Showing papers by "Qingming Luo published in 2014"

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

Abstract: Next-generation sequencing technology has made the generation of huge amounts of genetic data possible, but phenotype characterization remains slow and difficult. Here the authors develop a high-throughput phenotyping facility for rice that is able to accurately identify and characterize traits related to morphology, biomass and yield.

Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging.

Abstract: Resin embedding is a well-established technique to prepare biological specimens for microscopic imaging. However, it is not compatible with modern green-fluorescent protein (GFP) fluorescent-labelling technique because it significantly quenches the fluorescence of GFP and its variants. Previous empirical optimization efforts are good for thin tissue but not successful on macroscopic tissue blocks as the quenching mechanism remains uncertain. Here we show most of the quenched GFP molecules are structurally preserved and not denatured after routine embedding in resin, and can be chemically reactivated to a fluorescent state by alkaline buffer during imaging. We observe up to 98% preservation in yellow-fluorescent protein case, and improve the fluorescence intensity 11.8-fold compared with unprocessed samples. We demonstrate fluorescence microimaging of resin-embedded EGFP/EYFP-labelled tissue block without noticeable loss of labelled structures. This work provides a turning point for the imaging of fluorescent protein-labelled specimens after resin embedding.

Review: Tissue Optical Clearing Window for Blood Flow Monitoring

Abstract: The tissue optical clearing (TOC) technique could significantly improve the biomedical optical imaging depth, but most current investigations are limited to in vitro studies. For in vivo applications, the TOC method must provide a rapid treatment process, sufficient transparency, and safety for animals, which makes it more difficult. Recently developed innovative optical clearing methods for in vivo use show great potential for enhancing the contrast and resolution of laser speckle contrast imaging (LSCI) for blood flow monitoring. This paper gives an overview of recent progress in the use of TOC for vascular visualization with LSCI. First, the principle of TOC-induced improvement of LSCI and a quantitative analysis method for evaluating the improvement are described briefly. Second, the paper introduces transparent windows, including various skin windows and a cranial window, that permit LSCI to monitor dermal or cortical blood flow, respectively, with high resolution and contrast. Third, preliminary investigations of the safety of TOC demonstrate that the transparent skin window is switchable, which enables LSCI to repeatedly image blood flow. However, research on in vivo TOC is currently less advanced than that on in vitro TOC. Future work should focus on developing a highly effective, safe method and extending its applications.

Studying hemispheric lateralization during a Stroop task through near-infrared spectroscopy-based connectivity

Abstract: . Near-infrared spectroscopy (NIRS) is a developing and promising functional brain imaging technology. Developing data analysis methods to effectively extract meaningful information from collected data is the major bottleneck in popularizing this technology. In this study, we measured hemodynamic activity of the prefrontal cortex (PFC) during a color-word matching Stroop task using NIRS. Hemispheric lateralization was examined by employing traditional activation and novel NIRS-based connectivity analyses simultaneously. Wavelet transform coherence was used to assess intrahemispheric functional connectivity. Spearman correlation analysis was used to examine the relationship between behavioral performance and activation/functional connectivity, respectively. In agreement with activation analysis, functional connectivity analysis revealed leftward lateralization for the Stroop effect and correlation with behavioral performance. However, functional connectivity was more sensitive than activation for identifying hemispheric lateralization. Granger causality was used to evaluate the effective connectivity between hemispheres. The results showed increased information flow from the left to the right hemispheres for the incongruent versus the neutral task, indicating a leading role of the left PFC. This study demonstrates that the NIRS-based connectivity can reveal the functional architecture of the brain more comprehensively than traditional activation, helping to better utilize the advantages of NIRS.

Nasopharyngeal cancer-specific therapy based on fusion peptide-functionalized lipid nanoparticles.

Abstract: Current treatment of advanced-stage nasopharyngeal carcinoma (NPC) is not satisfactory. Targeted therapies offer hope for extending survival. Here, we developed simple, robust, and NPC-specific therapeutic lipid nanoparticles based on a fusion peptide, α-NTP, made up of an amphipathic α-helical peptide (α-peptide) linked to an NPC-specific therapeutic peptide (NTP). We found that α-NTP not only retained the sub-30 nm nanostructure-controlling ability of the α-peptide but also displayed the enhanced NPC-targeting ability of the NTP, in which the α-peptide accelerated the uptake of the NTP by NPC cells, with a 4.8-fold increase. Following uptake, α-NTP-based lipid nanoparticles (α-NTP-LNs) exerted coordinated cytotoxicity by inducing cell death via apoptosis and autophagy. In vivo and ex vivo optical imaging data showed that systemically administered α-NTP-LNs efficiently accumulated in the NPC xenograft tumor and displayed high contrast between tumor and normal tissues, which was further confirmed by flow cytometry that there had been a 13-fold uptake difference between tumor cells and hepatocytes. More importantly, the therapeutic efficacy of α-NTP-LNs was specific to NPC xenograft formed with 5-8F cells but not to fibrosarcoma xenograft formed with HT1080 cells in vivo. The growth of 5-8F tumors was significantly inhibited by α-NTP-LNs, with more than 85% inhibition relative to control groups (e.g., α-NTP and PBS treatment). In a lung metastasis model of NPC, survival was significantly improved by α-NTP-LN treatment. In a word, these excellent properties of α-NTP-LNs worked in sync and synergistically, maximizing the therapeutic efficacy of α-NTP-LNs against NPC and its metastasis.

Reweighted L1 regularization for restraining artifacts in FMT reconstruction images with limited measurements

Abstract: In fluorescence molecular tomography (FMT), many artifacts exist in the reconstructed images because of the inherently ill-posed nature of the FMT inverse problem, especially with limited measurements. A new method based on iterative reweighted L1 (IRL1) regularization is proposed for reducing artifacts with limited measurements. Phantom experiments demonstrate that the reconstructed images have fewer artifacts even with very limited measurements. This indicates that FMT based on IRL1 can obtain high-quality images and thus has the potential to observe dynamic changes in fluorescence-targeted molecules.

Multiresolution analysis of pathological changes in cerebral venous dynamics in newborn mice with intracranial hemorrhage: adrenorelated vasorelaxation.

Abstract: Intracranial hemorrhage (ICH) is the major problem of modern neonatal intensive care. Abnormalities of cerebral venous blood flow (CVBF) can play a crucial role in the development of ICH in infants. The mechanisms underlying these pathological processes remain unclear; however it has been established that the activation of the adrenorelated vasorelaxation can be an important reason. Aiming to reach a better understanding of how the adrenodependent relaxation of cerebral veins contributes to the development of ICH in newborns, we study here the effects of pharmacological stimulation of adrenorelated dilation of the sagittal sinus by isoproterenol on the cerebral venous hemodynamics. Our study is performed in newborn mice at different stages of ICH using the laser speckle contrast imaging and wavelet analysis of the vascular dynamics of CVBF. We show that the dilation of the sagittal sinus with the decreased velocity of blood flow presides to the stress-induced ICH in newborn mice. These morphofunctional vascular changes are accompanied by an increased variance of the wavelet-coefficients in the areas of endothelial and non-endothelial (KATP-channels activity of vascular muscle) sympathetic components of the CVBF variability. Changes in the cerebral venous hemodynamics at the latent stage of ICH are associated with a high responsiveness of the sagittal sinus to isoproterenol quantifying by wavelet-coefficients related to a very slow region of the frequency domain. The obtained results certify that a high activation of the adrenergic-related vasodilatory responses to severe stress in newborn mice can be one of the important mechanisms underlying the development of ICH. Thus, the venous insufficiency with the decreased blood outflow from the brain associated with changes in the endothelial and the sympathetic components of CVBF-variability can be treated as prognostic criteria for the risk of ICH during the first days after birth.

An automated three-dimensional detection and segmentation method for touching cells by integrating concave points clustering and random walker algorithm

Abstract: Characterizing cytoarchitecture is crucial for understanding brain functions and neural diseases. In neuroanatomy, it is an important task to accurately extract cell populations' centroids and contours. Recent advances have permitted imaging at single cell resolution for an entire mouse brain using the Nissl staining method. However, it is difficult to precisely segment numerous cells, especially those cells touching each other. As presented herein, we have developed an automated three-dimensional detection and segmentation method applied to the Nissl staining data, with the following two key steps: 1) concave points clustering to determine the seed points of touching cells; and 2) random walker segmentation to obtain cell contours. Also, we have evaluated the performance of our proposed method with several mouse brain datasets, which were captured with the micro-optical sectioning tomography imaging system, and the datasets include closely touching cells. Comparing with traditional detection and segmentation methods, our approach shows promising detection accuracy and high robustness.

Dynamic monitoring of optical clearing of skin using photoacoustic microscopy and ultrasonography

Abstract: Tissue optical clearing technique has shown great potential for enhancing the imaging depth and contrast of optical imaging modalities. However, the mechanism of optical clearing is still in controversy. In this manuscript, we combined photoacoustic microscopy with ultrasonography to monitor the dermic changes induced by optical clearing agents at different immersion time points. The measured parameters were correlated with the optical clearing process, and could be used to assess the optical clearing effect. Both in vitro and in vivo results demonstrated that photoacoustic microscopy and ultrasonography can potentially be used as a powerful tool in screening optical clearing agents and exploring the mechanism of optical clearing.

Multiscale photoacoustic microscopy with continuously tunable resolution.

Abstract: A multiscale photoacoustic microscope with continuously tunable lateral resolution is developed The tunable resolution is achieved by using an electrical varifocal lens and an optical fiber bundle The varifocal lens is used to generate a size tunable focused laser spot on the tip of the fiber bundle Laser beams emerging from the other end of the fiber bundle are imaged into the object as the excitation light spot for acoustic generation The verified lateral resolution of the system can be tuned from ∼1 μm to more than 448 μm, which span from optical resolution to acoustic resolution Additionally, a mouse ear was imaged in vivo using three different resolutions to demonstrate the feasibility of the multiscale imaging capability of our system

Preclinical evidence of mitochondrial nicotinamide adenine dinucleotide as an effective alarm parameter under hypoxia

Abstract: Early detection of tissue hypoxia in the intensive care unit is essential for effective treatment. Reduced nicotinamide adenine dinucleotide (NADH) has been suggested to be the most sensitive indicator of tissue oxy- genation at the mitochondrial level. However, no experimental evidence comparing the kinetics of changes in NADH and other physiological parameters has been provided. The aim of this study is to obtain the missing data in a systematic and reliable manner. We constructed four acute hypoxia models, including hypoxic hypoxia, hypemic hypoxia, circulatory hypoxia, and histogenous hypoxia, and measured NADH fluorescence, tissue reflectance, cerebral blood flow, respiration, and electrocardiography simultaneously from the induction of hypo- xia until death. We found that NADH was not always the first onset parameter responding to hypoxia. The order of responses was mainly affected by the cause of hypoxia. However, NADH reached its alarm level earlier than the other monitored parameters, ranging from several seconds to >10 min. As such, we suggest that the NADH can be used as a hypoxia indicator, although the exact level that should be used must be further investigated. When the NADH alarm is detected, the body still has a chance to recover if appropriate and timely treatment is provided. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in

Multi-Scale Optical Imaging of the Delayed Type Hypersensitivity Reaction Attenuated by Rapamycin

Abstract: Neutrophils and monocytes/macrophages (MMs) play important roles in the development of cell-mediated delayed type hypersensitivity (DTH). However, the dynamics of neutrophils and MMs during the DTH reaction and how the immunosuppressant rapamycin modulates their behavior in vivo are rarely reported. Here, we take advantage of multi-scale optical imaging techniques and a footpad DTH reaction model to non-invasively investigate the dynamic behavior and properties of immune cells from the whole field of the footpad to the cellular level. During the classic elicitation phase of the DTH reaction, both neutrophils and MMs obviously accumulated at inflammatory foci at 24 h post-challenge. Rapamycin treatment resulted in advanced neutrophil recruitment and vascular hyperpermeability at an early stage (4 h), the reduced accumulation of neutrophils (> 50% inhibition ratio) at 48 h, and the delayed involvement of MMs in inflammatory foci. The motility parameters of immune cells in the rapamycin-treated reaction at 4 h post-challenge displayed similar mean velocities, arrest durations, mean displacements, and confinements as the classic DTH reaction at 24 h. These results indicate that rapamycin treatment shortened the initial preparation stage of the DTH reaction and attenuated its intensity, which may be due to the involvement of T helper type 2 cells or regulatory T cells.

Evaluation of path-history-based fluorescence Monte Carlo method for photon migration in heterogeneous media.

Abstract: The path-history-based fluorescence Monte Carlo method used for fluorescence tomography imaging reconstruction has attracted increasing attention. In this paper, we first validate the standard fluorescence Monte Carlo (sfMC) method by experimenting with a cylindrical phantom. Then, we describe a path-history-based decoupled fluorescence Monte Carlo (dfMC) method, analyze different perturbation fluorescence Monte Carlo (pfMC) methods, and compare the calculation accuracy and computational efficiency of the dfMC and pfMC methods using the sfMC method as a reference. The results show that the dfMC method is more accurate and efficient than the pfMC method in heterogeneous medium.

Cerebral hemodynamic change and metabolic alteration in severe hemorrhagic shock.

Abstract: Understanding the biological mechanism and identifying biomarkers of hemorrhagic shock is important for diagnosis and treatment. We aim to use optical imaging to study how the cerebral blood circulation and metabolism change during the progression of severe hemorrhagic shock, especially the decompensatory stage. We used a multi-parameter (blood pressure (BP), cerebral blood flow (CBF), functional vascular density (FVD), blood oxygenation and mitochondrial NADH signal) cerebral cortex optical imaging system to observe brain hemodynamic change and metabolic alteration of rats in vivo for 4 h. Cerebral circulation and mitochondrial metabolism could be well preserved in the compensatory stage but impaired during the decompensatory stage. The changes of brain hemodynamics and metabolism may provide sensitive indicators for various shock stages including the transition from compensatory stage to decompensatory stage. Our novel imaging observations of hemodynamic and metabolic signals in vivo indicated that the rat brains under hemorrhagic shock suffered irreversible damage which could not be compensated by the autoregulation mechanism, probably due to injured mitochondria.

Early identification of acute hypoxia based on brain NADH fluorescence and cerebral blood flow

Abstract: Hypoxia is closely related to many diseases and often leads to death. Early detection and identification of the hypoxia causes may help to promptly determine the right rescue plan and reduce the mortality. We proposed a new multiparametric monitoring method employing mitochondrial reduced nicotinamide adenine dinucleotide (NADH) fluorescence, regional reflectance, regional cerebral blood flow (CBF), electrocardiography (ECG), and respiration under six kinds of acute hypoxia in four categories to investigate a correlation between the parameter variances and the hypoxia causes. The variation patterns of the parameters were discussed, and the combination of NADH and CBF may contribute to the identification of the causes of hypoxia.

Characterisation and photocatalytic activity of SnO2 films via plasma electrolytic oxidation

Abstract: SnO2 films were prepared by plasma electrolytic oxidation technology in solution containing different concentrations. The structure and photocatalytic activity of the films were characterised by X-ray diffraction, SEM, EDX, Brunauer–Emmett–Teller (BET) and UV-vis spectrophotometer. The result shows that films consisted of pure SnO2, but the grain size increased with the increase of concentration. Porous and rough SnO2 films were formed on the substrate. The BET surface area increased with the increase of concentration and reached its maximum when the concentration of was 0·05M. The absorption edge of the films shifted from 370 to 408 nm when the concentration of increased from 0·01 to 0·03M. Degradation of rhodamine indicated that photocatalytic activity of film formed in 0·03M was highest due to its smaller grain, larger BET surface area and greater photon absorption.

Optimization of sample cooling temperature for redox cryo-imaging.

Abstract: Cryo-imaging techniques have been widely used to measure the metabolic state of tissues by capturing reduced nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) autofluorescence. However, NADH and FAD fluorescence is sensitive to changes in temperature, which may result in unreliable redox ratio calculations. Here, the relationship between the measured redox ratio and sample surface temperature was analyzed using a standard phantom solution and biological tissues. The results indicated that a temperature <−100°C was a suitable cryo-imaging temperature window in which redox ratio measuring was immune to temperature fluctuations. These results may serve as a reference for designing and optimizing redox cryo-imaging experiments for quantitatively mapping the metabolic state of biological samples.

Refractory period modulates the spatiotemporal evolution of cortical spreading depression: a computational study.

Abstract: Cortical spreading depression (CSD) is a pathophysiological phenomenon, which underlies some neurological disorders, such as migraine and stroke, but its mechanisms are still not completely understood One of the striking facts is that the spatiotemporal evolution of CSD wave is varying Observations in experiments reveal that a CSD wave may propagate through the entire cortex, or just bypass some areas of the cortex In this paper, we have applied a 2D reaction-diffusion equation with recovery term to study the spatiotemporal evolution of CSD By modulating the recovery rate from CSD in the modeled cortex, CSD waves with different spatiotemporal evolutions, either bypassing some areas or propagating slowly in these areas, were present Moreover, spiral CSD waves could also be induced in case of the transiently altered recovery rate, ie block release from the absolute refractory period These results suggest that the refractory period contributes to the different propagation patterns of CSD, which may help to interpret the mechanisms of CSD propagation

Multi-color laser beam dynamic compensation synchronous scanning method based on acousto-optic deflector

Abstract: The invention discloses a multi-color laser beam dynamic compensation synchronous scanning method based on an acousto-optic deflector. After undergoing independent dynamic compensation, multi-color laser beams are combined relative to reference light, meanwhile, the combined multi-color laser beams enter the acousto-optic deflector for simultaneous scanning, and therefore deviation angles of the laser beams different in wavelength are kept consistent all the time, and the scanning light beams coincide accurately. Compared with an existing method for achieving multi-color simultaneous scanning in a mechanical scanning mode, the method has the advantages of being free of mechanical inertia, capable of selecting any point for scanning, stable for a long time, high in speed and the like. The method has promotion and application value in the fields of microscopic imaging, laser displaying and recording, laser printing, laser processing and the like.

Visible Brain-wide Networks at Single-neuron Resolution with Micro-Optical Sectioning Tomography

Abstract: We report a protocol combining a novel resin-embedding method for maintaining fluorescence, an automated fluorescence MOST system for long-term stable imaging, and a digital reconstruction-registration-annotation pipeline for tracing the axonal pathways individually in the mouse brain.

Studying hemispheric lateralization during a Stroop task by near-infrared spectroscopy

Abstract: We measured hemodynamic activity of the prefrontal cortex (PFC) during a Chinese color-word matching Stroop task using a homemade continuous-wave NIRS system. Two probes were placed separately over the left and the right PFC. Wavelet transform coherence (WTC) analysis was employed to calculate coherences between all channels of the same probe pairwise to obtain the intrahemispheric functional connectivity for each side of the PFC. The intrahemispheric functional connectivities in both sides of PFC were stronger during the incongruent task compared to that of the neutral task, but only the left intrahemispheric functional connectivity showed a significant Stroop effect. In addition to the Stroop effect, for the incongruent or the neutral task, there was also a leftward lateralization. The results indicate that, compared with traditional activation, NIRS-based connectivity is more sensitive for identifying hemispheric lateralization.

Technical considerations on confocal based fluorescence micro-optical sectioning tomography for visualizing brain circuits

Abstract: Imaging brain circuits is the basis for us to understand brain function and dysfunction. However, imaging axon at micrometer resolution while tracing the centimeter-scale axon projection across the whole-brain is still challenging. Here, we developed a fluorescence micro-optical sectioning tomography (fMOST) imaging system based on confocal fluorescence imaging scheme that can obtain whole brain image stack for visualizing brain circuits at neurite level. We use confocal detection to remove fluorescence background to clearly see one single neurite and use acoustical optical deflector (AOD), an inertia-free beam scanner to realize fast and prolonged stable imaging. We had acquired several complete datasets of whole-mouse brain at a one-micron voxel resolution. Based on these datasets, the uninterrupted tracing of brain-wide, long-distance axonal projections was demonstrated for the first time using a systematic reconstruction and annotation pipeline. Our method is believed to open an avenue to exploring both local and long-distance neural circuits that are related to brain functions and brain diseases down to the neurite level.