Bayesian sparse‐based reconstruction in bioluminescence tomography improves localization accuracy and reduces computational time

Bioluminescence tomography (BLT) provides fundamental insight into biological processes in vivo. To fully realize its potential, it is important to develop image reconstruction algorithms that accurately visualize and quantify the bioluminescence signals taking advantage of limited boundary measurements. In this study, a new 2‐step reconstruction method for BLT is developed by taking advantage of the sparse a priori information of the light emission using multispectral measurements. The first step infers a wavelength‐dependent prior by using all multi‐wavelength measurements. The second step reconstructs the source distribution based on this developed prior. Simulation, phantom and in vivo results were performed to assess and compare the accuracy and the computational efficiency of this algorithm with conventional sparsity‐promoting BLT reconstruction algorithms, and results indicate that the position errors are reduced from a few millimeters down to submillimeter, and reconstruction time is reduced by 3 orders of magnitude in most cases, to just under a few seconds. The recovery of single objects and multiple (2 and 3) small objects is simulated, and the recovery of images of a mouse phantom and an experimental animal with an existing luminescent source in the abdomen is demonstrated. Matlab code is available at https://github.com/jinchaofeng/code/tree/master .      

Sparse‐graph manifold learning method for bioluminescence tomography

In preclinical researches, bioluminescence tomography (BLT) has widely been used for tumor imaging and monitoring, imaged‐guided tumor therapy, and so forth. For these biological applications, both tumor spatial location and morphology analysis are the leading problems needed to be taken into account. However, most existing BLT reconstruction methods were proposed for some specific applications with a focus on sparse representation or morphology recovery, respectively. How to design a versatile algorithm that can simultaneously deal with both aspects remains an impending problem. In this study, a Sparse‐Graph Manifold Learning (SGML) method was proposed to balance the source sparseness and morphology, by integrating non‐convex sparsity constraint and dynamic Laplacian graph model. Furthermore, based on the nonconvex optimization theory and some iterative approximation, we proposed a novel iteratively reweighted soft thresholding algorithm (IRSTA) to solve the SGML model. Numerical simulations and in vivo experiments result demonstrated that the proposed SGML method performed much superior to the comparative methods in spatial localization and tumor morphology recovery for various source settings. It is believed that the SGML method can be applied to the related optical tomography and facilitate the development of optical molecular tomography.     

Integrated photoacoustic and diffuse optical tomography system for imaging of human finger joints in vivo

In this study, we developed a dual‐modality tomographic system that integrated photoacoustic imaging (PAI) and diffuse optical tomography (DOT) into a single platform for imaging human finger joints with fine structures and associated optical properties. In PAI, spherical focused transducers were utilized to collect acoustic signals, and the concept of virtual detector was applied in a conventional back‐projection algorithm to improve the image quality. A finite‐element based reconstruction algorithm was employed to quantitatively recover optical property distribution in the objects for DOT. The phantom results indicate that PAI has a maximum lateral resolution of 70 µm in resolving structures of targets. DOT was able to recover both optical absorption and reduced scattering coefficients of targets accurately. To validate the potential of this system in clinical diagnosis of joint diseases, the distal interphalangeal (DIP) joints of 4 healthy female volunteers were imaged. We successfully obtained high‐resolution images of the phalanx and the surrounding soft tissue via PAI, and recovered both optical absorption and reduced scattering coefficients of phalanx using DOT. The in vivo results suggest that this dual‐modality system has the potential for the early diagnosis of joint diseases such as osteoarthritis (OA) and rheumatoid arthritis (RA).

Integrated PAI/DOT imaging interface (top) and typical reconstruction of structures and associated optical properties of a female finger joint via PAI and DOT (bottom).     

In vivo nonlinear optical imaging to monitor early microscopic changes in a murine cutaneous squamous cell carcinoma model

Early detection of cutaneous squamous cell carcinoma (cSCC) can enable timely therapeutic and preventive interventions for patients. In this study, in vivo nonlinear optical imaging (NLOI) based on two‐photon excitation fluorescence (TPEF) and second harmonic generation (SHG), was used to non‐invasively detect microscopic changes occurring in murine skin treated topically with 7,12‐dimethylbenz(a)anthracene (DMBA). The optical microscopic findings and the measured TPEF‐SHG index show that NLOI was able to clearly detect early cytostructural changes in DMBA treated skin that appeared clinically normal. This suggests that in vivo NLOI could be a non‐invasive tool to monitor early signs of cSCC.

In vivo axial NLOI scans of normal murine skin (upper left), murine skin with preclinical hyperplasia (upper right), early clinical murine skin lesion (lower left) and late or advanced murine skin lesion (lower right).     

Nucleic acid oxidation: an early feature of Alzheimer's disease

Studies of oxidative damage during the progression of Alzheimer's disease (AD) suggest its central role in disease pathogenesis. To investigate levels of nucleic acid oxidation in both early and late stages of AD, levels of multiple base adducts were quantified in nuclear and mitochondrial DNA from the superior and middle temporal gyri (SMTG), inferior parietal lobule (IPL), and cerebellum (CER) of age‐matched normal control subjects, subjects with mild cognitive impairment, preclinical AD, late‐stage AD, and non‐AD neurological disorders (diseased control; DC) using gas chromatography/mass spectrometry. Median levels of multiple DNA adducts in nuclear and mitochondrial DNA were significantly (p ≤ 0.05) elevated in the SMTG, IPL, and CER in multiple stages of AD and in DC subjects. Elevated levels of fapyguanine and fapyadenine in mitochondrial DNA suggest a hypoxic environment early in the progression of AD and in DC subjects. Overall, these data suggest that oxidative damage is an early event not only in the pathogenesis of AD but is also present in neurodegenerative diseases in general.

     

A simple approach for non‐invasive transcranial optical vascular imaging (nTOVI)

In vivo imaging of cerebral vasculature is highly vital for clinicians and medical researchers alike. For a number of years non‐invasive optical‐based imaging of brain vascular network by using standard fluorescence probes has been considered as impossible. In the current paper controverting this paradigm, we present a robust non‐invasive optical‐based imaging approach that allows visualize major cerebral vessels at the high temporal and spatial resolution. The developed technique is simple to use, utilizes standard fluorescent dyes, inexpensive micro‐imaging and computation procedures. The ability to clearly visualize middle cerebral artery and other major vessels of brain vascular network, as well as the measurements of dynamics of blood flow are presented. The developed imaging approach has a great potential in neuroimaging and can significantly expand the capabilities of preclinical functional studies of brain and notably contribute for analysis of cerebral blood circulation in disorder models.

An example of 1 × 1.5 cm color‐coded image of brain blood vessels of mouse obtained in vivo by transcranial optical vascular imaging (TOVI) approach through the intact cranium.     

Elevation of striatal urate in experimental models of Parkinson's disease: a compensatory mechanism triggered by dopaminergic nigrostriatal degeneration?

Epidemiological studies have indicated an inverse association between high uricemia and incidence of Parkinson's disease (PD). To investigate the link between endogenous urate and neurotoxic changes involving the dopaminergic nigrostriatal system, this study evaluated the modifications in the striatal urate levels in two models of PD. To this end, a partial dopaminergic degeneration was induced by 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) in mice, while a severe dopaminergic degeneration was elicited by unilateral medial forebrain bundle infusion of 6‐hydroxydopamine (6‐OHDA) in rats. Urate levels were measured by in vivo microdialysis at 7 or 14 days from toxin exposure. The results obtained demonstrated higher urate levels in the dopamine‐denervated striatum of 6‐OHDA‐lesioned rats compared with the intact striatum. Moreover, an inverse correlation between urate and dopamine levels was observed in the same area. In contrast, only a trend to significant increase in striatal urate was observed in MPTP‐treated mice. These results demonstrate that a damage to the dopaminergic nigrostriatal system elevates the striatal levels of urate, and suggest that this could be an endogenous compensatory mechanism to attenuate dopaminergic neurodegeneration. This finding may be important in light of the epidemiological and preclinical evidences that indicate a link between urate and development of PD.

     

Real-time Imaging of Leukotriene B4 Mediated Cell Migration and BLT1 Interactions with β-arrestin

G-protein coupled receptors (GPCRs) belong to the seven transmembrane protein family and mediate the transduction of extracellular signals to intracellular responses. GPCRs control diverse biological functions such as chemotaxis, intracellular calcium release, gene regulation in a ligand dependent manner via heterotrimeric G-proteins^1-2. Ligand binding induces a series of conformational changes leading to activation of heterotrimeric G-proteins that modulate levels of second messengers such as cyclic adenosine monophosphate (cAMP), inositol triphosphate (IP3) and diacyl glycerol (DG). Concomitant with activation of the receptor ligand binding also initiates a series of events to attenuate the receptor signaling via desensitization, sequestration and/or internalization. The desensitization process of GPCRs occurs via receptor phosphorylation by G-protein receptor kinases (GRKs) and subsequent binding of β-arrestins³. β-arrestins are cytosolic proteins and translocate to membrane upon GPCR activation, binding to phosphorylated receptors (most cases) there by facilitating receptor internalization ^4-6.Leukotriene B₄ (LTB₄) is a pro-inflammatory lipid molecule derived from arachidonic acid pathway and mediates its actions via GPCRs, LTB₄ receptor 1 (BLT1; a high affinity receptor) and LTB₄ receptor 2 (BLT2; a low affinity receptor)^7-9. The LTB₄-BLT1 pathway has been shown to be critical in several inflammatory diseases including, asthma, arthritis and atherosclerosis^10-17. The current paper describes the methodologies developed to monitor LTB₄-induced leukocyte migration and the interactions of BLT1 with β-arrestin and , receptor translocation in live cells using microscopy imaging techniques^18-19.Bone marrow derived dendritic cells from C57BL/6 mice were isolated and cultured as previously described ^20-21. These cells were tested in live cell imaging methods to demonstrate LTB₄ induced cell migration. The human BLT1 was tagged with red fluorescent protein (BLT1-RFP) at C-terminus and β-arrestin1 tagged with green fluorescent protein (β-arr-GFP) and transfected the both plasmids into Rat Basophilic Leukomia (RBL-2H3) cell lines^18-19. The kinetics of interaction between these proteins and localization were monitored using live cell video microscopy. The methodologies in the current paper describe the use of microscopic techniques to investigate the functional responses of G-protein coupled receptors in live cells. The current paper also describes the use of Metamorph software to quantify the fluorescence intensities to determine the kinetics of receptor and cytosolic protein interactions.Download video file.^{(88M, mov)}     

APOE‐modulated Aβ‐induced neuroinflammation in Alzheimer's disease: current landscape,novel data,and future perspective

Chronic glial activation and neuroinflammation induced by the amyloid‐β peptide (Aβ) contribute to Alzheimer's disease (AD) pathology. APOE4 is the greatest AD‐genetic risk factor; increasing risk up to 12‐fold compared to APOE3, with APOE4‐specific neuroinflammation an important component of this risk. This editorial review discusses the role of APOE in inflammation and AD, via a literature review, presentation of novel data on Aβ‐induced neuroinflammation, and discussion of future research directions. The complexity of chronic neuroinflammation, including multiple detrimental and beneficial effects occurring in a temporal and cell‐specific manner, has resulted in conflicting functional data for virtually every inflammatory mediator. Defining a neuroinflammatory phenotype (NIP) is one way to address this issue, focusing on profiling the changes in inflammatory mediator expression during disease progression. Although many studies have shown that APOE4 induces a detrimental NIP in peripheral inflammation and Aβ‐independent neuroinflammation, data for APOE‐modulated Aβ‐induced neuroinflammation are surprisingly limited. We present data supporting the hypothesis that impaired apoE4 function modulates Aβ‐induced effects on inflammatory receptor signaling, including amplification of detrimental (toll‐like receptor 4‐p38α) and suppression of beneficial (IL‐4R‐nuclear receptor) pathways. To ultimately develop APOE genotype‐specific therapeutics, it is critical that future studies define the dynamic NIP profile and pathways that underlie APOE‐modulated chronic neuroinflammation.

     

Topographic prominence as a method for cluster identification in single‐molecule localisation data

Single‐molecule localisation based super‐resolution fluorescence imaging produces maps of the coordinates of fluorescent molecules in a region of interest. Cluster analysis algorithms provide information concerning the clustering characteristics of these molecules, often through the generation of cluster heat maps based on local molecular density. The goal of this study was to generate a new cluster analysis method based on a topographic approach. In particular, a topographic map of the level of clustering across a region is generated based on Getis' variant of Ripley's K‐function. By using the relative heights (topographic prominence, TP) of the peaks in the map, cluster characteristics can be identified more accurately than by using previously demonstrated height thresholds. Analogous to geological TP, the concepts of wet and dry TP and topographic isolation are introduced to generate binary maps. The algorithm is validated using simulated and experimental data and found to significantly outperform previous cluster identification methods.

Illustration of the topographic prominence based cluster analysis algorithm.     

Quantitative IR microscopy and spectromics open the way to 3D digital pathology

Currently, only mass‐spectrometry (MS) microscopy brings a quantitative analysis of chemical contents of tissue samples in 3D. Here, the reconstruction of a 3D quantitative chemical images of a biological tissue by FTIR spectro‐microscopy is reported. An automated curve‐fitting method is developed to extract all intense absorption bands constituting IR spectra. This innovation benefits from three critical features: (1) the correction of raw IR spectra to make them quantitatively comparable; (2) the automated and iterative data treatment allowing to transfer the IR‐absorption spectrum into a IR‐band spectrum; (3) the reconstruction of an 3D IR‐band matrix (x, y, z for voxel position and a 4^th dimension with all IR‐band parameters). Spectromics, which is a new method for exploiting spectral data for tissue metadata reconstruction, is proposed to further translate the related chemical information in 3D, as biochemical and anatomical tissue parameters. An example is given with oxidative stress distribution and the reconstruction of blood vessels in tissues. The requirements of IR microscopy instrumentation to propose 3D digital histology as a clinical routine technology is briefly discussed.

     

Toward the measurement of multiple fluorescence lifetimes in flow cytometry: maximizing multi‐harmonic content from cells and microspheres

Flow cytometry is a powerful means for in vitro cellular analyses where multi‐fluorescence and multi‐angle light scattering can indicate unique biochemical or morphological features of single cells. Yet, to date, flow cytometry systems have lacked the ability to capture complex fluorescence dynamics due to the transient nature of flowing cells. In this contribution we introduce a simple approach for measuring multiple fluorescence lifetimes from a single cytometric event. We leverage square wave modulation, Fourier analysis, and high frequency digitization and show the ability to resolve more than one fluorescence lifetime from fluorescently‐labelled cells and microspheres.

Illustration of a flow cytometer capable of capturing multiple fluorescence lifetime measurements; creating potential for multi‐parametric, time‐resolved signals to be captured for every color channel.     

Nitrate or ammonium: Influences of nitrogen source on the physiology of a green alga

In freshwaters, algal species are exposed to different inorganic nitrogen (N_i) sources whose incorporation varies in biochemical energy demand. We hypothesized that due to the lesser energy requirement of ammonium ()‐use, in contrast to nitrate ()‐use, more energy remains for other metabolic processes, especially under CO₂‐ and phosphorus (P_i) limiting conditions. Therefore, we tested differences in cell characteristics of the green alga Chlamydomonas acidophila grown on or under covariation of CO₂ and P_i‐supply in order to determine limitations, in a full‐factorial design. As expected, results revealed higher carbon fixation rates for ‐grown cells compared to growth with under low CO₂ conditions. ‐grown cells accumulated more of the nine analyzed amino acids, especially under P_i‐limited conditions, compared to cells provided with . This is probably due to a slower protein synthesis in cells provided with . In contrast to our expectations, compared to ‐grown cells ‐grown cells had higher photosynthetic efficiency under P_i‐limitation. In conclusion, growth on the N_i‐source did not result in a clearly enhanced C_i‐assimilation, as it was highly dependent on P_i and CO₂ conditions (replete or limited). Results are potentially connected to the fact that C. acidophila is able to use only CO₂ as its inorganic carbon (C_i) source.     

Inside Cover: In vivo monitoring of thrombosis in mice by optical coherence tomography (J. Biophotonics 11/2019)

Thrombosis monitoring in vivo in small animals is of great value in basic research. The aim of this study is to utilize OCT to monitor thrombosis progression in femoral vein of mice from various measurement criteria, and to validate its use in evaluation the efficacy of the antithrombotic drug. The proved capability of obtaining thrombodynamics information in mice model provide valuable use in preclinical studies for anti‐thrombotic drugs development research. Further details can be found in the article by Yao Yu, Menghan Yu, Jian Liu, et al. ( e201900105 ).

     

Multiple sulphur isotopic interpretations of biosynthetic pathways: implications for biological signatures in the sulphur isotope record

Isotopic fractionations produced by biosynthetic processes are the result of networks of individual biochemical reactions that operate at differing efficiencies and with distinct fractionation factors. These reaction networks determine the magnitude and direction of the net isotopic fractionation associated with a given process. Here we examine the ways that biological reaction networks control mass‐dependent isotopic fractionations of multiple sulphur isotopes. We describe how material‐flow through some networks can produce characteristic multiple‐sulphur‐isotope signatures that differ from those produced by their constituent steps and demonstrate that experimental results with Archaeaglobus fulgidus can be evaluated using multiple sulphur isotopes in the context of previously published models for dissimilatory sulphate reduction. Our evaluation of these data is consistent with the interpretation that the dependence of sulphur isotope fractionation on external sulphate concentration is rooted in differences between the forward and reverse  ? adenosine‐5′‐phosphosulphate (APS) ?  steps. The framework provided by our analysis has the potential to evaluate the biosynthetic pathways that produce the isotopic fractionations, to isolate the primary sources of isotopic fractionations (sulphate reduction or disproportionation reactions) and to establish criteria to identify the signature of specific sulphur metabolisms in the geological record. The results highlight the new types of information that can be obtained by including measurements of δ³³S {δ³³S = [(³³S/³²S)_sample/(³³S/³²S)_reference ? 1]*1000} with measurements of δ³⁴S.     

Monte Carlo method for bioluminescence tomography

Bioluminescence imaging plays an important role in the areas of cancer biology, cell biology, gene therapy, and so on. The 2D planar bioluminescent imaging has been transformed into a 3D framework by bioluminescence tomography (BLT) that enables bioluminescent source reconstruction in a mouse using a modality fusion approach. To solve this BLT problem, a geometrical model of the mouse is usually built from a CT/micro-CT/micro-MRI scan, which facilitates the assignment of optical parameters to various anatomical regions in the model. This optical model is then used to facilitate BLT. The forward model is based on Monte Carlo simulation to calculate the diffuse light flux on the surface of the mouse. The forward model data are used to define the imaging system and perform the BLT reconstruction. In this paper, we report the reconstruction of sources inside a heterogeneous highly scattering physical phantom to demonstrate the feasibility of this Monte Carlo based BLT method.     

Front Cover: Spectrally encoded coherence tomography and reflectometry: Simultaneous en face and cross‐sectional imaging at 2 gigapixels per second (J. Biophotonics 4/2018)

SECTR is a novel multimodal imaging platform for combined volumetric optical coherence tomography (OCT) and en face spectrally encoded reflectometry (SER). The authors demonstrate three‐dimensional motion‐tracking with millisecond temporal and micron spatial resolution using complementary data from OCT and SER, and preliminary algorithms and results showing real‐time image aiming and multi‐volumetric mosaicking for reconstruction of wide‐field composites. The image shows a noninvasively imaged nine‐field mosaic of in vivo human retina and depth‐resolved visualization of tissue microstructures. Further details can be found in the article by Mohamed T. El‐Haddad, Ivan Bozic, and Yuankai K. Tao ( e201700268 )

     

N‐nitrosomelatonin enhances photic synchronization of mammalian circadian rhythms

Most physiological processes in mammals are synchronized to the daily light:dark cycle by a circadian clock located in the hypothalamic suprachiasmatic nucleus. Signal transduction of light‐induced phase advances of the clock is mediated through a neuronal nitric oxide synthase‐guanilyl cyclase pathway. We have employed a novel nitric oxide‐donor, N‐nitrosomelatonin, to enhance the photic synchronization of circadian rhythms in hamsters. The intraperitoneal administration of this drug before a sub‐saturating light pulse at circadian time 18 generated a twofold increase of locomotor rhythm phase‐advances, having no effect over saturating light pulses. This potentiation was also obtained even when inhibiting suprachiasmatic nitric oxide synthase activity. However, N‐nitrosomelatonin had no effect on light‐induced phase delays at circadian time 14. The photic‐enhancing effects were correlated with an increased suprachiasmatic immunoreactivity of FBJ murine osteosarcoma viral oncogene and period1. Moreover, in vivo nitric oxide release by N‐nitrosomelatonin was verified by measuring nitrate and nitrite levels in suprachiasmatic nuclei homogenates. The compound also accelerated resynchronization to an abrupt 6‐h advance in the light:dark cycle (but not resynchronization to a 6‐h delay). Here, we demonstrate the chronobiotic properties of N‐nitrosomelatonin, emphasizing the importance of nitric oxide‐mediated transduction for circadian phase advances.

     

Striatal serotonin 2C receptors decrease nigrostriatal dopamine release by increasing GABA‐A receptor tone in the substantia nigra

Drugs acting at the serotonin‐2C (5‐HT2C) receptor subtype have shown promise as therapeutics in multiple syndromes including obesity, depression, and Parkinson's disease. While it is established that 5‐HT2C receptor stimulation inhibits DA release, the neural circuits and the localization of the relevant 5‐HT2C receptors remain unknown. This study used dual‐probe in vivo microdialysis to investigate the relative contributions of 5‐HT2C receptors localized in the rat substantia nigra (SN) and caudate‐putamen (CP) in the control of nigrostriatal DA release. Systemic administration (3.0 mg/kg) of the 5‐HT2C receptor selective agonist Ro 60‐0175 [(αS)‐6‐Chloro‐5‐fluoro‐α‐methyl‐1H‐indole‐1‐ethanamine fumarate] decreased, whereas intrastriatal infusions of the selective 5‐HT2C antagonist SB 242084 [6‐Chloro‐2,3‐dihydro‐5‐methyl‐N‐[6‐[(2‐methyl‐3‐pyridinyl)oxy]‐3‐pyridinyl]‐1H‐indole‐1‐carboxyamide; 1.0 μM] increased, basal DA in the CP. Depending on the site within the SN pars reticulata (SNpr), infusions of SB 242084 had more modest but significant effects. Moreover, infusions of the GABA‐A receptor agonist muscimol (10 μM) into the SNpr completely reversed the increases in striatal DA release produced by intrastriatal infusions of SB 242084. These findings suggest a role for 5‐HT2C receptors regulating striatal DA release that is highly localized. 5‐HT2C receptors localized in the striatum may represent a primary site of action that is mediated by the actions on GABAergic activity in the SN.

     

Kinetic modeling of [18F]VAT,a novel radioligand for positron emission tomography imaging vesicular acetylcholine transporter in non‐human primate brain

Molecular imaging of vesicular acetylcholine transporter (VACh T) in the brain provides an important cholinergic biomarker for the pathophysiology and treatment of dementias including Alzheimer's disease. In this study, kinetics modeling methods were applied and compared for quantifying regional brain uptake of the VACh T‐specific positron emission tomography radiotracer, ((?)‐(1‐(‐8‐(2‐fluoroethoxy)‐3‐hydroxy‐1,2,3,4‐tetrahydronaphthalen‐2‐yl)piperidin‐4‐yl)(4‐fluorophenyl)‐methanone) ([¹⁸F]VAT ) in macaques. Total volume distribution (V _T ) estimates were compared for one‐tissue compartment model (1TCM ), two‐tissue compartment model (2TCM ), Logan graphic analysis (LoganAIF ) and multiple linear analysis (MA 1) with arterial blood input function using data from three macaques. Using the cerebellum‐hemispheres as the reference region with data from seven macaques, three additional models were compared: reference tissue model (RTM ), simplified RTM (SRTM ), and Logan graphic analysis (LoganREF ). Model selection criterion indicated that a) 2TCM and SRTM were the most appropriate kinetics models for [¹⁸F]VAT ; and b) SRTM was strongly correlated with 2TCM (Pearson's coefficients r  > 0.93, p  < 0.05). Test–retest studies demonstrated that [¹⁸F]VAT has good reproducibility and reliability (TRV < 10%, ICC > 0.72). These studies demonstrate [¹⁸F]VAT is a promising VACh T positron emission tomography tracer for quantitative assessment of VACh T levels in the brain of living subjects.