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Biology subjects

Dodd, J.

Publications and source records attributed to Dodd, J..

3 recordsLinked to original sources

GelGenie: an AI-powered framework for gel electrophoresis image analysis

Gel electrophoresis is a ubiquitous laboratory method for the separation and semi-quantitative analysis of biomolecules. However, gel image analysis principles have barely advanced for decades, in stark contrast to other fields where AI has revolutionised data processing. Here, we show that an AI-based system can automatically identify gel bands in seconds for a wide range of experimental conditions, far surpassing the capabilities of current software. We used a dataset containing 500+ images of manually-labelled gels to train various U-Nets to accurately identify bands through segmentation, i.e. classifying pixels as band or background. When applied to gel electrophoresis data from other laboratories, our system generated results that quantitatively matched those of the original authors. We have publicly released our models through GelGenie, an open-source application that allows users to extract bands from gel images on their own devices, with no expert knowledge or experience required.

molecular biology↗

Spatial ecology and population dynamics of brown trout Salmo trutta L. in reservoirs and headwater tributaries

This investigation compared the spatial ecology and population dynamics of brown trout Salmo trutta L. between reservoirs with (impact; Langsett Reservoir) and without (control; Grimwith Reservoir) barriers to fish movements into afferent headwater tributaries, including the effectiveness of a fish pass to remediate connectivity. Passive Integrated Transponder (PIT) telemetry revealed fish that emigrated from Langsett and Grimwith reservoirs were 1-3 and 0-2 years old, respectively, and predominantly did so in March-May and October-December in both. Weirs at Langsett Reservoir (emigration rate = 26%) appeared to thwart emigration relative to Grimwith Reservoir (emigration rate = 85%). Acoustic telemetry (2D positions) in the impact reservoir revealed the largest home range was in October - December (monthly K95 {+/-} S.D. up to 26.9 {+/-} 6.69 ha in November), activity was influenced by both month and time of day, and fish occupied shallow water depths (relative to reservoir depth), especially at night. Large proportions of brown trout tagged in Grimwith and Langsett reservoirs (42.9% and 64.1%, respectively) and fish that emigrated (37.2% and 27.7%, respectively) were detected moving upstream into tributaries. At both reservoirs, peak immigration for 3- and [≥]4-year-old fish occurred in October-December, although upstream movements occurred throughout the year and by all age classes. Three brown trout passed upstream of each of the weirs on River Little Don (prior to fish pass construction; 3% of those that approached from downstream) and Thickwoods Brook (throughout the study; 2%). Overall fish pass solution passage efficiency was 14% but was higher for 2- and 3-year-old fish (32%), which was comparable to fish translocated from upstream (33%). Passage predominantly occurred at lower river levels than fish pass entrance / attraction, which was also lower than during approaches to the weir. A Before-After Control-Impact (BACI) design found that although juvenile (0+, but not >0+) brown trout densities were lower after fish pass construction, the reduction was significantly less than at control sites, i.e., the fish pass had a positive effect. Overall, this investigation significantly furthers our understanding of brown trout spatial ecology and population dynamics in reservoirs and headwater tributaries.

ecology↗

Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord

Spinal neurons are highly heterogeneous in location, transcriptional identity and function. To understand their contributions to sensorimotor circuits, it is essential to map the positions of identified subsets of neurons in relation to others throughout the spinal cord (SC), but we lack tools for whole SC sample preparation, imaging and in toto analysis. To overcome this problem, we have (1) designed scaffolds (SpineRacks) that facilitate efficient and ordered cryo-sectioning of the entire SC in a single block, (2) constructed a 3D reference atlas of adult mouse SC and (3) developed software (SpinalJ) to register images of sections and for standardized analysis of cells and projections in atlas space. We have verified mapping accuracies for known neurons and demonstrated the usefulness of this platform to reveal unknown neuronal distributions. Together, these tools provide high-throughput analyses of whole mouse SC and enable direct comparison of 3D spatial information between animals and studies.

neuroscience↗