Optical molecular imaging for systems biology: from molecule to organism

Photodynamic effect of indocyanine green and its application to hepatocellular carcinoma treatment

Hepatocellular carcinoma (HCC) stands as the primary cause of liver cancers, with limited treatment options outside of surgical resection or transplant. Photodynamic therapy (PDT) using indocyanine green (ICG) as a photosensitizer offers a promising therapeutic option for HCC. ICG PDT has demonstrated efficacy in vitro and in vivo , providing a safe treatment option for patients ineligible for resection or transplant. Challenges in PDT optimization include limited light delivery, poor photosensitizer optimization, and low oxygen generation. Innovative solutions, such as ICG incorporation into nanostructures and direct administration for HCC cases, show promise. Combining ICG PDT with Lentinula edodes mycelia (LEM) and hydrogen gas inhalation may address oxygen production limitations. Utilizing a combination of therapeutic approaches and therapies may increase the efficacy of ICG PDT, making it the safer and more effective treatment option for patients. ICG’s proven clinical safety may expedite potential approval for its use in PDT. Advancements in photosensitizer technology, such as aggregation-induced emission photosensitizers (AIE-PSs), and combination therapies will enhance PDT efficacy shortly, as developments show promise for improved outcomes. For HCC patients, ICG PDT presents a valuable therapeutic option. This work is novel because it explores new combination therapy approaches, leveraging the benefits of PDT with ICG and the developments in photosensitizer technology, nanotechnology, and the combination of other treatments such as LEM and hydrogen gas, which could potentially revolutionize the treatment of HCC and offer a better prognosis for patients.

In vivo optical molecular imaging of inflammation and immunity

Inflammation is the phenotypic form of various diseases. Recent development in molecular imaging provides new insights into the diagnostic and therapeutic evaluation of different inflammatory diseases as well as diseases involving inflammation such as cancer. While conventional imaging techniques used in the clinical setting provide only indirect measures of inflammation such as increased perfusion and altered endothelial permeability, optical imaging is able to report molecular information on diseased tissue and cells. Optical imaging is a quick, noninvasive, nonionizing, and easy-to-use diagnostic technology which has been successfully applied for preclinical research. Further development of optical imaging technology such as optoacoustic imaging overcomes the limitations of mere fluorescence imaging, thereby enabling pilot clinical applications in humans. By means of endogenous and exogenous contrast agents, sites of inflammation can be accurately visualized in vivo. This allows for early disease detection and specific disease characterization, enabling more rapid and targeted therapeutic interventions. In this review, we summarize currently available optical imaging techniques used to detect inflammation, including optical coherence tomography (OCT), bioluminescence, fluorescence, optoacoustics, and Raman spectroscopy. We discuss advantages and disadvantages of the different in vivo imaging applications with a special focus on targeting inflammation including immune cell tracking.

Coupling of Laser Ablation and the Liquid Sampling-Atmospheric Pressure Glow Discharge Plasma for Simultaneous, Comprehensive Mapping: Elemental, Molecular, and Spatial Analysis

The spatial distributions of elemental and molecular species are vital pieces of information for a broad number of applications such as material development and bio/environmental analysis. There is currently no single analytical method that can simultaneously acquire elemental, molecular, and spatial information from a single sample. This paper presents the coupling of an NWR213 laser ablation (LA) system to the liquid sampling-atmospheric pressure glow discharge (LS-APGD) microplasma for combined atomic and molecular (CAM) analysis. The work demonstrates a fundamental balance that must be considered between the extent of fragmentation of molecules and ionization of atoms for CAM analysis. Detailed studies showed that the interelectrode gap to be a critical parameter for controlling the ionization efficiency of atomic and molecular species. Utilizing Design-of-Experiment (DoE) procedures, the discharge current was also found to be a significant parameter to control. Elemental lead, caffeine, and simultaneous lead and caffeine analysis via LA-LS-APGD-MS was made possible through improved understanding of the influence of plasma parameters on the product mass spectra of laser-ablated particles. Finally, a chemical map of elemental lead and molecular caffeine, from lead nitrate and caffeine residues, was generated, demonstrating the comprehensive mapping capabilities of LA-LS-APGD-MS. The practical relevance of the capabilities is demonstrated by mapping glutamic acid from a cryosectioned chicken breast with a thallium spike deposited within the tissue. It is believed that the LA-LS-APGD-MS could be a valuable methodology for the simultaneous mapping of elemental and molecular species from a variety of samples.

Label-free optical imaging in developmental biology [Invited]

Application of optical imaging in developmental biology marks an exciting frontier in biomedical optics. Optical resolution and imaging depth allow for investigation of growing embryos at subcellular, cellular, and whole organism levels, while the complexity and variety of embryonic processes set multiple challenges stimulating the development of various live dynamic embryonic imaging approaches. Among other optical methods, label-free optical techniques attract an increasing interest as they allow investigation of developmental mechanisms without application of exogenous markers or fluorescent reporters. There has been a boost in development of label-free optical imaging techniques for studying embryonic development in animal models over the last decade, which revealed new information about early development and created new areas for investigation. Here, we review the recent progress in label-free optical embryonic imaging, discuss specific applications, and comment on future developments at the interface of photonics, engineering, and developmental biology.

Molecular Imaging of the Heart

Multimodality cardiovascular imaging is routinely used to assess cardiac function, structure, and physiological parameters to facilitate the diagnosis, characterization, and phenotyping of numerous cardiovascular diseases (CVD), as well as allows for risk stratification and guidance in medical therapy decision-making. Although useful, these imaging strategies are unable to assess the underlying cellular and molecular processes that modulate pathophysiological changes. Over the last decade, there have been great advancements in imaging instrumentation and technology that have been paralleled by breakthroughs in probe development and image analysis. These advancements have been merged with discoveries in cellular/molecular cardiovascular biology to burgeon the field of cardiovascular molecular imaging. Cardiovascular molecular imaging aims to noninvasively detect and characterize underlying disease processes to facilitate early diagnosis, improve prognostication, and guide targeted therapy across the continuum of CVD. The most-widely used approaches for preclinical and clinical molecular imaging include radiotracers that allow for high-sensitivity in vivo detection and quantification of molecular processes with single photon emission computed tomography and positron emission tomography. This review will describe multimodality molecular imaging instrumentation along with established and novel molecular imaging targets and probes. We will highlight how molecular imaging has provided valuable insights in determining the underlying fundamental biology of a wide variety of CVDs, including: myocardial infarction, cardiac arrhythmias, and nonischemic and ischemic heart failure with reduced and preserved ejection fraction. In addition, the potential of molecular imaging to assist in the characterization and risk stratification of systemic diseases, such as amyloidosis and sarcoidosis will be discussed. © 2019 American Physiological Society. Compr Physiol 9:477-533, 2019.

Superparamagnetic graphene quantum dot as a dual-modality contrast agent for confocal fluorescence microscopy and magnetomotive optical coherence tomography

A magnetic graphene quantum dot (MGQD) nanoparticle, synthesized by hydrothermally reducing and cutting graphene oxide-iron oxide sheet, was demonstrated to possess the capabilities of simultaneous confocal fluorescence and magnetomotive optical coherence tomography (MMOCT) imaging. This MGQD shows low toxicity, significant tunable blue fluorescence and superparamagnetism, which can thus be used as a dual-modality contrast agent for confocal fluorescence microscopy (CFM) and MMOCT. The feasibility of applying MGQD as a tracer of cells is shown by imaging and visualizing MGQD labeled cells using CFM and our in-house MMOCT. Since MMOCT and CFM can offer anatomical structure and intracellular details, respectively, the MGQD for cell tracking could provide a more comprehensive diagnosis.

Molecular Imaging of Acute Cardiac Transplant Rejection: Animal Experiments and Prospects

Acute rejection (AR) remains the biggest challenge during the first year after heart transplantation despite advances in immunosuppressive therapy. The early detection and curbing of AR are crucial to the survival of transplant recipients. However, as the criterion standard for AR, endomyocardial biopsy has several limitations because of its inherent invasiveness and morbidity. Traditional imaging techniques, such as echocardiography and cardiac magnetic resonance imaging, are of certain value for AR, but their diagnostic criteria and accuracy remain in question. Molecular imaging sheds new light on AR diagnosis because it can provide information about gene expression and the location of molecules and cells. This article reviews the latest research and applications of several typical modalities of molecular imaging used in AR and discusses their advantages and disadvantages.

Triethylene glycol-modified iridium(iii) complexes for fluorescence imaging of Schistosoma japonicum

Schistosomiasis, an infectious disease caused by the Schistosoma parasitic worm, presents a serious public health issue. To date, investigation of anti-Schistosomiasis drug mechanisms through fluorescence imaging remains challenging due to the lack of appropriate dyes as fluorescent probes. Phosphorescent Ir(iii) complexes have been attracting substantial attention among various classes of fluorophores given their excellent photophysical properties. Herein, four phosphorescent Ir(iii) complexes were synthesized, two of which contained a triethylene glycol (TEG) hydrophilic group. The phosphorescent emission range of the four complexes lay between 500 and 750 nm, and their quantum yields ranged from 0.031 to 0.146. Furthermore, under the experimental concentration conditions, the TEG-modified complexes had low cytotoxicity. Cell fluorescence labeling experiments indicated that the TEG-modified complexes had good membrane permeability. Finally, the TEG-modified complexes showed remarkable labeling effects in adult Schistosoma fluorescence imaging. Thus, TEG-modified Ir(iii) complexes could be used as a new class of bilharzial fluorescent probes.

Ternary graphene quantum dot-polydopamine-Mn3O4 nanoparticles for optical imaging guided photodynamic therapy and T1-weighted magnetic resonance imaging

Imaging-guided therapy, which bridges treatment and diagnosis, plays an important role in overcoming the limitations of classical cancer therapy. To provide a more exact location of the tumor and to reduce side effects to normal tissues, a multifunctional probe was designed to serve as both an imaging agent and a therapeutic agent. Ternary hybrid nanoparticles comprised of visible red-responsive graphene, the T1-weighted magnetic resonance imaging (MRI) agent Mn3O4 and a mussel-inspired linker polydopamine. The conjugation of graphene to Mn3O4 through polydopamine enhanced the water solubility of Mn3O4, enabling an efficient uptake by cancer cells as well as tumor accumulation when the nanoparticles were intravenously administered into mice. These nanoparticles, when localized at a tumor site, exhibited low cytotoxicity in the dark, while light irradiation of the cancer cells transfected with the nanoparticles resulted in significant phototherapeutic effects, apparently by generating toxic reactive oxygen species. These nanoparticles also allowed excellent T1-weighted MR imaging in a human lung cancer xenograft model and were successfully used for combined visible red-imaging-guided photodynamic therapy and T1-weighted MRI.

Antibody-based imaging strategies for cancer

Although mainly developed for preclinical research and therapeutic use, antibodies have high antigen specificity, which can be used as a courier to selectively deliver a diagnostic probe or therapeutic agent to cancer. It is generally accepted that the optimal antigen for imaging will depend on both the expression in the tumor relative to normal tissue and the homogeneity of expression throughout the tumor mass and between patients. For the purpose of diagnostic imaging, novel antibodies can be developed to target antigens for disease detection, or current FDA-approved antibodies can be repurposed with the covalent addition of an imaging probe. Reuse of therapeutic antibodies for diagnostic purposes reduces translational costs since the safety profile of the antibody is well defined and the agent is already available under conditions suitable for human use. In this review, we will explore a wide range of antibodies and imaging modalities that are being translated to the clinic for cancer identification and surgical treatment.

Photosensitizer conjugated iron oxide nanoparticles for simultaneous in vitro magneto-fluorescent imaging guided photodynamic therapy

A hybrid nanoparticle composed of a photodynamic agent pheophorbide A linked with Fe₃O₄ through heparin and APTES for MR imaging and phototherapy.

Three-dimensional fuse deposition modeling of tissue-simulating phantom for biomedical optical imaging

Biomedical optical devices are widely used for clinical detection of various tissue anomalies. However, optical measurements have limited accuracy and traceability, partially owing to the lack of effective calibration methods that simulate the actual tissue conditions. To facilitate standardized calibration and performance evaluation of medical optical devices, we develop a three-dimensional fuse deposition modeling (FDM) technique for freeform fabrication of tissue-simulating phantoms. The FDM system uses transparent gel wax as the base material, titanium dioxide (TiO2 ) powder as the scattering ingredient, and graphite powder as the absorption ingredient. The ingredients are preheated, mixed, and deposited at the designated ratios layer-by-layer to simulate tissue structural and optical heterogeneities. By printing the sections of human brain model based on magnetic resonance images, we demonstrate the capability for simulating tissue structural heterogeneities. By measuring optical properties of multilayered phantoms and comparing with numerical simulation, we demonstrate the feasibility for simulating tissue optical properties. By creating a rat head phantom with embedded vasculature, we demonstrate the potential for mimicking physiologic processes of a living system.

New researches and application progress of commonly used optical molecular imaging technology

Optical molecular imaging, a new medical imaging technique, is developed based on genomics, proteomics and modern optical imaging technique, characterized by non-invasiveness, non-radiativity, high cost-effectiveness, high resolution, high sensitivity and simple operation in comparison with conventional imaging modalities. Currently, it has become one of the most widely used molecular imaging techniques and has been applied in gene expression regulation and activity detection, biological development and cytological detection, drug research and development, pathogenesis research, pharmaceutical effect evaluation and therapeutic effect evaluation, and so forth, This paper will review the latest researches and application progresses of commonly used optical molecular imaging techniques such as bioluminescence imaging and fluorescence molecular imaging.

Light microscopy applications in systems biology: opportunities and challenges

Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular processes work on a cellular scale. However, imaging can also be used as a top-down approach to study the behavior of a system without detailed prior knowledge about its underlying molecular mechanisms. In this review, we highlight the recent developments on microscopy-based systems analyses and discuss the complementary opportunities and different challenges with high-content screening and high-throughput imaging. Furthermore, we provide a comprehensive overview of the available platforms that can be used for image analysis, which enable community-driven efforts in the development of image-based systems biology.

Estimation of neoplasia-related biological parameters through modeling and sensitivity analysis of optical molecular imaging data

We combine system's biology approaches with in vivo optical molecular imaging of epithelial neoplasia for estimating disease-specific biological parameters. Molecular imaging measures and maps the dynamic optical effects, generated by the topical application of acetic acid diluted solution. The dynamic characteristics of the in vivo measured optical signal are governed by the epithelial transport effects of the biomarker. Nine biological parameters, both structural and functional, have been identified to be potentially correlated with the neoplasia growth and to be manifested to the measured data in a convoluted manner. A compartmental model of the cervical neoplastic epithelium has been developed, which predicts the dynamic optical effects in all possible parameter value combinations. We have performed global sensitivity analysis for the purpose of identifying the subset of the input parameters that are the key determinants of the model's output. Finally, we have for the first time shown that it is possible to estimate, from in vivo measured dynamic optical data, the following neoplasia related parameters: number of neoplastic layers, intracellular and extracellular space dimensions, functionality of tight junctions, and extracellular pH. These findings have been (in part) validated with optical data and biopsies obtained from 30 women with cervical neoplasia.

Multiscale imaging and computational modeling of blood flow in the tumor vasculature

The evolution in our understanding of tumor angiogenesis has been the result of pioneering imaging and computational modeling studies spanning the endothelial cell, microvasculature and tissue levels. Many of these primary data on the tumor vasculature are in the form of images from pre-clinical tumor models that provide a wealth of qualitative and quantitative information in many dimensions and across different spatial scales. However, until recently, the visualization of changes in the tumor vasculature across spatial scales remained a challenge due to a lack of techniques for integrating micro- and macroscopic imaging data. Furthermore, the paucity of three-dimensional (3-D) tumor vascular data in conjunction with the challenges in obtaining such data from patients presents a serious hurdle for the development and validation of predictive, multiscale computational models of tumor angiogenesis. In this review, we discuss the development of multiscale models of tumor angiogenesis, new imaging techniques capable of reproducing the 3-D tumor vascular architecture with high fidelity, and the emergence of "image-based models" of tumor blood flow and molecular transport. Collectively, these developments are helping us gain a fundamental understanding of the cellular and molecular regulation of tumor angiogenesis that will benefit the development of new cancer therapies. Eventually, we expect this exciting integration of multiscale imaging and mathematical modeling to have widespread application beyond the tumor vasculature to other diseases involving a pathological vasculature, such as stroke and spinal cord injury.

FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins

We report a new technique to detect enzyme activity inside cells. The method based on Fluorescence Lifetime Imaging (FLIM) technology allows one to follow sensor cleavage by proteolytic enzyme caspase-3. Specifically, we use the FLIM FRET of living cells via the confocal fluorescence microscopy. A specially designed lentivector pLVT with the DNA fragment of TagRFP-23-KFP was applied for transduction of A549 cell lines. Computer simulations are carried out to estimate FRET efficiency and to analyze possible steric restrictions of the reaction between the substrate TagRFP-23-KFP and caspase-3 dimer. Successful use of the fuse protein TagRFP-23-KFP to register the caspase-3 activation based on average life-time measurements is demonstrated. We show that the average life-time distribution is dramatically changed for cells with the modified morphology that is typical for apoptosis. Namely, the short-lived component at 1.8-2.1 ns completely disappears and the long-lived component appears at 2.4-2.6 ns. The latter is a fingerprint of the TagRFP molecule released after cleavage of the TagRFP-23-KFP complex by caspase-3. Analysis of life-time distributions for population of cells allows us to discriminate apoptotic and surviving cells within single frame and to peform statistical analysis of drug efficiency. This system can be adjusted for HTS by using special readers oriented on measurements of fluorescence life-time.

Selective targeting of microglia by quantum dots

Background

Microglia, the resident immune cells of the brain, have been implicated in brain injury and various neurological disorders. However, their precise roles in different pathophysiological situations remain enigmatic and may range from detrimental to protective. Targeting the delivery of biologically active compounds to microglia could help elucidate these roles and facilitate the therapeutic modulation of microglial functions in neurological diseases.

Methods

Here we employ primary cell cultures and stereotaxic injections into mouse brain to investigate the cell type specific localization of semiconductor quantum dots (QDs) in vitro and in vivo. Two potential receptors for QDs are identified using pharmacological inhibitors and neutralizing antibodies.

Results

In mixed primary cortical cultures, QDs were selectively taken up by microglia; this uptake was decreased by inhibitors of clathrin-dependent endocytosis, implicating the endosomal pathway as the major route of entry for QDs into microglia. Furthermore, inhibiting mannose receptors and macrophage scavenger receptors blocked the uptake of QDs by microglia, indicating that QD uptake occurs through microglia-specific receptor endocytosis. When injected into the brain, QDs were taken up primarily by microglia and with high efficiency. In primary cortical cultures, QDs conjugated to the toxin saporin depleted microglia in mixed primary cortical cultures, protecting neurons in these cultures against amyloid beta-induced neurotoxicity.

Conclusions

These findings demonstrate that QDs can be used to specifically label and modulate microglia in primary cortical cultures and in brain and may allow for the selective delivery of therapeutic agents to these cells.

NIR-mbc94, a fluorescent ligand that binds to endogenous CB(2) receptors and is amenable to high-throughput screening

High-throughput screening (HTS) of chemical libraries is often used for the unbiased identification of compounds interacting with G protein-coupled receptors (GPCRs), the largest family of therapeutic targets. However, current HTS methods require removing GPCRs from their native environment, which modifies their pharmacodynamic properties and biases the screen toward false positive hits. Here, we developed and validated a molecular imaging (MI) agent, NIR-mbc94, which emits near infrared (NIR) light and selectively binds to endogenously expressed cannabinoid CB(2) receptors, a recognized target for treating autoimmune diseases, chronic pain and cancer. The precision and ease of this assay allows for the HTS of compounds interacting with CB(2) receptors expressed in their native environment.

A near-infrared optical tomography system based on photomultiplier tube

Diffuse optical tomography (DOT) is a rapidly growing discipline in recent years. It plays an important role in many fields, such as detecting breast cancer and monitoring the cerebra oxygenation. In this paper, a relatively simple, inexpensive, and conveniently used DOT system is presented in detail, in which only one photomultiplier tube is employed as the detector and an optical multiplexer is used to alter the detector channels. The 32-channel imager is consisted of 16-launch fibers and 16-detector fibers bundles, which works in the near-infrared (NIR) spectral range under continuous-wave (CW) model. The entire imaging system can work highly automatically and harmoniously. Experiments based on the proposed imaging system were performed, and the desired results can be obtained. The experimental results suggested that the proposed imaging instrumentation is effective.

A chemical signal generator for resolving temporal dynamics of single cells

To investigate rapid cell signaling, analytical methods are required that can generate repeatable chemical signals for stimulating live cells with high temporal resolution. Here, we present a chemical signal generator based on hydrodynamic gating, permitting flexible stimulation of single adherent cells with a temporal resolution of 20 ms. Studies of adenosine triphosphate (ATP)-induced calcium signaling in HeLa cells were demonstrated using this developed method. Consecutive treatment of the cells with ATP pulses of 20 or 1 s led to an increase of latency, which might be another indicator of receptor desensitization in addition to the decrease in the amplitude of calcium spikes. With increasing duration of ATP pulses from milliseconds to a few seconds, the cellular responses transitioned from single calcium spikes to calcium oscillation gradually. We expected this method to open up a new avenue for potential investigation of rapid cell signaling.

Combined Cerenkov luminescence and nuclear imaging of radioiodine in the thyroid gland and thyroid cancer cells expressing sodium iodide symporter: initial feasibility study

Radioiodine (RI) such as (131)I or (124)I, can generate luminescent emission and be detected with an optical imaging (OI) device. To evaluate the possibility of a novel Cerenkov luminescence imaging (CLI) for application in thyroid research, we performed feasibility studies of CLI by RI in the thyroid gland and human anaplastic thyroid carcinoma cells expressing sodium iodide symporter gene (ARO-NIS). For in vitro study, FRTL-5 and ARO-NIS were incubated with RI, and the luminometric and CLI intensity was measured with luminometer and OI device. Luminescence intensity was compared with the radioactivity measured with γ-counter. In vivo CLI of the thyroid gland was performed in mice after intravenous injection of RI with and without thyroid blocking. Mice were implanted with ARO-NIS subcutaneously, and CLI was performed with injection of (124)I. Small animal PET or γ-camera imaging was also performed. CLI intensities of thyroid gland and ARO-NIS were quantified, and compared with the radioactivities measured from nuclear images (NI). Luminometric assay and OI confirmed RI uptake in the cells in a dose-dependent manner, and luminescence intensity was well correlated with radioactivity of the cells. CLI clearly demonstrated RI uptake in thyroid gland and xenografted ARO-NIS cells in mice, which was further confirmed by NI. A strong positive correlation was observed between CLI intensity and radioactivity assessed by NI. We successfully demonstrated dual molecular imaging of CLI and NI using RI both in vitro and in vivo. CLI can provide a new OI strategy in preclinical thyroid studies.

In vivo dynamic imaging, in silico modeling and global sensitivity analysis for the study and the diagnosis of epithelial neoplasia

We present a method for detecting and studying neoplasia-specific functional and structural features through the combination of in vivo dynamic imaging, in silico modeling and global sensitivity analysis. We particularly present the case of cervical epithelium interacting with acetic acid solution, which is employed as an optical biomarker. The in vivo measured dynamic scattering characteristics are strongly correlated with the output of the biomarker's pharmacokinetic model that we have developed. Model global sensitivity analysis has shown that the measured/modeled bio-optical processes can be used for probing, in vivo, the number of neoplastic layers, the extracellular pH, the intracellular buffering efficiency and the size of the extracellular space.

Lifetime imaging of FRET between red fluorescent proteins

Numerous processes in cells can be traced by using fluorescence resonance energy transfer (FRET) between two fluorescent proteins. The novel FRET pair including the red fluorescent protein TagRFP and kindling fluorescent protein KFP for sensing caspase-3 activity is developed. The lifetime mode of FRET measurements with a nonfluorescent protein KFP as an acceptor is used to minimize crosstalk due to its direct excitation. The red fluorescence is characterized by a better penetrability through the tissues and minimizes the cell autofluorescence signal. The effective transfection and expression of the FRET sensor in eukaryotic cells is shown by FLIM. The induction of apoptosis by camptothecine increases the fluorescence lifetime, which means effective cleavage of the FRET sensor by caspase-3. The instruments for detecting whole-body fluorescent lifetime imaging are described. Experiments on animals show distinct fluorescence lifetimes for the red fluorescent proteins possessing similar spectral properties.

A review of current applications of mass spectrometry for neuroproteomics in epilepsy

The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology-based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large-scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far-reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society.

Polyfluorophores on a DNA backbone: a multicolor set of labels excited at one wavelength

We recently described the assembly of fluorescent deoxyriboside monomers ("fluorosides") into DNA-like phosphodiester oligomers (oligodeoxyfluorosides or ODFs) in which hydrocarbon and heterocyclic aromatic fluorophores interact both physically and electronically. Here we report the identification of a multicolor set of water-soluble ODF dyes that display emission colors across the visible spectrum, and all of which can be simultaneously excited by long-wavelength UV light at 340-380 nm. Multispectral dye candidates were chosen from a library of 4096 tetramer ODFs constructed on PEG-polystyrene beads using a simple long-pass filter to observe all visible colors at the same time. We resynthesized and characterized a set of 23 ODFs containing one to four individual chromophores and included 2-3 spacer monomers to increase aqueous solubility and minimize aggregation. Emission maxima of this set range from 376 to 633 nm, yielding apparent colors from violet to red, all of which can be visualized directly. The spectra of virtually all ODFs in this set varied considerably from the simple combination of monomer components, revealing extensive electronic interactions between the presumably stacked monomers. In addition, comparisons of anagrams in the set (isomers having the same components in a different sequence) reveal the importance of nearest-neighbor interactions in the emissive behavior. Preliminary experiments with human tumor (HeLa) cells, observing two ODFs by laser confocal microscopy, showed that they can penetrate the outer cellular membrane, yielding cytoplasmic localization. In addition, a set of four distinctly colored ODFs was incubated with live zebrafish embryos, showing tissue penetration, apparent biostability, and no apparent toxicity. The results suggest that ODF dyes may be broadly useful as labels in biological systems, allowing the simultaneous tracking of multiple species by color, and allowing visualization in moving systems where classical fluorophores fail.

ULTRASHORT PULSE MULTISPECTRAL NONLINEAR OPTICAL MICROSCOPY

Ultrashort pulse, multispectral nonlinear optical microscopy (NLOM) is developed and used to image, simultaneously, a mixed population of cells expressing different fluorescent protein mutants in a 3D tissue model of angiogenesis. Broadband, sub-10-fs pulses are used to excite multiple fluorescent proteins and generate second harmonic in collagen simultaneously. A 16-channel multispectral detector is used to delineate the multiple nonlinear optical signals, pixel by pixel, in NLOM. The ability to image multiple fluorescent protein mutants and collagen, simultaneously, enables serial measurements of cell-cell and cell-matrix interactions in our 3D tissue model and characterization of fundamental processes in angiogenic morphogenesis.

Imaging the glycome

Molecular imaging enables visualization of specific molecules in vivo and without substantial perturbation to the target molecule's environment. Glycans are appealing targets for molecular imaging but are inaccessible with conventional approaches. Classic methods for monitoring glycans rely on molecular recognition with probe-bearing lectins or antibodies, but these techniques are not well suited to in vivo imaging. In an emerging strategy, glycans are imaged by metabolic labeling with chemical reporters and subsequent ligation to fluorescent probes. This technique has enabled visualization of glycans in living cells and in live organisms such as zebrafish. Molecular imaging with chemical reporters offers a new avenue for probing changes in the glycome that accompany development and disease.

Mass spectrometry in systems biology: an overview

As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and methodologies in genomics, proteomics, transcriptomics and metabolomics will be further elaborated individually. Undoubtedly, more applications of mass spectrometry in systems biology can be expected in the near future.

Quantum dot probes for bacteria distinguish Escherichia coli mutants and permit in vivo imaging

Fluorescent quantum dots coated with zinc(ii)-dipicolylamine coordination complexes can selectively stain a rough Escherichia coli mutant that lacks an O-antigen element and permit optical detection in a living mouse leg infection model.

Multiphoton excitation fluorescence: A versatile detection method for capillary electrophoresis

Multiphoton excitation is a relatively old concept in quantum optics. But using multiphoton excitation fluorescence (MPEF) for bioanalysis is still in its infancy. Recently, MPEF has been introduced into the microseparation field, particularly CE, as a novel detection method. In this paper, MPEF detection for CE is reviewed, including MPEF fundamentals, approaches to achieving MPEF, detector configurations and applications in biological and environmental analyses. Emphasis will be placed on some recent advances of CE-MPEF in our laboratory. Challenges and future prospects are also discussed.