Biology subjects

Fong, J.

Publications and source records attributed to Fong, J..

8 recordsLinked to original sources

bioRxiv2026

Revealing the benefit of eye motion for acuity under emulated cone loss

Retinal degenerative diseases progressively erode the cone photoreceptor mosaic, reducing the retinas spatial sampling power, yet visual acuity is remarkably resilient to cone loss. Prior work has shown that clinically normal visual acuity (20/25 or better) can persist despite up to 50% of cone cells being lost (Ratnam et al. 2013, Foote et al. 2018). However, studies on individuals with retinal degeneration cannot control for patients stage of disease progression, creating the need for an experimental paradigm that can mimic these diseases in healthy subjects. The Oz Vision system creates visual percepts through programmable, per-cell stimulation of thousands of cone cells. We reprogram this system to emulate cone loss in healthy eyes by withholding stimulation from a subset of randomly-selected cones, rendering them inactive, in a method we term "cone dropout." Using this approach, we characterize the visual systems robustness to cone loss, showing that visual acuity declines nonlinearly with increasing cone dropout. Importantly, we uncover the compensatory benefit that eye motion provides under cone-deprived conditions, finding that at the highest level of dropout, a visual system with eye motion has an equivalent acuity to a static dropout condition with nearly twice as many sampling elements. Through analysis of eye motion and stimulation data, we find that this benefit arises from the additional information accumulated by "surviving" cones as they sample more of the letter through fixational eye motion.

neuroscience↗

bioRxiv2025

Targeting Aurora kinases as essential cell cycle regulators to deliver multi-stage antimalarials against Plasmodium falciparum

Kinases that play critical roles in the development and adaptation of Plasmodium falciparum present novel opportunities for chemotherapeutic intervention. Of particular interest are mitotic kinases that regulate the proliferation of the parasites by controlling nuclear division, segregation and cytokinesis. We evaluated the potential of human Aurora kinase (Aur) inhibitors to inhibit P. falciparum development by targeting members of the Aurora-related kinase (Ark) family in this parasite. Several human AurB inhibitors exhibited multistage potency (<250 nM) against all proliferative stages of parasite development, including asexual blood stages, liver schizonts and male gametes. Among the most potent compounds, hesperadin and AT83 exhibit >1000x selectivity towards the parasite without concerns about mammalian cell toxicity. Importantly, we identified PfArk1 as the principal vulnerable Ark family member, with specific inhibition of PfArk1 as the primary target for hesperadin and the human anaplastic lymphoma kinase (ALK) inhibitor TAE684. Hesperadins whole-cell and protein activity validates it as a unique PfArk1 tool compound. Inhibition of PfArk1 results in the parasites inability to complete mitotic processes, presenting with unsegregated, multi-lobed nuclei caused by aberrant microtubule organization. This suggests that PfArk1 is the main Aur mitotic kinase in proliferative stages of Plasmodium, characterized by bifunctional AurA and B activity. This paves the way for drug discovery campaigns based on hesperadin targeting PfArk1.

molecular biology↗

bioRxiv2024

Comprehensive proteolytic profiling of Aedes aegypti mosquito midgut extracts: Unraveling the blood meal protein digestion system

To sustain the gonotrophic cycle, the Aedes aegypti mosquito must acquire a blood meal from a human or other vertebrate host. However, in the process of blood feeding, the mosquito may facilitate the transmission of several bloodborne viral pathogens (e.g., dengue, Zika, and chikungunya). The blood meal is essential as it contains proteins that are digested into polypeptides and amino acid nutrients that are eventually used for egg production. These proteins are digested by several midgut proteolytic enzymes. As such, the female mosquitos reliance on blood may serve as a potential target for vector and viral transmission control. However, this strategy may prove to be challenging since midgut proteolytic activity is a complex process dependent on several exo- and endo-proteases. Therefore, to understand the complexity of Ae. aegypti blood meal digestion, we used Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS) to generate global proteolytic profiles of sugar- and blood-fed midgut tissue extracts, along with substrate profiles of recombinantly expressed midgut proteases. Our results reveal a shift from high exoproteolytic activity in sugar-fed mosquitoes to an expressive increase in endoproteolytic activity in blood-fed mosquitoes. This approach allowed for the identification of 146 cleaved peptide bonds (by the combined 6 h and 24 h blood-fed samples) in the MSP-MS substrate library, and of these 146, 99 (68%) were cleaved by the five recombinant proteases evaluated. These reveal the individual contribution of each recombinant midgut protease to the overall blood meal digestion process of the Ae. aegypti mosquito. Further, our molecular docking simulations support the substrate specificity of each recombinant protease. Therefore, the present study provides key information of midgut proteases and the blood meal digestion process in mosquitoes, which may be exploited for the development of potential inhibitor targets for vector and viral transmission control strategies. Author SummaryThe Aedes aegypti mosquito is a vector of viral pathogens that can be transmitted directly to humans. For instance, the transmission of dengue, Zika, or chikungunya viruses may happen during the Ae. aegypti acquisition of an infected blood meal. This blood meal is important for the anautogenous mosquito because without the digestion of blood proteins the mosquito will not obtain the necessary nutrients needed for egg production. After imbibing a blood meal, midgut digestive enzymes (proteases) are expressed and secreted into the lumen. To fully understand their roles in blood meal digestion, we used a special technique called Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS). This method allows us to generate global proteolytic activity profiles of Ae. aegypti midgut tissue extracts that were fed with sugar or blood. In addition, we generated substrate cleavage profiles of recombinantly expressed midgut proteases allowing us to understand the enzyme preferences for blood proteins. Therefore, utilizing this approach, we found the contribution of each individual recombinant protease tested relative to the global activity profile of blood-fed midgut tissue extracts. This may be a starting point for the validation of midgut protease inhibition and the development of a new potential vector control strategy.

biochemistry↗

bioRxiv2022

Characterizing Cone Spectral Classification by Optoretinography

Light propagation in photoreceptor outer segments is affected by photopigment absorption and the phototransduction amplification cascade. Photopigment absorption has been studied using retinal densitometry, while recently, optoretinography (ORG) has provided an avenue to probe changes in outer segment optical path length due to phototransduction. With adaptive optics (AO), both densitometry and ORG have been used for cone spectral classification, based on the differential bleaching signatures of the three cone types. Here, we characterize cone classification by ORG, implemented in an AO line-scan OCT and compare it against densitometry. The cone mosaics of five color normal subjects were classified using ORG showing high probability ([~]0.99), low error (<0.22%), high test-retest reliability ([~]97%) and short imaging durations (< 1 hour). Of these, the cone spectral assignments in two subjects were compared against AOSLO densitometry. High agreement (mean: 91%) was observed between the two modalities in these 2 subjects, with measurements conducted 6-7 years apart. Overall, ORG benefits from higher sensitivity and dynamic range to probe cone photopigments compared to densitometry, and thus provides greater fidelity for cone spectral classification.

neuroscience↗

bioRxiv2021

Dissecting the Roles of the Tuberin Protein in the Subcellular Localization of the G2/M Cyclin, Cyclin B1

Tuberin is a major component of the protein regulatory complex known as the Tuberous Sclerosis Complex and plays a crucial role in cell cycle progression and protein synthesis. Mutations in the Tuberin gene, TSC2, lead to the formation of benign tumors in many organ systems and causes the Tuberous Sclerosis Complex disorder. Genotypes ranging from point mutations to large deletions in the TSC2 gene have been clinically characterized with a wide range of phenotypes from skin tumors to large brain tumors. Our current work investigates the molecular mechanisms behind Tuberin and its ability to regulate the cell cycle through its binding to the G2/M cyclin, Cyclin B1. After creating an early stop codon in a critical region of the Tuberin, our results show the in vitro phenotype that occurs from a truncated Tuberin protein. Herein we demonstrate that this clinically relevant truncated form of Tuberin promotes an increased nuclear accumulation of Cyclin B1 and a subsequent increase in cell proliferation supporting the phenotypic data seen in the clinic with Tuberous Sclerosis Complex patients showing deletions within the TSC2 gene. This data provides an insight into some of the functional and molecular consequences of truncated proteins that are seen in clinical patients.

cell biology↗

bioRxiv2021

Tuberin levels during cellular differentiation in brain development

Tuberin is a member of a large protein complex, Tuberous Sclerosis Complex, and acts as a sensor for nutrient status regulating protein synthesis and cell cycle progression. Mutations in the Tuberin gene, TSC2, lead to the formation of tumors and developmental defects in many organ systems, including the central nervous system. Tuberin is expressed in the brain throughout development and levels of Tuberin have been found to decrease during neuronal differentiation in cell lines in vitro. Our current work investigates the levels of Tuberin at two stages of embryonic development in vivo, and we study the mRNA and protein levels during a time course using immortalized cell lines in vitro. Our results show that Tuberin levels remain stable in the olfactory bulb but decrease in the Purkinje cell layer during embryonic mouse brain development. We show here that Tuberin levels are higher when cells are cultured as neurospheres, and knockdown of Tuberin results in a reduction in the number of neurospheres. These data provide support for the hypothesis that Tuberin is an important regulator of stemness and the reduction of Tuberin levels might support functional differentiation in the central nervous system. Understanding how Tuberin expression is regulated throughout neural development is essential to fully comprehend the role of this protein in several developmental and neural pathologies. HIGHLIGHTSO_LITuberin protein levels are decreased in the Purkinje cell layer in later stages of embryonic development. C_LIO_LITuberin protein and mRNA levels decrease as cells undergo neuronal differentiation. C_LIO_LIDownregulation of Tuberin impairs neurosphere formation. C_LIO_LITuberin is implicated in the maintenance of stemness in the developing brain. C_LI

developmental biology↗

bioRxiv2020

Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM

Epigenetic changes, such as aberrant DNA methylation, contribute to cancer clonal expansion and disease progression. However, identifying subpopulation-level changes in a heterogeneous sample remains challenging. Thus, we have developed a computational approach, DXM, to deconvolve the methylation profiles of major allelic subpopulations from the bisulfite sequencing data of a heterogeneous sample. DXM does not require prior knowledge of the number of subpopulations or types of cells to expect. We benchmark DXMs performance and demonstrate improvement over existing methods. We further experimentally validate DXM predicted allelic subpopulation-methylation profiles in four Diffuse Large B-Cell Lymphomas (DLBCLs). Lastly, as proof-of-concept, we apply DXM to a cohort of 31 DLBCLs and relate allelic subpopulation methylation profiles to relapse. We thus demonstrate that DXM can robustly find allelic subpopulation methylation profiles that may contribute to disease progression using bisulfite sequencing data of any heterogeneous sample.

bioinformatics↗

bioRxiv2017

Synergy of Quorum Quenching Enzyme and Quorum Sensing Inhibitor in Inhibiting P. aeruginosa Quorum Sensing

The threat of antibiotic resistant bacteria has called for alternative antimicrobial strategies that would mitigate the increase of classical resistance mechanism. Many bacteria employ quorum sensing (QS) to govern the production of virulence genes and formation of drug-resistance biofilms. Blocking QS mechanisms have proven to be a functional alternative to conventional antibiotic control of infections. The concepts of quorum sensing inhibitors (QSI) and quorum quenching enzymes (QQ) have been investigated separately. In this study however, we simulated the synergistic effect of QQ and QSI in blocking bacterial QS. This effect was validated by experiments using AiiA and G1 as QQ and QSI respectively on Pseudomonas aeruginosa LasR/I and RhlR/I QS circuits. The combination of a QQ and a QSI almost completely blocked the P. aeruginosa QS las and rhl system. Our findings provided a potential application strategy for bacterial QS disruption.

microbiology↗