Biology subjects

Murray, K. L.

Publications and source records attributed to Murray, K. L..

3 recordsLinked to original sources

bioRxiv2021

Effects of α-crystallin gene knockout on zebrafish lens development

The -crystallin small heat shock proteins contribute to the transparency and refractive properties of the vertebrate eye lens and prevent the protein aggregation that would otherwise produce lens cataracts, the leading cause of human blindness. There are conflicting data in the literature as to what role the -crystallins may play in early lens development. In this study, we used CRISPR gene editing to produce zebrafish lines with null mutations for each of the three -crystallin genes (cryaa, cryaba and cryabb). The absence of normal protein was confirmed by mass spectrometry, and lens phenotypes were assessed with differential interference contrast microscopy and histology. Loss of A-crystallin produced a variety of lens defects with varying severity in larval lenses at 3 and 4 dpf but little substantial change in normal fiber cell denucleation. Loss of either Ba- or full-length Bb-crystallin produced no substantial lens defects. Mutation of each -crystallin gene did not alter the mRNA levels of the remaining two, suggesting a lack of genetic compensation. These data confirm a developmental role for A-crystallin in lens development, but the range of phenotype severity suggests that its loss simply increases the chance for defects and that the protein is not essential. Our finding that cryaba and cryabb mutants lack noticeable lens defects is congruent with insubstantial transcript levels in lens epithelial and fiber cells. Future experiments can explore the molecular consequences of cryaa mutation and causes of lens defects in this null mutant, as well as the roles of other genes in lens development and function.

developmental biology↗

bioRxiv2021

Automated classification of bat echolocation call recordings with artificial intelligence

Acoustic recorders are commonly used to remotely monitor and collect data on bats (Order Chiroptera). These efforts result in many acoustic recordings that must be classified by a bat biologist with expertise in call classification in order to obtain useful information. The rarity of this expertise and time constraints have prompted efforts to automatically classify bat species in acoustic recordings using a variety of learning methods. There are several software programs available for this purpose, but they are imperfect and the United States Fish and Wildlife Service often recommends that a qualified acoustic analyst review bat call identifications even if using these software programs. We sought to build a model to classify bat species using modern computer vision techniques. We used images of bat echolocation calls (i.e., plots of the pulses) to train deep learning computer vision models that automatically classify bat calls to species. Our model classifies 10 species, five of which are protected under the Endangered Species Act. We evaluated our models using standard model validation procedures, but we also performed two out-of-distribution tests. For the out-of-distribution tests, an entire dataset was withheld from the procedure before splitting the data into training and validation sets. We found that our validation accuracy (93%) and out-of-distribution accuracy (90%) were higher than when we used Kaleidoscope Pro and BCID software (65% and 61% accuracy, respectively) to evaluate the same calls. Our results suggest that our approach is effective at classifying bat species from acoustic recordings, and our trained model will be incorporated into new bat call identification software: WEST-EchoVision.

ecology↗

bioRxiv2019

Why does the zebrafish cloche mutant develop lens cataract?

The zebrafish has become a valuable model for examining ocular lens development, physiology and disease. The zebrafish cloche mutant, first described for its loss of hematopoiesis, also shows reduced eye and lens size, interruption in lens cell differentiation and a cataract likely caused by abnormal protein aggregation. To facilitate the use of the cloche mutant for studies on cataract development and prevention we characterized variation in the lens phenotype, quantified changes in gene expression by qRT-PCR and RNA-Seq and compared the ability of two promoters to drive expression of introduced proteins into the cloche lens. We found that the severity of cloche embryo lens cataract varied, while the decrease in lens diameter and retention of nuclei in differentiating lens fiber cells was constant. We found very low expression of both B-crystallin genes (cryaba and cryabb) at 4 days post fertilization (dpf) by both qRT-PCR and RNA-Seq in cloche, cloche sibling and wildtype embryos and no significant difference in A-crystallin (cryaa) expression. RNA-Seq analysis of 4 dpf embryos identified transcripts from 25,281 genes, with 1,329 showing statistically significantly different expression between cloche and wildtype samples. Downregulation of eight lens {beta}- and {gamma}M-crystallin genes and 22 retinal related genes may reflect a general reduction in eye development and growth. Six stress response genes were upregulated. We did not find misregulation of any known components of lens development gene regulatory networks. These results suggest that the cloche lens cataract is not caused by loss of A-crystallin or changes to lens gene regulatory networks. Instead, we propose that the cataract results from general physiological stress related to loss of hematopoiesis. Our finding that the zebrafish A-crystallin promoter drove strong GFP expression in the cloche lens demonstrates its use as a tool for examining the effects of introduced proteins on lens crystallin aggregation and cataract prevention.

developmental biology↗