Methow subbasin, mean eDNA concentration was higher in August compared to June, especially in smaller tributaries, probably resulting from the arrival of spring Chinook adults, reduced discharge, or both. Chinook eDNA concentrations did not appear to change in the Okanogan subbasin from June to August. Contrary to our expectations about downstream eDNA accumulation, Chinook eDNA did not decrease in concentration in upstream reaches (0–120 km). Further examination of factors influencing spatial distribution of eDNA in lotic systems may allow for greater inference of local population densities along stream networks or watersheds. These results demonstrate the potential effectiveness of eDNA detection methods for determining landscape-level distribution of anadromous salmonids in large river systems

Investigating Coexistence Between Trout and Long-Toed Salamanders and the Indirect Effects of Fish Predators

In many, formerly fishless lakes in western North America, trout have been introduced for recreational fishing, replacing native amphibians as top predators. Trout are associated with reducing the abundance of amphibians and have extirpated populations of long-toed salamanders (Ambystoma macrodactylum). Salamanders and trout may coexist in some lakes, as larvae often are able to alter foraging behavior, use of open water, and time in refugia in response to predatory cues. However, salamanders are still subject to attacks and may have different body morphology in environments with fish. We sought to estimate minimum population sizes of long-toed salamanders, as well as investigate indirect effects of fish on salamander morphology. We sampled lakes with and without fish in northwestern Montana during the summers of 2012 and 2013. We caught salamander larvae using minnow traps, took several body measurements, and compared capture rates and morphological measurements between lakes with and without fish. Preliminary results suggest that more salamanders were captured per trap in lakes with fish (1.8 salamanders/trap, 95% CI = 1.3-2.4), compared to lakes without fish (0.58 salamanders/trap, 0.36-0.81), which could reflect higher population sizes or increased use of traps as refugia. However, salamanders in lakes with fish were smaller: they weighed less, had shorter snout-vent lengths, and had shorter and narrower tails. Even if salamanders are more abundant in lakes with fish, growth may be reduced. Further research into the coexistence of long-toed salamanders and trout may aid in developing conservation strategies for these and other amphibians affected by novel predators

A Post-Fire Index For Describing Mixed Severity Outcomes After Wildfire

Kimmins (1997) argues that “words” and their correct usage are important and that the “careless use of language often causes confusion and misunderstanding and is a factor in many conflicts.” The public often lacks the technical knowledge to understand and interpret the use of inconsistent terminology and each discipline within resource science and management has developed their own definitions and application of specific terms. The fire community is no different. The only consistent component in the fire literature is the interchangeable use of the terms fire intensity, fire severity, and burn severity. Moreover, within each of these definitions, the terms low, moderate, and high severity and/or intensity and associated definitions are also inconsistent. Although some recognize the inconsistent use in terminology to describe different aspects of fire behavior and effects, discussions tend to favor the continuation of the incompatible use of terms. Furthermore, some suggest that a severity description should be specific to a particular interest, leaving it up to the reader to decipher the meaning of the terms. The objective of this oral presentation is to present a post-fire index (PFI) for temperate forests designed to diminish the inconsistent application of severity. We developed this index by synthesizing current severity literature and its potential relation to chemical, physical, and biological responses. We then validated the index using actual data collected post-fire from landscapes that contain mixed-severity fire regimes within the cold, moist, and dry forests within the Rocky Mountains of the United States

Occupancy and Abundance of American Badgers and Piute Ground Squirrels in the Sagebrush-Steppe: Implications of the Fire-Cheatgrass Cycle

Sagebrush-steppe is experiencing vast changes due to biological invasions and changing fire characteristics. Understanding how these changes influence functionally important animals is essential for ecosystem management. American Badgers (Taxidea taxus) are an apex predator and ecosystem engineer within sagebrush ecosystems. Piute Ground Squirrels (Urocitellus mollis) are also an ecosystem engineer as well as an essential prey source for many predators.  Our objective was to evaluate the relative importance of large-scale changes, abiotic processes, and biotic processes on badgers and ground squirrels. We samples 163 1-ha plots across a gradient of burn histories within a 1,962 km2 area in Southern Idaho, USA. At each plot, we characterized ground squirrel and badger occupancy, ground squirrel relative abundance, and many environmental variables. We used information-theoretic approaches to evaluate competing hypotheses concerning occupancy of ground squirrels and badgers, and ground squirrel relative abundance. Results suggest that ground squirrel occupancy was positively associated with abiotic characteristics (e.g., higher precipitation and finer textured soil). Badger occupancy was positively associated with ground squirrel occupancy and agriculture. Relative abundance of ground squirrels was positively associated with finer textured soils, but negatively associated with cheatgrass (Bromus tectorum), fire frequency, agriculture and shrubs. Managers can focus restoration efforts on areas with high cheatgrass and shrub cover, if ground squirrels are a management objective. These results support previous hypotheses suggesting abiotic processes are important for herbivore occupancy. However, we provide support that a combination of abiotic, biotic and disturbance processes are important for mesocarnivore occupancy and herbivore abundance

Forecasting Natural Regeneration of Sagebrush After Wildfires Using Population Models and Spatial Matching

Context Addressing ecosystem degradation in the Anthropocene will require ecological restoration across large spatial extents. Identifying areas where natural regeneration will occur without direct resource investment will improve scalability of restoration actions. Objectives An ecoregion in need of large scale restoration is the Great Basin of the Western US, where increasingly large and frequent wildfires threaten ecosystem integrity and its foundational shrub species. We develop a framework to forecast where postwildfire regeneration of sagebrush cover (Artemisia spp.) is likely to occur within the burnt areas across the region (\u3e900,000 km2). Methods First, we parameterized population models using Landsat satellite-derived time series of sagebrush cover. Second, we evaluated the out-of-sample performance by predicting natural regeneration in wildfres not used for model training. This model assessment reproduces a management-oriented scenario: making restoration decisions shortly after wildfires with minimal local information. Third, we asked how accounting for increasingly fine-scale spatial heterogeneity could improve model forecasting accuracy. Results Regional-level models revealed that sagebrush post-fire recovery is slow, estimating \u3e 80-year time horizon to reach an average cover at equilibrium of 16.6% (CI95% 9–25). Accounting for wildfre and within-wildfre spatial heterogeneity improved out-ofsample forecasts, resulting in a mean absolute error of 3.5 ± 4.3% cover, compared to the regional model with an error of 7.2 ± 5.1% cover. Conclusions We demonstrate that combining population models and non-parametric spatial matching provides a fexible framework for forecasting plant population recovery. Models for population recovery applied to Landsat-derived time series will assist restoration decision-making, including identifying priority targets for restoration

The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology

1. Knowledge of species distribution is critical to ecological management and conservation biology. Effective management requires the detection of populations, which can sometimes be at low densities and is usually based on visual detection and counting. 2. Recently, there has been considerable interest in the detection of short species-specific environmental DNA (eDNA) fragments to allow aquatic species monitoring within different environments due to the potential of greater sensitivity over traditional survey methods which can be time-consuming and costly. 3. Environmental DNA analysis is increasingly being used in the detection of rare or invasive species and has also been applied to eDNA persistence studies and estimations of species biomass and distribution. When combined with next-generation sequencing methods, it has been demonstrated that entire faunas can be identified. 4. Different environments require different sampling methodologies, but there remain areas where laboratory methodologies could be standardized to allow results to be compared across studies. 5. Synthesis and applications. We review recently published studies that use eDNA to moni- tor aquatic populations, discuss the methodologies used and the application of eDNA analysis as a survey tool in ecology. We include innovative ideas for how eDNA can be used for conservation and management citing test cases, for instance, the potential for on-site analyses, including the application of eDNA analysis to carbon nanotube platforms or laser transmission spectroscopy to facilitate rapid on-site detections. The use of eDNA monitoring is already being adopted in the UK for ecological surveys

Cedar Grove, Orange County : an action-oriented community diagnosis : findings and next steps of action

During the 2000-2001 academic year, four students from the Department of Health Behavior and Health Education at the School of Public Health at the University of North Carolina Chapel Hill, under the guidance of a preceptor from the Orange County Health Department and faculty of their program, conducted an Action Oriented Community Diagnosis of Cedar Grove, Orange County, North Carolina. The purpose of this document is to summarize that process. A brief description of the Cedar Grove community is presented to provide background information about the context of the process. This is followed by a description of the qualitative methodology used by the student team to conduct the diagnosis. Results of the process, including a discussion of themes identified as important by community members and a description of the community meeting, the concluding event of the diagnosis, are presented. This is followed by a summary of future plans made by community members and service providers as well as recommendations for future action made by the student team. While many valid and important concerns were identified through the diagnosis, the Cedar Grove community has a history of successful problem-solving. It is our hope that this process has renewed the interest of community members and service providers alike in working together to address issues related to the future vitality of Cedar Grove. We hope that this document will be of use to them in those efforts.Master of Public Healt