Biology subjects

Gabay, M.

Publications and source records attributed to Gabay, M..

7 recordsLinked to original sources

bioRxiv2025

The effect of virtual reality modality level of immersion and locomotion on spatial learning and gaze measures

The widespread adoption of head-mounted display (HMD) virtual reality (VR) systems has emerged in various fields, including spatial learning research. This study investigated the effects of VR modality level of immersion, locomotion interface, and proprioception on spatial learning and physiological measures using eye-tracking (ET) in VR. We translated the classic T-maze task from Barnes et al. (1980) to humans for the first time, comparing three VR modalities: 3D HMD VR with physical walking, 3D HMD VR with controller-based movement, and 2D desktop VR. Results revealed that human participants employed a mixture of cue, place, and response strategies when navigating the virtual T-maze, mirroring rodent behavior. In both samples, no significant differences were found between the two HMD VR conditions in learning performance, nor consistent ones in strategy choices. However, 2D desktop navigation was associated with slower initial learning, though this discrepancy diminished in subsequent sessions. These results were supported by spatial presence, immersion, and naturalness reports. Gaze measures showed that participants who physically walked devoted more visual attention to environmental cues compared to controller users. Predictive models for identifying spatial learning strategies based on ET and behavioral measures demonstrated significant accuracy in some models, particularly in the VR walking condition and second session. Our findings enhance the understanding of spatial learning strategies and the effects of VR modality on cognition and gaze behavior. This work demonstrates the potential of integrated ET data and holds implications for early detection and personalized rehabilitation of neurodegenerative conditions related to spatial cognition.

neuroscience↗

bioRxiv2024

Genetically encoded biosensor for fluorescence lifetime imaging of PTEN dynamics in the intact brain

The phosphatase and tensin homolog (PTEN) is a vital signaling protein which maintains an inhibitory brake that is critical for cellular metabolism, proliferation, and growth. The importance of PTEN signaling is evident from the broad spectrum of human pathologies associated with its loss of function. Moreover, loss or gain of PTEN function in animal models leads to aberrant cellular morphology, function, and metabolic regulation. However, despite the important role of PTEN signaling, there is currently no method to dynamically monitor its activity with cellular specificity within intact biological systems. Here, we describe the development of a novel PTEN biosensor, optimized for two-photon fluorescence lifetime imaging microscopy (2pFLIM). This biosensor is designed to measure PTEN activity within intact cells, tissues, and organisms. Our approach is based on monitoring FRET-dependent changes in PTEN conformation, which serves as a proxy for the activity state in living cells. We identify a point mutation that allow us to express this biosensor with minimal interference to endogenous PTEN signaling and cellular function. We demonstrate the utility of imaging PTEN signaling in cell lines, developing C. elegans, and in the living mouse brain. To complement this approach, we developed a red-shifted PTEN sensor variant that permits simultaneous imaging with GFP-based sensors. Finally, we use in vivo PTEN imaging in the mouse brain to identify cell-type specific dynamics of PTEN activity in excitatory and inhibitory cortical cells. In summary, our approach enables dynamic imaging of PTEN activity in vivo with unprecedented spatial and temporal resolution.

neuroscience↗

bioRxiv2024

Making the Monitoring Framework of the Kunming-Montreal Global Biodiversity Framework fit for purpose.

The Kunming-Montreal Global Biodiversity Framework (GBF) is the most ambitious agreement on biodiversity conservation and sustainable use to date. It calls for a whole-of government and whole-of-society approach to halt and reverse biodiversity loss worldwide. The Monitoring Framework of the GBF lays out how Parties to the Convention on Biological Diversity (CBD) are expected to report their progress. A CBD expert group provided guidance on its implementation, including a gap analysis to identify the strengths and limitations of the indicators in the Monitoring Framework. We present the results of the gap analysis, highlight where more work is needed and provide recommendations on implementing and improving monitoring to allow effective and comprehensive tracking of the GBFs ambition. We find that with the headline and binary indicators, which Parties are required to use, the Monitoring Framework fully covers 19% of the GBFs ambition and partially covers an additional 40%. Including disaggregations of the headline indicators improves coverage to 22% fully and an additional 41% partially. Adding optional (component and complementary) indicators brings full coverage to 29% with an additional 47% partial coverage. No indicators are available for 12% of the GBF. In practice, the coverage of the Monitoring Framework will depend on which indicators (headline and binary as well as component and complementary) and disaggregations are used by countries. Disaggregations are particularly relevant to monitor the cross-cutting considerations defined under section C. Substantial investment is required to collect the necessary data to compute indicators, infer change, and effectively monitor progress. We highlight important next steps to progressively improve the efficacy of the Monitoring Framework.

ecology↗

bioRxiv2024

Anti-fungal recombinant psoriasin effectively inhibits Candida albicans growth on denture base

Oral candidiasis leading to denture stomatitis is a fungal infection resulting from unregulated growth and adhesion mainly of Candida albicans onto acrylic denture base. Once the biofilm is formed, it is immune resistant and mainstay treatments involve toxic chemical antifungal agents or mechanical cleaning techniques, both offer limited efficacy. Consequently, there is an urgent need for more effective and safer therapeutic approaches. While biological modalities are expanding in general medicine, the exploration of protein-based therapeutics in dental medicine remains limited. This research evaluates the inhibitory effect of recombinantly expressed psoriasin on the growth of Candida albicans on polymethyl methacrylate denture bases. Psoriasin, also known as S100-A7, has shown promise in treating microbial skin infections, and its natural presence in saliva makes it a promising candidate for treating oral microbial infections. Our findings indicate that psoriasin exhibits a strong, dose-dependent inhibition of Candida albicans growth. Further, we incubated a polymethyl methacrylate denture base within the psoriasin solution. Notably, immersing the denture base in the solution completely eradicated fungal growth. Our research utilizes natural antifungal proteins within biomedical devices like denture bases, suggesting psoriasin as a safe alternative to chemical antifungals in dental medicine.

biochemistry↗

bioRxiv2024

Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium

Methionine biosynthesis relies on the sequential catalysis of multiple enzymes. Escherichia coli, the main bacteria used in research and industry for protein production and engineering, utilizes the three-step trans-sulfurylation pathway catalyzed by L-homoserine O-succinyl transferase, cystathionine gamma synthase and cystathionine beta lyase to convert L-homoserine to L-homocysteine. However, most bacteria employ the two-step direct-sulfurylation pathway involving L-homoserine O-acetyltransferases and O-acetyl homoserine sulfhydrylase. We previously showed that a methionine-auxotroph E. coli strain (MG1655) with deletion of metA, encoding for L-homoserine O-succinyl transferase, and metB, encoding for cystathionine gamma synthase, could be complemented by introducing the genes metX, encoding for L-homoserine O-acetyltransferases and metY, encoding for O-acetyl homoserine sulfhydrylase, from various sources, thus altering the Escherichia coli methionine biosynthesis metabolic pathway to direct-sulfurylation. However, introducing metX and metY from Corynebacterium glutamicum failed to complement methionine auxotrophy. Herein, we generated a randomized genetic library based on the metX and metY of Corynebacterium glutamicum and transformed it into a methionine-auxotrophic E. coli strain lacking the metA and metB genes. Through multiple enrichment cycles, we successfully isolated active clones capable of growing in M9 minimal media without external methionine supplementation. The dominant metX mutations in the evolved methionine-autotrophs Escherichia coli were L315P and H46R. Interestingly, we found that a metY gene encoding only the N-terminus 106 out of 438 amino acids of the wild-type MetY enzyme is functional and supports the growth of the methionine auxotroph. Recloning the new genes into the original plasmid and transforming them to methionine auxotroph Escherichia coli validated their functionality. These results show that directed enzyme-evolution enables the fast engineering of new active variants within the Escherichia coli methionine direct-sulfurylation pathway, leading to efficient complementation.

biochemistry↗

bioRxiv2023

Conversion of methionine biosynthesis in E. coli from trans- to direct-sulfurylation enhances extracellular methionine levels

Methionine is an essential amino acid in mammals and a critical metabolite in all organisms. As such, various applications, including food, feed, and pharmaceuticals, necessitate the addition of L-methionine. Although amino acids and other metabolites are commonly produced through bacterial fermentation, high-yield biosynthesis of L-methionine remains a significant challenge due to the strict cellular regulation of the biosynthesis pathway. As a result, methionine is produced primarily synthetically, resulting in a racemic mixture of D,L-methionine. This study aimed to enhance methionine bio-production yields in E. coli by replacing its highly regulated trans-sulfurylation pathway with the more common direct-sulfurylation pathway used by other bacteria. To this end, we generated an auxotroph E. coli strain (MG1655) by simultaneously deleting metA and metB genes and complementing them with metX and metY from different bacteria. Complementation of the genetically modified E. coli with metX/metY from Cyclobacterium marinum or Deinococcus geothermalis, together with the deletion of the global repressor metJ and overexpression of the transporter YjeH, resulted in a substantial increase of up to 126 and 160-fold methionine relative to the wild-type strain, respectively, and accumulation of up to 700 mg/L using minimal MOPS medium and 2 ml culture. Our findings provide a method to study methionine biosynthesis and a chassis for enhancing L-methionine production by fermentation. HighlightsO_LIReplacement of E. coli metA and metB with metX and metY recovered its growth C_LIO_LIThe engineered E. coli has a 160-fold increase in extracellular methionine levels C_LIO_LISelection of different metX and metY leads to varying growth rates and enhanced methionine levels C_LI

biochemistry↗

bioRxiv2022

Passive identification of subjective preferences towards individual items using eye-tracking in a virtual reality environment

Usage of Virtual reality (VR) has been growing in many fields of research and therapy thanks to its immersive and gamified nature. Detection of the subjective experience of the users is thus essential for effective personalization of content. Eye-tracking (ET) data and specifically gaze, in two-dimensional tasks has been linked to value-based choices and emotional states. Therefore, here we aimed to develop a method for passive identification of subjective preferences based on ET data collected during a VR experience. For this purpose, we developed a naturalistic dynamic VR task where participants searched and looked at complex objects of pets and control shapes that appeared in pre-defined locations in random order. At the end of the task, participants ranked their preference, valence, and arousal of the items they saw during the task. ET data was recorded using a built-in binocular eye-tracker within the VR headset. We found that the median distance of gaze from the center of objects and the median gaze scan speed showed a significant interaction with object type (pets/shapes), as well as a significant positive relation to preference and valence rankings of pets. Our results suggest that ET could be used as a passive biomarker for detecting individual preferences and pleasantness, and in the future may enable successful personalization of VR content in real time for various applications.

neuroscience↗