Biology subjects

Lewis, T. R.

Publications and source records attributed to Lewis, T. R..

11 recordsLinked to original sources

bioRxiv2026

A novel methodology for assessing reinforcement choice in primates under human care

Positive Reinforcement Training is a technique commonly employed in zoological collections to elicit a desired behaviour from an animal under human care. Typically, a food item is offered as a reward for performing that behaviour. Three non-human primate species (Mandrillus sphinx, Pan troglodytes, and Hylobates lar) were offered four different foods (banana, grape, apple, and sweet potato) in a series of choice experiments. Latent variable models were employed to investigate which foods were the best selection to use as reinforcement items. Results show that food preference varies between the three primate species. Pan troglodytes and H. lar showed strong preferences for grape and banana, whereas M. sphinx showed a very strong preference for sweet potato. This study indicates that foraging ecology might play an important part in fruit selection and preference in primates. The findings highlight that understanding a species' natural behaviour and dietary preferences is key to informing reinforcement and training decisions.

zoology↗

bioRxiv2026

Clathrin-coated tubules mediate rapid and selective protein absorption by lysosome-rich enterocytes

In the digestive tract of neonatal mammals and in fish, lysosome-rich enterocytes (LREs) internalize dietary proteins and digest them intracellularly within a large lysosomal vacuole. Impaired LRE function leads to growth stunting and poor survival in zebrafish and mice. Previous work has shown that protein uptake relies on a scavenger receptor complex. However, how LREs can internalize proteins rapidly enough to support organismal growth is unclear. Here, using live and electron microscopy and genetic manipulations in zebrafish, we find that LREs contain apical micron-sized clathrin-coated endocytic tubules (ETs) that perform rapid internalization of proteins and other soluble cargoes, while excluding resident apical membrane proteins. Dab2, an endocytic adaptor linking clathrin to scavenger receptors, controls both the biogenesis and function of ETs by recruiting unconventional myosin Myo6 and by influencing dynamin activity. Our findings suggest that continuous pinching of vesicles from ETs allows for rapid, high-capacity internalization of dietary protein.

cell biology↗

bioRxiv2025

RPE pseudopods maintain photoreceptor outer segment renewal despite subretinal space expansion in Adam9 knockout mice

Vision begins in the outer segment compartment of photoreceptor cells, which is constantly renewed through the addition of membrane material at its base and ingestion of mature membranes at its tip by the retinal pigment epithelium (RPE). The close apposition of outer segments to the RPE is believed to be critical for maintaining this renewal process. Yet, in several retinal diseases, expansion of the subretinal space separating photoreceptors from the RPE does not immediately impact photoreceptor functionality. Here, we analyzed outer segment function and renewal in the Adam9 knockout mouse characterized by a major expansion of the subretinal space. Surprisingly, photoreceptor-RPE separation affected neither the sensitivity of photoreceptor light-responses nor the normal rate of outer segment renewal in this mouse prior to the onset of photoreceptor degeneration. The latter is achieved through the formation of elongated RPE "pseudopods" extending across the enlarged subretinal space to ingest outer segment tips. This work suggests that pseudopod formation may underlie the persistence of photoreceptor function in human diseases accompanied by photoreceptor-RPE separation, such as vitelliform macular dystrophy or age-related macular degeneration associated with subretinal drusenoid deposits.

cell biology↗

bioRxiv2024

Inpp5e is a Critical Regulator of Protein Transport to Photoreceptor Outer Segments

In humans, inositol polyphosphate-5-phosphatase e (INPP5E) mutations cause retinal degeneration as part of Joubert and MORM syndromes and can also cause non-syndromic blindness. In mice, mutations cause a spectrum of brain, kidney, and other anomalies and prevent the formation of photoreceptor outer segments. To further explore the function of Inpp5e in photoreceptors, we generated conditional and inducible knockouts of mouse Inpp5e where the gene was deleted either during outer segment formation or after outer segments were fully formed. In both cases, the loss of Inpp5e led to severe defects in photoreceptor outer segment morphology and ultimately photoreceptor cell loss. The primary morphological defect consisted of outer segment shortening and reduction in the number of newly forming discs at the outer segment base. This was accompanied by structural abnormalities of the Golgi apparatus, mislocalized rhodopsin, and an accumulation of extracellular vesicles. In addition, knockout cells showed a reduction in the size and prevalence of the actin network at the site of new disc morphogenesis and the occasional formation of membrane whorls instead of discs in a subset of cells. Together, these data demonstrate that Inpp5e plays a critical role in maintaining the outer segment and the normal process of outer segment renewal depends on the activity of this enzyme.

cell biology↗

bioRxiv2024

Human rod photoreceptor outer segments are supported by accessory inner segment structures

The first steps in vision take place in photoreceptor cells, which are highly compartmentalized neurons exhibiting significant structural variation across species. The light-sensitive ciliary compartment, called the outer segment, is located atop of the cell soma, called the inner segment. In this study, we present an ultrastructural analysis of human photoreceptors, which reveals that, in contrast to this classic arrangement, the inner segment of human rods extends alongside the outer segment to form a structure hereby termed the "accessory inner segment". While reminiscent of the actin-based microvilli known as "calyceal processes" observed in other species, the accessory inner segment is a unique structure: (1) it contains an extensive microtubule-based cytoskeleton, (2) it extends far alongside the outer segment, (3) its diameter is comparable to that of the outer segment, (4) it contains numerous mitochondria, and (5) it forms electron-dense structures that likely mediate adhesion to the outer segment. Given that the spacing of extrafoveal human photoreceptors is more sparse than in non-primate species, with vast amounts of interphotoreceptor matrix present between cells, the closely apposed accessory inner segment likely provides structural support to the outer segment. This discovery expands our understanding of the human retina and directs future studies of human photoreceptor function in health and disease.

cell biology↗

bioRxiv2023

ROM1 is redundant to PRPH2 as a molecular building block of photoreceptor disc rims

Visual signal transduction takes place within a stack of flattened membranous "discs" enclosed within the light-sensitive photoreceptor outer segment. The highly curved rims of these discs, formed in the process of disc enclosure, are fortified by large hetero-oligomeric complexes of two homologous tetraspanin proteins, PRPH2 (a.k.a. peripherin-2 or rds) and ROM1. While mutations in PRPH2 affect the formation of disc rims, the role of ROM1 remains poorly understood. In this study, we found that the knockout of ROM1 causes a compensatory increase in the disc content of PRPH2. Despite this increase, discs of ROM1 knockout mice displayed a delay in disc enclosure associated with a large diameter and lack of incisures in mature discs. Strikingly, further increasing the level of PRPH2 rescued these morphological defects. We next showed that disc rims are still formed in a knockin mouse in which the tetraspanin body of PRPH2 was replaced with that of ROM1. Together, these results demonstrate that, despite its contribution to the formation of disc rims, ROM1 can be replaced by an excess of PRPH2 for timely enclosure of newly forming discs and establishing normal outer segment structure.

cell biology↗

bioRxiv2023

Photoreceptor disc incisures form as an adaptive mechanism ensuring the completion of disc enclosure

The first steps of vision take place within a stack of tightly packed disc-shaped membranes, or "discs", located in the outer segment compartment of photoreceptor cells. In rod photoreceptors, discs are enclosed inside the outer segment and contain deep indentations in their rims called "incisures". The presence of incisures has been documented in a variety of species, yet their role remains elusive. In this study, we combined traditional electron microscopy with three-dimensional electron tomography to demonstrate that incisures are formed only after discs become completely enclosed. We also observed that, at the earliest stage of their formation, discs are not round as typically depicted but rather are highly irregular in shape and resemble expanding lamellipodia. Using genetically manipulated mice and frogs and measuring outer segment protein abundances by quantitative mass spectrometry, we further found that incisure size is determined by the molar ratio between peripherin-2, a disc rim protein critical for the process of disc enclosure, and rhodopsin, the major structural component of disc membranes. While a high perpherin-2 to rhodopsin ratio causes an increase in incisure size and structural complexity, a low ratio precludes incisure formation. Based on these data, we propose a model whereby normal rods express a modest excess of peripherin-2 over the amount required for complete disc enclosure in order to ensure that this important step of disc formation is accomplished. Once the disc is enclosed, the excess peripherin-2 incorporates into the rim to form an incisure.

cell biology↗

bioRxiv2023

Absolute quantification of photoreceptor outer segment proteins

Photoreceptor cells generate neuronal signals in response to capturing light. This process, called phototransduction, takes place in a highly specialized outer segment organelle. There are significant discrepancies in the reported amounts of many proteins supporting this process, particularly those of low abundance, which limits our understanding of their molecular organization and function. In this study, we used quantitative mass spectrometry to simultaneously determine the abundances of twenty key structural and functional proteins residing in mouse rod outer segments. We computed the absolute number of molecules of each protein residing within an individual outer segment and the molar ratio amongst all twenty proteins. The molar ratios of proteins comprising three well-characterized constitutive complexes in outer segments differed from the established subunit stoichiometries of these complexes by less than 7%, highlighting the exceptional precision of our quantification. Overall, this study resolves multiple existing discrepancies regarding the outer segment abundances of these proteins, thereby advancing our understanding of how the phototransduction pathway functions as a single, well-coordinated molecular ensemble.

biochemistry↗

bioRxiv2020

Unusual mode of dimerization of retinitis pigmentosa-associated F220C rhodopsin

Mutations in the G protein-coupled receptor (GPCR) rhodopsin are a common cause of autosomal dominant retinitis pigmentosa, a blinding disease. Rhodopsin self-associates in the membrane, and the purified monomeric apo-protein opsin dimerizes in vitro as it transitions from detergent micelles to reconstitute into a lipid bilayer. We previously reported that the retinitis pigmentosa-linked F220C opsin mutant fails to dimerize in vitro, reconstituting as a monomer. Using fluorescence-based assays and molecular dynamics simulations we now report that whereas wildtype and F220C opsin display distinct dimerization propensities in vitro as previously shown, they both dimerize in the plasma membrane of HEK293 cells. Unexpectedly, molecular dynamics simulations show that F220C opsin forms an energetically favored dimer in the membrane when compared with the wild-type protein. The conformation of the F220C dimer is unique, with transmembrane helices 5 and 6 splayed apart, promoting widening of the intracellular vestibule of each protomer and influx of water into the protein interior. FRET experiments with SNAP-tagged wild-type and F220C opsin expressed in HEK293 cells are consistent with this conformational difference. We speculate that the unusual mode of dimerization of F220C opsin in the membrane may have physiological consequences.

biophysics↗

bioRxiv2020

Assessing bird collisions in the United Kingdom: Modelling frequency of bird-strike from road and rail mortality using a Bayesian hierarchical approach

Roads are an important way to transport people and goods, but they sometimes have negative impacts on wildlife. One of the leading causes of mortality for several species is identified as road strikes, and the most significant remains bird-vehicle collisions. This study aimed to investigate what species of birds are most affected, and what other factors impact in their susceptibility in road collisions, such as age, sex, season, and type of transports. A total of N=5413 records, and 140 bird species were documented by BTO ringers. For analysis four Bayesian Hierarchical Models were used, with random effects results showing that Barn owls were most affected by collisions. Road mortality presents the highest cause of mortality among species when contrasted with rail mortality. Age and sexual bias was detected across all species, however juveniles and males did appear to be prominent in relation to other age classes. Winter and early spring were the months with most reported casualties and 2016 had lower abundance of mortality across the 10-year period. 75% of birds were found within a week, which may indicate some bias interference from scavenging animals, as true figures could be up to 16 times more. This study discusses some mitigation measures found in current research, that could dramatically reduce numbers of birds affected each year by road mortality.

ecology↗

bioRxiv2018

Kif17 phosphorylation regulates its ciliary localization and photoreceptor outer segment turnover

BackgroundKIF17, a kinesin-2 motor that functions in intraflagellar transport, can regulate the onset of photoreceptor outer segment development. However, the function of KIF17 in a mature photoreceptor remains unclear. Additionally, the ciliary localization of KIF17 is regulated by a C-terminal consensus sequence (KRKK) that is immediately adjacent to a conserved residue (mouse S1029/zebrafish S815) previously shown to be phosphorylated by CaMKII. Yet, whether this phosphorylation can regulate the localization, and thus function, of KIF17 in ciliary photoreceptors remains unknown.\n\nResultsUsing transgenic expression in both mammalian cells and zebrafish photoreceptors, we show that phospho-mimetic KIF17 has enhanced localization to cilia. Importantly, expression of phospho-mimetic KIF17 is associated with greatly enhanced turnover of the photoreceptor outer segment through disc shedding in a cell-autonomous manner, while genetic mutants of kif17 in zebrafish and mice have diminished disc shedding. Lastly, cone expression of constitutively active tCaMKII leads to a kif17-dependent increase in disc shedding.\n\nConclusionsTaken together, our data support a model in which phosphorylation of KIF17 promotes its ciliary localization. In cone photoreceptor outer segments, this promotes disc shedding, a process essential for photoreceptor maintenance and homeostasis. While disc shedding has been predominantly studied in the context of the mechanisms underlying phagocytosis of outer segments by the retinal pigment epithelium, this work implicates photoreceptor-derived signaling in the underlying mechanisms of disc shedding.

cell biology↗