Biology subjects

Thompson, L.

Publications and source records attributed to Thompson, L..

24 records · Page 2Linked to original sources

bioRxiv2021

How much does it take to be old? Modelling the time since the last harvesting to infer the distribution of mature forests in France

AimThe distribution of overmature forests in metropolitan France is poorly known, with only a few well-studied prominent sites, and has never been evaluated countrywide. Here, we modelled French forest reserves time since the last harvesting operation - a proxy for forest maturity - then inferred the current statistical distribution of overmature forests (i.e. forests over 50 years without harvesting) in France. LocationMetropolitan France MethodsWe used inventories from forest reserves and managed forests to calibrate a generalised linear mixed model explaining the time since the last harvesting with selected structural attributes and environmental variables. We then projected this model on the independent National Forest Inventory dataset. We thus obtained an updated estimation of the proportion and a rough distribution of overmature forest stands in metropolitan France. ResultsWe found that high basal area of very large trees, high volumes of standing and downed deadwood, high diversity of tree-related microhabitats and more marginally diversity of decay stages best characterized the time since the last harvesting. Volumes of stumps and high density of coppices translating legacy of past forest management also distinguished more overmature plots. Our projection yielded an estimated 3% of French forests over 50 years without harvesting mostly located in more inaccessible areas (i.e. mountainous areas) and a promising proportion of future overmature forests if left unharvested. Main conclusionsOur study showed that the time since the last harvesting is a good proxy for a combination of stand structure attributes key in characterising overmature temperate forests. It gives the first robust statistical estimate of the proportion of overmature forests and may serve to report on their status in metropolitan France. Our method could be implemented at a larger spatial scale, notably in countries with accessible National Forest Inventory and calibration data, to produce indicators at international level.

ecology↗

bioRxiv2020

ENSO drives lateral separation of FAD-associated skipjack and bigeye tuna in the Western Tropical Pacific

Incidental capture of juvenile bigeye tuna in fish aggregating device (FAD)-associated purse seine fisheries targeting skipjack tuna have contributed significantly to the degradation of bigeye stocks in the Western Tropical Pacific (WTP) Ocean. One way to reduce this incidental catch is to simply limit purse seine fishing effort; however, skipjack tuna stocks are healthy and economically important to many small island nations in the region. Here we assess whether there is sufficient lateral separation of skipjack and bigeye within FAD-associated purse seine fisheries in the WTP to allow limiting bigeye catch while maintaining a robust skipjack fishery. Based on monthly 5{degrees}-longitude-by-5{degrees}-latitude catch and effort data, FAD-associated bigeye and skipjack catch per unit effort (CPUE) covary tightly throughout the WTP, such that lateral separation between the two species is generally small. There are, however, significant variations in the amount of separation over both space and time. Waters within the Party to the Nauru Agreement exclusive economic zones (EEZs) belonging to Palau, Solomon Islands, and Tuvalu regularly exhibit some of the smallest bigeye-to-skipjack catch ratios, especially during El Nino. In contrast, waters within Kiribatis Phoenix Islands EEZ regularly exhibit some of the largest bigeye-to-skipjack catch ratios, which are particularly high during La Nina. In general, El Nino lowers bigeye-to-skipjack catch ratios east of 170{degrees}E, while La Nina lowers bigeye-to-skipjack catch ratios west of 170{degrees}E. These ENSO-driven variations in separability are larger and more widespread than those driven by seasonality, due to larger associated variations in environmental conditions. Sea surface height anomalies may be particularly useful for demarcating the different environments preferred by skipjack and bigeye throughout the WTP. Sea surface temperatures, temperatures at 100 m, and thermocline depths may also help distinguish between the two species preferred habitats in many areas. These analyses can help better inform the complex decisions made by both fishers during operations and fisheries managers during creation of effective, dynamic policies to preserve bigeye stocks in the WTP. They also show that climate variability can have substantial effects on the spatial distributions of top pelagic predators and their interactions with one another.

ecology↗

bioRxiv2019

VIRAL DELIVERY OF GDNF PROMOTES FUNCTIONAL INTEGRATION OF HUMAN STEM CELL GRAFTS IN PARKINSONS DISEASE

The derivation of neurotransmitter and region-specific neuronal populations from human pluripotent stem cells (PSC) provides impetus for advancing cell therapies into the clinic. At the forefront is our ability to generate ventral midbrain (VM) dopaminergic (DA) progenitors, suitable for transplantation in Parkinsons disease (PD). Pre-clinical studies, however, have highlighted the low proportion of DA neurons within these grafts and their inferior plasticity by comparison to human fetal donor transplants. Here we sought to examine whether modification of the host environment, through viral delivery of a developmentally critical molecule, glial cell line-derived neurotrophic factor (GDNF), could improve graft survival, integration and function in Parkinsonian rodents. Utilising LMX1A- and PITX3-GFP hPSC reporter lines, we tracked the response of DA progenitors implanted into either a GDNF-rich environment, or in a second group, after a 3-week delay in onset of exposure. We found that early exposure of the graft to GDNF promoted survival of DA and non-DA cells, leading to enhanced motor recovery in PD rats. Delayed overexpression of intrastriatal GDNF also promoted motor recovery in transplanted rats, through alternate selective mechanisms including enhanced A9/A10 specification, increased DA graft plasticity, greater activation of striatal neurons and elevated DA metabolism. Lastly, transcriptional profiling of the grafts highlighted novel genes underpinning these changes. Collectively these results demonstrate the potential of targeted neurotrophic gene therapy strategies to improve human PSC graft outcomes.

neuroscience↗

bioRxiv2019

Optimized but not maximized cue integration for 3D visual perception

Reconstructing three-dimensional (3D) scenes from two-dimensional (2D) retinal images is an ill-posed problem. Despite this, our 3D perception of the world based on 2D retinal images is seemingly accurate and precise. The integration of distinct visual cues is essential for robust 3D perception in humans, but it is unclear if this mechanism is conserved in non-human primates, and how the underlying neural architecture constrains 3D perception. Here we assess 3D perception in macaque monkeys using a surface orientation discrimination task. We find that perception is generally accurate, but precision depends on the spatial pose of the surface and available cues. The results indicate that robust perception is achieved by dynamically reweighting the integration of stereoscopic and perspective cues according to their pose-dependent reliabilities. They further suggest that 3D perception is influenced by a prior for the 3D orientation statistics of natural scenes. We compare the data to simulations based on the responses of 3D orientation selective neurons. The results are explained by a model in which two independent neuronal populations representing stereoscopic and perspective cues (with perspective signals from the two eyes combined using nonlinear canonical computations) are optimally integrated through linear summation. Perception of combined-cue stimuli is optimal given this architecture. However, an alternative architecture in which stereoscopic cues and perspective cues detected by each eye are represented by three independent populations yields two times greater precision than observed. This implies that, due to canonical computations, cue integration for 3D perception is optimized but not maximized.\n\nAuthor summaryOur eyes only sense two-dimensional projections of the world (like a movie on a screen), yet we perceive the world in three dimensions. To create reliable 3D percepts, the human visual system integrates distinct visual signals according to their reliabilities, which depend on conditions such as how far away an object is located and how it is oriented. Here we find that non-human primates similarly integrate different 3D visual signals, and that their perception is influenced by the 3D orientation statistics of natural scenes. Cue integration is thus a conserved mechanism for creating robust 3D percepts by the primate brain. Using simulations of neural population activity, based on neuronal recordings from the same animals, we show that some computations which occur widely in the brain facilitate 3D perception, while others hinder perception. This work addresses key questions about how neural systems solve the difficult problem of generating 3D percepts, identifies a plausible neural architecture for implementing robust 3D vision, and reveals how neural computation can simultaneously optimize and curb perception.

neuroscience↗

bioRxiv2018

Real-time experimental control using network-based parallel processing

Modern neuroscience research often requires the coordination of multiple processes such as stimulus generation, real-time experimental control, as well as behavioral and neural measurements. The technical demands required to simultaneously manage these processes with high temporal fidelity limits the number of labs capable of performing such work. Here we present an open-source network-based parallel processing framework that eliminates these barriers. The Real-Time Experimental Control with Graphical User Interface (REC-GUI) framework offers multiple advantages: (i) a modular design agnostic to coding language(s) and operating system(s) that maximizes experimental flexibility and minimizes researcher effort, (ii) simple interfacing to connect measurement and recording devices, (iii) high temporal fidelity by dividing task demands across CPUs, and (iv) real-time control using a fully customizable and intuitive GUI. Testing results demonstrate that the REC-GUI framework facilitates technically demanding, behavior-contingent neuroscience research. Sample code and hardware configurations are downloadable, and future developments will be regularly released.

neuroscience↗

bioRxiv2017

Neurochondrin interacts with the SMN protein suggesting a novel mechanism for Spinal Muscular Atrophy pathology.

Spinal Muscular Atrophy (SMA) is an inherited neurodegenerative condition caused by reduction in functional Survival Motor Neurones Protein (SMN). SMN has been implicated in transport of mRNA in neural cells for local translation. We previously identified microtubule-dependant mobile vesicles rich in SMN and the splicing factor SmB, a member of the Sm protein family, in neural cells. By comparing the proteome of SmB to that of SmN, a neural-specific Sm protein, we now show that the essential neural protein neurochondrin (NCDN) interacts with Sm proteins and SMN in the context of mobile vesicles in neurites. NCDN has roles in protein localisation in neural cells, and in maintenance of cell polarity. NCDN is required for the correct localisation of SMN, suggesting they may both be required for formation and transport of trafficking vesicles. NCDN provides a potential therapeutic target for SMA together with, or in place of, those targeting SMN expression.

cell biology↗