bioRxiv Science⌕ Search

Biology subjects

Schneider, S. A.

Publications and source records attributed to Schneider, S. A..

3 recordsLinked to original sources

A pilot computer-vision model trained to identify slide-mounted scale insect pests from the family Rhizoecidae

The emerging field of image classification using computer vision has yet to address a rather challenging group of insect pests--soft-bodied insects that are preserved on microscope slides. This includes many notoriously invasive herbivores that have a significant impact on agriculture, such as members of the hemipteran suborder Sternorrhyncha. Using root mealybugs (Hemiptera: Rhizoecidae) as a test case, we gathered high-resolution extended depth of field images from museum specimens and trained a convolutional neural network (CNN) to identify and distinguish among 16 root mealybug species that are encountered as agricultural pests in plant quarantine or greenhouses. A pretrained EfficientNetV2-M model was trained using BioEncoder. Our dataset contained 1,607 images, with 41 to 239 images per category. Performance was improved through the adoption of augmentation techniques. Upon completion of training, the model achieved macro precision, recall, and F1 scores of 80.1%, 79.3%, and 79.1%, respectively. The model demonstrated classification metrics >= 80% for seven species. Gradient-weighted Class Activation Mapping (Grad-CAM) was used to visualize the morphological features associated with the test-image classification. Grad-CAM images highlighted meaningful diagnostic features to distinguish among species rather than focusing on uninformative visual artifacts or specimen damage, demonstrating the models utility for identification purposes. The results suggest that further development of the model should incorporate at least 200 training images per species with a minimum resolution of 600x600 pixels. The model was designed to be adaptable; images can be added to improve its performance, and more species can be incorporated as specimens become available, expanding on the taxonomic breadth of its application. Computer-vision identification tools have the potential to enhance rapid response capabilities in plant quarantine at ports-of-entry in the United States and globally.

zoology↗

Loss of NPC1 enhances phagocytic uptake and impairs lipid trafficking in microglia

Niemann-Pick type C disease is a rare neurodegenerative disorder mainly caused by mutations in Npc1, resulting in abnormal late endosomal/lysosomal lipid storage. Although microgliosis is a prominent pathological feature, consequences of NPC1 loss on microglial function remain uncharacterized. Here, we provide an in-depth characterization of microglial proteomic signatures and phenotypes in a NPC1-deficient (Npc1-/-) murine model and patient blood-derived macrophages. We demonstrate enhanced phagocytic uptake and impaired lipid trafficking in Npc1-/- microglia that precede neuronal death. Loss of NPC1 compromises microglial developmental functions as revealed by increased synaptic pruning and deficient myelin turnover. Undigested myelin accumulates within multi-vesicular bodies of Npc1-/- microglia while lysosomal degradation remains preserved. To translate our findings to human disease, we generated novel ex vivo assays using patient macrophages that displayed similar proteomic disease signatures and lipid trafficking defects as murine Npc1-/- microglia. Thus, peripheral macrophages provide a novel promising clinical tool for monitoring disease progression and therapeutic efficacy in NPC patients. Our study underscores an essential role for NPC1 in immune cells and implies microglial therapeutic potential.

neuroscience↗

Repeat expansion and methylation state analysis with nanopore sequencing

Expansions of short tandem repeats are genetic variants that have been implicated in neuropsychiatric and other disorders but their assessment remains challenging with current molecular methods. Here, we developed a Cas12a-based enrichment strategy for nanopore sequencing that, combined with a new algorithm for raw signal analysis, enables us to efficiently target, sequence and precisely quantify repeat numbers as well as their DNA methylation status. Taking advantage of these single molecule nanopore signals provides therefore unprecedented opportunities to study pathological repeat expansions.

genetics↗