Biology subjects

Jacques, S. L.

Publications and source records attributed to Jacques, S. L..

5 recordsLinked to original sources

bioRxiv2022

Graphics processing unit-accelerated Monte Carlo simulation of polarized light in complex three-dimensional media

SignificanceMonte Carlo (MC) methods have been applied for studying interactions between polarized light and biological tissues, but most existing MC codes supporting polarization modeling can only simulate homogeneous or multi-layered domains, resulting in approximations when handling realistic tissue structures. AimOver the past decade, the speed of MC simulations has seen dramatic improvement with massively-parallel computing techniques. Developing hardware-accelerated MC simulation algorithms that can accurately model polarized light inside 3-D heterogeneous tissues can greatly expand the utility of polarization in biophotonics applications. ApproachHere we report a highly efficient polarized MC algorithm capable of modeling arbitrarily complex media defined over a voxelated domain. Each voxel of the domain can be associated with spherical scatters of various radii and densities. The Stokes vector of each simulated photon packet is updated through photon propagation, creating spatially resolved polarization measurements over the detectors or domain surface. ResultsWe have implemented this algorithm in our widely disseminated MC simulator, Monte Carlo eXtreme (MCX). It is validated by comparing with a reference CPU-based simulator in both homogeneous and layered domains, showing excellent agreement and a 931-fold speedup. ConclusionThe polarization-enabled MCX (pMCX) offers biophotonics community an efficient tool to explore polarized light in bio-tissues, and is freely available at http://mcx.space/.

biophysics↗

bioRxiv2021

Fiberoptic Probe For Hemodynamic Spectroscopy in Freely Moving Mice Shows Cerebrovascular Dysregulation In Alzheimers and Glioma Models

SignificanceCerebral vascular reactivity is critical parameters of brain homeostasis in health and disease, but the investigational value of brain oxymetry is diminished by anesthesia and mechanical fixation of the mouse scull. AimWe needed to reduce the physical restrictivity of hemodynamic spectroscopy to enable Alzheimers disease (AD) studies in freely-moving mice. ApproachWe combined spectroscopy, spectral analysis software and a magnetic, implantable device to measure vascular reactivity in unanesthetized, freely-moving mice. We measured cerebral blood volume fraction (CBVF) and oxygen saturation (SO2). ResultsWe validated that our system could detect delayed cerebrovascular recovery from hypoxia in an orthotopic xenograft glioma model under anesthetized condition and we also found increased CBVF and impaired vascular reactivity during hypercapnia in a freely-moving mouse model of AD compared to wild-type littermates. ConclusionsOur optomechanical approach to reproducibly getting light into and out of the brain enabled us to successfully measure CBVF and SO2 during hypercapnia in unanesthetized freely-moving mice. We present hardware and software enabling oximetric analysis of metabolic activity, which provides a safe and reliable method for rapid assessment of vascular reactivity in murine disease models as well as CBVF and SO2.

neuroscience↗

bioRxiv2020

Light-harvesting in mesophotic corals is powered by a spatially efficient photosymbiotic system between coral host and microalgae

The coral-algal photosymbiosis fuels global coral-reef primary productivity, extending from sea level to as deep as 150 m (i.e., mesophotic). Currently, it is largely unknown how such mesophotic reefs thrive despite extremely limited light conditions. Here, we show that corals exhibit a plastic response to mesophotic conditions that involves a spatially optimized regulation of the bio-optical properties by coral host and symbiont. In contrast to shallow corals, mesophotic corals absorbed up to three-fold more light, resulting in excellent photosynthetic response under light conditions of only ~3% of the incident surface irradiance. The enhanced light harvesting capacity of mesophotic corals is regulated by average refractive index fluctuations in the coral skeleton that give rise to optical scattering and facilitate light transport and absorption by densely pigmented host tissue. The results of this study provide fundamental insight into the energy efficiency and light-harvesting mechanisms underlying the productivity of mesophotic coral reef ecosystems, yet also raise concerns regarding their ability to withstand prolonged environmental disturbances.

biophysics↗

bioRxiv2018

Microscale light management and inherent optical properties of intact corals studied with optical coherence tomography

Coral reefs are highly productive photosynthetic systems and coral optics studies suggest that such high efficiency is due to optimised light scattering by coral tissue and skeleton. Here, we characterise the inherent optical properties, i.e., the scattering coefficient, s, and the anisotropy of scattering, g, of 8 intact coral species using optical coherence tomography (OCT). Specifically, we describe light scattering by coral skeletons, coenoarc tissues, polyp tentacles and areas covered by fluorescent pigments (FP). Our results reveal that light scattering between coral species ranges from s = 3 mm-1 (Stylophora pistillata) to s= 25 mm-1 (Echinopora lamelosa). For Platygyra pini, s was 10-fold higher for tissue vs skeleton, while in other corals (e.g. Hydnophora pilosa) no difference was found between tissue and skeletal scattering. Tissue scattering was 3-fold enhanced in coenosarc tissues (s = 24.6 mm-1) vs polyp tentacles (s = 8.3 mm-1) in Turbinaria reniformis. FP scattering was almost isotropic when FP were organized in granule chromatophores (g=0.34) but was forward directed when FP were distributed diffusely in the tissue (g=0.96). Our study provides detailed measurements of coral scattering and establishes a rapid approach for characterising optical properties of photosynthetic soft tissues via OCT in vivo.

biophysics↗

bioRxiv2016

In vivo imaging of coral tissue and skeleton with optical coherence tomography

Optical coherence tomography (OCT) is a non-invasive three-dimensional imaging technique with micrometer resolution allowing microstructural characterization of tissues in vivo and in real time. We present the first application of OCT for in vivo imaging of tissue and skeleton structure of intact living corals spanning a variety of morphologies and tissue thickness. OCT visualized different coral tissue layers (e.g. endoderm vs ectoderm), special structures such as mesenterial filaments and skeletal cavities, as well as mucus release from living corals. We also developed a new approach for non-invasive imaging and quantification of chromatophores containing green fluorescent protein (GFP)-like host pigment granules in coral tissue. The chromatophore system is hyper-reflective and can thus be imaged with good optical contrast in OCT, enabling quantification of chromatophore size, distribution and abundance. Because of its rapid imaging speed, OCT can also be used to quantify coral tissue movement showing that maximal linear contraction velocity was ~120 m per second upon high light stimulation. Based on OCT imaging of tissue expansion and contraction, we made first estimates of dynamic changes in the coral tissue surface area, which varied by a factor of 2 between the contracted and expanded state of the coral Pocillopora damicornis. We conclude that OCT is an excellent novel tool for in vivo tomographic imaging of corals that can reveal tissue and skeleton organization as well as quantify dynamic changes in tissue structure and coral surface area non-invasively and at high spatio-temporal resolution.

biophysics↗