Biology subjects

Phillips, J. B.

Publications and source records attributed to Phillips, J. B..

6 recordsLinked to original sources

bioRxiv2025

Mini-Pcdh15b Gene Therapy Rescues Visual Deficits in a Zebrafish Model of Usher Syndrome Type 1F

Usher syndrome type 1F (USH1F) is a severe inherited disorder caused by mutations in PCDH15, resulting in congenital deafness, vestibular dysfunction, and progressive retinal degeneration leading to blindness. While cochlear implantation can restore hearing, no therapeutic interventions currently exist for vision loss. Gene augmentation therapy represents a promising approach; however, the PCDH15 coding sequence ([~]5.3 kb) exceeds the packaging capacity of adeno-associated virus (AAV) vectors. To overcome this limitation, we previously engineered shortened "mini-PCDH15" constructs that retain key structural and functional domains while fitting within a single AAV. Among these, the mini-PCDH15-V4 variant successfully restored hearing in Pcdh15-deficient mice. Here, we investigated the ability of a cone-targeted mini-pcdh15b-V4 transgene to rescue vision in a zebrafish model of USH1F. Untreated pcdh15b-deficient zebrafish exhibited severe structural and functional defects of the retina, including disorganized and shortened photoreceptor outer segments, disrupted calyceal processes, and markedly reduced electroretinogram (ERG) and optokinetic response (OKR) performance. Targeted expression of mini-pcdh15b-V4 recapitulated typical localization of Pcdh15b to calyceal processes and outer segment membranes, rescued photoreceptor architecture, and re-established both structural organization and functional output. Treated mutants exhibited improved visual tracking behavior and full recovery of ERG a-wave and b-wave amplitudes, indicating restoration of photoreceptor and synaptic function. Importantly, mini-pcdh15b-V4 expression produced no adverse effects in wild-type or heterozygous fish, supporting the safety of cone-specific expression. Together, these findings demonstrate that mini-pcdh15b-V4 can restore both photoreceptor structure and visual function in pcdh15b-deficient zebrafish. This work establishes the pcdh15b mutant zebrafish as a powerful preclinical model for studying USH1F retinopathy and supports the translational potential of rationally engineered mini-PCDH15 constructs as a feasible gene therapy approach for preventing or reversing vision loss in individuals with USH1F.

neuroscience↗

bioRxiv2023

Hexafluoro slows retinal degeneration and improves visual function in zebrafish models of Usher syndrome 1F

Usher syndrome is the leading genetic cause of deafblindness, affecting hundreds of thousands of people worldwide. The deafness can be addressed with hearing aids or cochlear implants, but there is currently no treatment for the vision loss, which is due to progressive degeneration of retinal photoreceptors. Studies in animal models of Usher syndrome have shown that photoreceptor degeneration is exacerbated by exposure to bright light, and other studies have shown that light-induced photostress reduces mitochondrial function. We previously synthesized hexafluoro and showed that it is a potent Sirt3 activator that promotes mitochondrial respiration. Here we examined the efficacy of hexafluoro as a potential therapeutic for treatment of vison loss in a zebrafish model of Usher syndrome type 1F, which exhibits early and severe vision defects along with vestibular dysfunction as seen in Usher type 1 pathology. We find that hexafluoro improves visual function, reduces photoreceptor degeneration, and protects the retina against exposure to bright light in this USH1F model.

neuroscience↗

bioRxiv2021

Breaking the Scale: Allometric scaling analysis in Carnivoran families

The analysis of scaling relationships, allometric scaling, has a long history of importance for modelling and predicting biological phenomena. Individual organisms are not truly independent, and as a result phylogenetic corrections are necessary to increase the accuracy of scaling relationships. The relationships between body mass and gestation length have not been previously reported at the Family level, as it was previously thought species had insufficient time to diverge evolutionarily leaving phylogenetic corrections unnecessary. Using a Carnivora supertree, we perform a phylogenetically generalised least squares (PGLS) analysis using life history information largely from the Pantheria dataset. Our results suggest that allometric relationships are maintained in four families: Canidae, Felidae, Herpestidae and Otariidae. Conversely, several evolutionary mechanisms may contribute to the lack of a significant scaling parameter in other families, such as diverse reproductive strategies or positive selection for genes affecting adiposity. In addition, low sample sizes or the inclusion of paternal body masses could alter the presence of significant scaling. Our results suggests that PGLS analyses are informative at the family level, and the absence of scaling can provide insight to understanding of the evolutionary mechanisms that work on the family taxonomic level or below. CCS CONCEPTS* Applied computing [->] Molecular evolution; * Computing methodologies [->] Modeling methodologies. ACM Reference FormatStefanie Navaratnam and Julie Baker Phillips. 2021. Breaking the Scale: Allometric scaling analysis in Carnivoran families. In BCB: ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 01-04, 2021, Virtual due to COVID-19. ACM, New York, NY, USA, 7 pages. https://doi.org/10.1145/1122445.1122456

evolutionary biology↗

bioRxiv2020

COPB2 haploinsufficiency causes a coatopathy with osteoporosis and developmental delay

Coatomer complexes function in the sorting and trafficking of proteins between subcellular organelles. Pathogenic variants in coatomer subunits or associated factors have been reported in multi-systemic disorders, i.e., coatopathies, that can affect the skeletal and central nervous systems. We have identified loss-of-function variants in COPB2, a component of the coatomer complex I (COPI), in individuals presenting with osteoporosis, fractures and developmental delay of variable severity. Because the role of COPB2 in bone has not been characterized, we studied the effect of COPB2 deficiency on skeletal development in mice and zebrafish. Copb2+/- mice showed low bone mass and decreased bone strength. In zebrafish, larvae carrying a copb2 heterozygous frameshift variant showed delayed mineralization. copb2-null embryos showed endoplasmic reticulum (ER) and Golgi disorganization, and embryonic lethality. COPB2 siRNA-treated fibroblasts showed delayed collagen trafficking with retention of type I collagen in the ER and Golgi, and altered distribution of Golgi markers. Our data suggest that COPB2 haploinsufficiency leads to disruption of intracellular collagen trafficking and osteoporosis, which may improve with ascorbic acid supplementation. This work highlights the role of COPI complex as a critical regulator of bone mass and identifies a new form of coatopathy due to COPB2 deficiency.

genetics↗

bioRxiv2020

Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map

The evolution of tRNA multigene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We improved FlyBase tRNA gene annotations from twelve Drosophila species, incorporating previously identified ortholog sets to compare substitution rates across tRNA bodies at single-site and base-pair resolution. All rapidly evolving sites fell within the same metal ion-binding pocket, that lies at the interface of the two major stacked helical domains. We applied our tRNA Structure-Function Mapper (tSFM) method independently to each Drosophila species and one outgroup species Musca domestica and found that, although predicted tRNA structure-function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidly-evolving ion-binding pocket -- Cytosine 17 (C17), ancestrally informative for lysylation identity -- independently gained asparaginylation identity and substituted in parallel across tRNAAsn paralogs at least once, possibly multiple times, during evolution of the genus. In D. melanogaster, most tRNALys and tRNAAsn genes are co-arrayed in one large heterologous gene cluster, suggesting that heterologous gene conversion as well as structural similarities of tRNA-binding interfaces in the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution in D. ananassae may have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsn paralogs in that lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure-function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multigene families.

molecular biology↗

bioRxiv2018

Genome wide association analysis identifies genetic variants associated with reproductive variation across domestic dog breeds and uncovers links to domestication

The diversity of eutherian reproductive strategies has led to variation in many traits, such as number of offspring, age of reproductive maturity, and gestation length. While reproductive trait variation has been extensively investigated and is well established in mammals, the genetic loci contributing to this variation remain largely unknown. The domestic dog, Canis lupus familiaris is a powerful model for studies of the genetics of inherited disease due to its unique history of domestication. To gain insight into the genetic basis of reproductive traits across domestic dog breeds, we collected phenotypic data for four traits - cesarean section rate (n = 97 breeds), litter size (n = 60), stillbirth rate (n = 57), and gestation length (n = 23) - from primary literature and breeders handbooks. By matching our phenotypic data to genomic data from the Cornell Veterinary Biobank, we performed genome wide association analyses for these four reproductive traits, using body mass and kinship among breeds as co-variates. We identified 14 genome-wide significant associations between these traits and genetic loci, including variants near CACNA2D3 with gestation length, MSRB3 with litter size, SMOC2 with cesarean section rate, MITF with litter size and still birth rate, KRT71 with cesarean section rate, litter size, and stillbirth rate, and HTR2C with stillbirth rate. Some of these loci, such as CACNA2D3 and MSRB3, have been previously implicated in human reproductive pathologies. Many of the variants that we identified have been previously associated with domestication-related traits, including brachycephaly (SMOC2), coat color (MITF), coat curl (KRT71), and tameness (HTR2C). These results raise the hypothesis that the artificial selection that gave rise to dog breeds also shaped the observed variation in their reproductive traits. Overall, our work establishes the domestic dog as a system for studying the genetics of reproductive biology and disease.

evolutionary biology↗