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1.  Microscopic study of electrical properties of CrSi2 nanocrystals in silicon 
Nanoscale Research Letters  2011;6(1):209.
Semiconducting CrSi2 nanocrystallites (NCs) were grown by reactive deposition epitaxy of Cr onto n-type silicon and covered with a 50-nm epitaxial silicon cap. Two types of samples were investigated: in one of them, the NCs were localized near the deposition depth, and in the other they migrated near the surface. The electrical characteristics were investigated in Schottky junctions by current-voltage and capacitance-voltage measurements. Atomic force microscopy (AFM), conductive AFM and scanning probe capacitance microscopy (SCM) were applied to reveal morphology and local electrical properties. The scanning probe methods yielded specific information, and tapping-mode AFM has shown up to 13-nm-high large-area protrusions not seen in the contact-mode AFM. The electrical interaction of the vibrating scanning tip results in virtual deformation of the surface. SCM has revealed NCs deep below the surface not seen by AFM. The electrically active probe yielded significantly better spatial resolution than AFM. The conductive AFM measurements have shown that the Cr-related point defects near the surface are responsible for the leakage of the macroscopic Schottky junctions, and also that NCs near the surface are sensitive to the mechanical and electrical stress induced by the scanning probe.
PMCID: PMC3211265  PMID: 21711727
2.  Two-photon microscopy of oxygen: polymersomes as probe carrier vehicles 
The journal of physical chemistry. B  2010;114(45):14373-14382.
Oxygen concentration distributions in biological systems can be imaged by the phosphorescence quenching method in combination with two-photon laser scanning microscopy. In this paper we identified the excitation regime in which the signal of a two-photon-enhanced phosphorescent probe1 is dependent quadratically on the excitation power (quadratic regime), and performed simulations that relate the photophysical properties of the probe to the imaging resolution. Further, we characterized polymersomes as a method of probe encapsulation and delivery. Photo-physical and oxygen sensing properties of the probe were found unchanged when the probe is encapsulated in polymersomes. Polymersomes were found capable of sustaining high probe concentrations, thereby serving to improve the signal-to-noise ratios for oxygen detection compared to the previously employed probe delivery methods. Imaging of polymersomes loaded with the probe was used as a test-bed for a new method.
PMCID: PMC2939231  PMID: 20462225
phosphorescence; oxygen; two-photon microscopy; polymersome; dendrimer; porphyrin
3.  Scanning probe recognition microscopy investigation of tissue scaffold properties 
Scanning probe recognition microscopy is a new scanning probe microscopy technique which enables selective scanning along individual nanofibers within a tissue scaffold. Statistically significant data for multiple properties can be collected by repetitively fine-scanning an identical region of interest. The results of a scanning probe recognition microscopy investigation of the surface roughness and elasticity of a series of tissue scaffolds are presented. Deconvolution and statistical methods were developed and used for data accuracy along curved nanofiber surfaces. Nanofiber features were also independently analyzed using transmission electron microscopy, with results that supported the scanning probe recognition microscopy-based analysis.
PMCID: PMC2676826  PMID: 18203431
tissue scaffold; tissue engineering; scanning probe recognition microscopy; regenerative medicine; image processing
4.  Targeted Nanoparticles for Imaging Incipient Pancreatic Ductal Adenocarcinoma  
PLoS Medicine  2008;5(4):e85.
Pancreatic ductal adenocarcinoma (PDAC) carries an extremely poor prognosis, typically presenting with metastasis at the time of diagnosis and exhibiting profound resistance to existing therapies. The development of molecular markers and imaging probes for incipient PDAC would enable earlier detection and guide the development of interventive therapies. Here we sought to identify novel molecular markers and to test their potential as targeted imaging agents.
Methods and Findings
Here, a phage display approach was used in a mouse model of PDAC to screen for peptides that specifically bind to cell surface antigens on PDAC cells. These screens yielded a motif that distinguishes PDAC cells from normal pancreatic duct cells in vitro, which, upon proteomics analysis, identified plectin-1 as a novel biomarker of PDAC. To assess their utility for in vivo imaging, the plectin-1 targeted peptides (PTP) were conjugated to magnetofluorescent nanoparticles. In conjunction with intravital confocal microscopy and MRI, these nanoparticles enabled detection of small PDAC and precursor lesions in engineered mouse models.
Our approach exploited a well-defined model of PDAC, enabling rapid identification and validation of PTP. The developed specific imaging probe, along with the discovery of plectin-1 as a novel biomarker, may have clinical utility in the diagnosis and management of PDAC in humans.
Kimberly Kelly and colleagues describe the discovery of plectin-1 as a novel biomarker for pancreatic ductal adenocarcinoma and the subsequent development of a specific imaging probe using this marker.
Editors' Summary
Pancreatic cancer is a leading cause of cancer-related death in the US. Like all cancers, it occurs when cells begin to grow uncontrollably and to move around the body (metastasize) because of changes (mutations) in their genes. If pancreatic cancer is found early, surgical removal of the tumor can sometimes provide a cure. Unfortunately, this cancer rarely causes any symptoms in its early stages and the symptoms it does eventually cause—jaundice, abdominal and back pain, and weight loss—are also seen in other illnesses. In addition, even though magnetic resonance imaging (MRI) or other noninvasive imaging techniques can be used to look at the pancreas, by the time tumors are large enough to show up on MRI scans, they have often already spread. Consequently, in most patients, pancreatic cancer is advanced by the time a diagnosis is made, hence surgery is no longer useful. These patients are given radiotherapy and chemotherapy but these treatments are rarely curative and most patients die within a year of diagnosis.
Why Was This Study Done?
If more pancreatic cancers could be found before they had metastasized, it should extend the life expectancy of patients with this type of cancer. An early detection method would be particularly useful for monitoring people at high risk of developing pancreatic cancer. These include people with certain inherited cancer syndromes, pancreatitis (inflammation of the pancreas), and diabetes. Because cancer cells have many mutations, they express different proteins on their cell surface from normal cells. If these proteins could be identified, it might be possible to develop an “imaging probe”—a molecule that binds to a protein found only on cancer cells and that can be detected with MRI, for example—for early detection of pancreatic cancer. In this study, the researchers use a technique called “phage display” to identify several peptides (short sequences of amino acids, the constituent parts of proteins) that specifically bind to pancreatic cancer cells early in their development. They then investigate the possibility of developing an imaging probe from one of these peptides.
What Did the Researchers Do and Find?
The researchers isolated early pancreatic cancer cells from a mouse model of human pancreatic ductal adenocarcinoma (PDAC; the commonest type of pancreatic cancer). Then, by mixing together these cells and normal mouse pancreatic cells with a library of phage clones (phages are viruses that infect bacteria; a clone is a group of genetically identical organisms), each engineered in the laboratory to express a random seven amino-acid peptide, they identified one clone, clone 27, that bound to the mouse tumor cells but not to normal cells. Clone 27 also showed up in the cancer cells in samples of mouse pancreatic intraepithelial neoplasias (PanINs; precursors to pancreatic cancer), mouse PDACs, and human PDACs.
The peptide in clone 27, the researchers report, binds to plectin-1, a protein present both inside and on the membrane of human and mouse PDAC cells but only on the inside of normal pancreatic cells. Finally, the researchers attached this plectin-1–targeted peptide (PTP) to a nanoparticles that was both magnetic and fluorescent (PTP-NP) and used special microscopy (which detects the fluorescent part of this very small particle) and MRI (which detects its magnetic portion) to show that this potential imaging probe was found in areas of PDAC (but not in normal pancreatic tissue) in the mouse model of human PDAC.
What Do These Findings Mean?
These findings identify PTP as a peptide that can distinguish normal pancreatic cells from pancreatic cancer cells. The discovery that plectin-1 (a cytoskeletal component) is abnormally expressed on the cell surface of PDACs provides new information about the development of pancreatic cancer that could eventually lead to new ways to treat this disease. These findings also show that PTP can be used to generate a nanoparticle-based imaging agent that can detect PDAC within a normal pancreas. These results need to be confirmed in people—results obtained in mouse models do not always reflect what happens in people. Nevertheless, they suggest that PTP-NPs might allow the noninvasive detection of early tumors in people at high risk of developing pancreatic cancer, an advance that could extend their lives by identifying tumors earlier, when they can be removed surgically.
Additional Information.
Please access these Web sites via the online version of this summary at
• The Panreatic Cancer Action Network and the Lustgarten Foundation for Pancreatic Cancer Research provide information, support, and advocacy for patients, families, and healthcare professionals
• The MedlinePlus Encyclopedia has a page on pancreatic cancer (in English and Spanish). Links to further information are provided by MedlinePlus
• The US National Cancer Institute has information about pancreatic cancer for patients and health professionals (in English and Spanish)
• The UK charity Cancerbackup also provides information for patients about pancreatic cancer
PMCID: PMC2292750  PMID: 18416599
5.  Imaging Microscopic Pigment Chemistry in Conjunctival Melanocytic Lesions Using Pump-Probe Laser Microscopy 
To report the application of a novel imaging technique, pump-probe microscopy, to analyze patterns of pigment chemistry of conjunctival melanocytic lesion biopsies.
Histopathologic specimens of eight previously excised conjunctival melanocytic lesions were analyzed with pump-probe microscopy. The technique uses a laser scanning microscope with a two-color pulsed laser source to distinguish hemoglobin, eumelanin, and pheomelanin pigment based on differences in transient excited state and ground state photodynamics. The pump-probe signatures of conjunctival melanins were compared with cutaneous melanins. The distributions of hemoglobin, eumelanin, and pheomelanin were analyzed, and pump-probe images were correlated with adjacent hematoxylin and eosin (H&E)-stained sections.
The pump-probe signatures of conjunctival melanins are similar, but not identical to cutaneous melanins. In addition, there are qualitative and quantitative differences in the structure and pigment chemistry of conjunctival benign nevi, primary acquired melanosis of the conjunctiva (PAM), and conjunctival melanomas. The pump-probe images correlated well with histopathologic features observed in the adjacent H&E-stained sections, and provided a label-free means of discerning conjunctival anatomic features and pathologic benign or malignant tissue.
Pump-probe laser microscopy shows promise as an adjuvant diagnostic tool in evaluation of ocular melanocytic lesions based on morphologic correlation with the histopathology results and pigment chemistry. This initial study suggests systematic differences in pigmentation patterns among conjunctival benign nevi, primary acquired melanosis, and melanomas. In addition, pump-probe microscopy has the potential for use as a noninvasive “in vivo” optical biopsy technique to aid clinical and surgical management of conjunctival melanocytic lesions.
Using pump-probe microscopy, a multiphoton technique that images absorptive pigments, we analyzed the microscopic distribution of melanins in biopsy sections of conjunctival melanocytic lesions, and found differences among conjunctival benign nevi, primary acquired melanosis, and melanomas.
PMCID: PMC3805089  PMID: 24065811
conjunctival melanoma; primary acquired melanosis; benign conjunctival nevus; pump-probe microscopy; multiphoton microscopy
6.  Assessment of Fluorochromes for Two-Photon Laser Scanning Microscopy of Biofilms 
A major limitation for the use of two-proton laser scanning microscopy (2P-LSM) in biofilm and other studies is the lack of a thorough understanding of the excitation-emission responses of potential fluorochromes. In order to use 2P-LSM, the utility of various fluorochromes and probes specific for a range of biofilm constituents must be evaluated. The fluorochromes tested in this study included classical nucleic acid-specific stains, such as acridine orange (AO) and 4",6"-diamidino-2-phenylindole (DAPI), as well as recently developed stains. In addition, stains specific for biofilm extracellular polymeric substances (EPS matrix components) were tested. Two-photon excitation with a Ti/Sapphire laser was carried out at wavelengths from 760 to 900 nm in 10-nm steps. It was found that autofluorescence of phototrophic organisms (cyanobacteria and green algae) resulted in strong signals for the entire excitation range. In addition, the coenzyme F420-related autofluorescence of methanogenic bacteria could be used to obtain images of dense aggregates (excitation wavelength, 780 nm). The intensities of the emission signals for the nucleic acid-specific fluorochromes varied. For example, the intensities were similar for excitation wavelengths ranging from 780 to 900 nm for AO but were higher for a narrower range, 780 to 810 nm, for DAPI. In selective excitation, fading, multiple staining, and combined single-photon-two-photon studies, the recently developed nucleic acid-specific fluorochromes proved to be more suitable regardless of whether they are intended for living or fixed samples. Probes specific for proteins and glycoconjugates allowed two-photon imaging of polymeric biofilm constituents. Selective excitation-emission was observed for Calcofluor White M2R (780 to 800 nm) and SyproOrange (880 to 900 nm). In addition, fluor-conjugated concanavalin A lectins were examined and provided acceptable two-photon emission signals at wavelengths ranging from 780 to 800 nm. Finally, CellTracker, a fluorochrome suitable for long-term labeling of microbial eucaryote cells, was found to give strong emission at wavelengths ranging from 770 to 810 nm. If fluorochromes have the same two-photon excitation cross section, they are suitable for multiple staining and multichannel recording. Generally, if an appropriate excitation wavelength and fluorochrome were used, it was possible to obtain more highly resolved images for thick biofilm samples with two-photon laser microscopy than with conventional single-photon laser microscopy. Due to its potential for higher resolution in light-scattering tissue-like material, such as biofilms, and extremely localized excitation, 2P-LSM is a valuable addition to conventional confocal laser scanning microscopy with single-photon excitation. However, further development of the method and basic research are necessary to take full advantage of nonlinear excitation in studies of interfacial microbial ecology.
PMCID: PMC126725  PMID: 11823234
7.  Neutral Red as a Probe for Confocal Laser Scanning Microscopy Studies of Plant Roots 
Annals of Botany  2006;97(6):1127-1138.
• Background and Aims Neutral red (NR), a lipophilic phenazine dye, has been widely used in various biological systems as a vital stain for bright-field microscopy. In its unprotonated form it penetrates the plasma membrane and tonoplast of viable plant cells, then due to protonation it becomes trapped in acidic compartments. The possible applications of NR for confocal laser scanning microscopy (CLSM) studies were examined in various aspects of plant root biology.
• Methods NR was used as a fluorochrome for living roots of Phaseolus vulgaris, Allium cepa, A. porrum and Arabidopsis thaliana (wild-type and transgenic GFP-carrying lines). The tissues were visualized using CLSM. The effect of NR on the integrity of the cytoskeleton and the growth rate of arabidopsis primary roots was analysed to judge potential toxic effects of the dye.
• Key Results The main advantages of the use of NR are related to the fact that NR rapidly penetrates root tissues, has affinity to suberin and lignin, and accumulates in the vacuoles. It is shown that NR is a suitable probe for visualization of proto- and metaxylem elements, Casparian bands in the endodermis, and vacuoles in cells of living roots. The actin cytoskeleton and the microtubule system of the cells, as well as the dynamics of root growth, remain unchanged after short-term application of NR, indicating a relatively low toxicity of this chemical. It was also found that NR is a useful probe for the observation of the internal structures of root nodules and of fungal hyphae in vesicular–arbuscular mycorrhizas.
• Conclusions Ease, low cost and absence of tissue processing make NR a useful probe for structural, developmental and vacuole-biogenetic studies of plant roots with CLSM.
PMCID: PMC2803381  PMID: 16520341
CLSM; Casparian band; xylem; vacuole biogenesis; lateral root development; root development; neutral red
8.  In Vivo Near-Infrared Imaging of Fibrin Deposition in Thromboembolic Stroke in Mice 
PLoS ONE  2012;7(1):e30262.
Thrombus and secondary thrombosis plays a key role in stroke. Recent molecular imaging provides in vivo imaging of activated factor XIII (FXIIIa), an important mediator of thrombosis or fibrinolytic resistance. The present study was to investigate the fibrin deposition in a thromboembolic stroke mice model by FXIIIa–targeted near-infrared fluorescence (NIRF) imaging.
Materials and Methods
The experimental protocol was approved by our institutional animal use committee. Seventy-six C57B/6J mice were subjected to thromboembolic middle cerebral artery occlusion or sham operation. Mice were either intravenously injected with the FXIIIa-targeted probe or control probe. In vivo and ex vivo NIRF imaging were performed thereafter. Probe distribution was assessed with fluorescence microscopy by spectral imaging and quantification system. MR scans were performed to measure lesion volumes in vivo, which were correlated with histology after animal euthanasia.
In vivo significant higher fluorescence intensity over the ischemia-affected hemisphere, compared to the contralateral side, was detected in mice that received FXIIIa-targeted probe, but not in the controlled mice. Significantly NIRF signals showed time-dependent processes from 8 to 96 hours after injection of FXIIIa-targeted probes. Ex vivo NIRF image showed an intense fluorescence within the ischemic territory only in mice injected with FXIIIa-targeted probe. The fluorescence microscopy demonstrated distribution of FXIIIa-targeted probe in the ischemic region and nearby micro-vessels, and FXIIIa-targeted probe signals showed good overlap with immune-fluorescent fibrin staining images. There was a significant correlation between total targeted signal from in vivo or ex vivo NIRF images and lesion volume.
Non-invasive detection of fibrin deposition in ischemic mouse brain using NIRF imaging is feasible and this technique may provide an in vivo experimental tool in studying the role of fibrin in stroke.
PMCID: PMC3260250  PMID: 22272319
9.  Quantitative operando visualization of the energy band depth profile in solar cells 
Nature Communications  2015;6:7745.
The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference.
The energy band alignment of solar cell materials is highly relevant to the device performance, but its measurement is challenging. Here, the authors report direct visualization of energy band alignment in operating organic photovoltaic devices using scanning Kelvin probe microscopy imaging.
PMCID: PMC4510960  PMID: 26166580
10.  Measuring bacterial cells size with AFM 
Brazilian Journal of Microbiology  2012;43(1):341-347.
Atomic Force Microscopy (AFM) can be used to obtain high-resolution topographical images of bacteria revealing surface details and cell integrity. During scanning however, the interactions between the AFM probe and the membrane results in distortion of the images. Such distortions or artifacts are the result of geometrical effects related to bacterial cell height, specimen curvature and the AFM probe geometry. The most common artifact in imaging is surface broadening, what can lead to errors in bacterial sizing. Several methods of correction have been proposed to compensate for these artifacts and in this study we describe a simple geometric model for the interaction between the tip (a pyramidal shaped AFM probe) and the bacterium (Escherichia coli JM-109 strain) to minimize the enlarging effect. Approaches to bacteria immobilization and examples of AFM images analysis are also described.
PMCID: PMC3768968  PMID: 24031837
Atomic force microscopy (AFM); Escherichia coli; cell dimensions; bacteria visualization
11.  Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction 
Nature Communications  2014;5:5653.
By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms.
Advances in electron microscopy are enabling ever smaller features to be probed, with the measurement of atomic electric fields standing as a major challenge. Towards that aim, Müller et al. present a simplified theoretical approach for enhancing the resolution in differential phase contrast microscopy.
PMCID: PMC4275586  PMID: 25501385
12.  Comprehensive confocal endomicroscopy of the esophagus in vivo  
Endoscopy International Open  2014;2(3):E135-E140.
Background and study aims: Biopsy sampling error can be a problem for the diagnosis of certain gastrointestinal tract diseases. Spectrally-encoded confocal microscopy (SECM) is a high-speed reflectance confocal microscopy technology that has the potential to overcome sampling error by imaging large regions of gastrointestinal tract tissues. The aim of this study was to test a recently developed SECM endoscopic probe for comprehensively imaging large segments of the esophagus at the microscopic level in vivo.
Methods: Topical acetic acid was endoscopically applied to the esophagus of a normal living swine. The 7 mm diameter SECM endoscopic probe was transorally introduced into the esophagus over a wire. Optics within the SECM probe were helically scanned over a 5 cm length of the esophagus. Confocal microscopy data was displayed and stored in real time.
Results: Very large confocal microscopy images (length = 5 cm; circumference = 2.2 cm) of swine esophagus from three imaging depths, spanning a total area of 33 cm2, were obtained in about 2 minutes. SECM images enabled the visualization of cellular morphology of the swine esophagus, including stratified squamous cell nuclei, basal cells, and collagen within the lamina propria.
Conclusions: The results from this study suggest that the SECM technology can rapidly provide large, contiguous confocal microscopy images of the esophagus in vivo. When applied to human subjects, the unique comprehensive, microscopic imaging capabilities of this technology may be utilized for improving the screening and surveillance of various esophageal diseases.
PMCID: PMC4440396  PMID: 26134959
13.  Condenser-free contrast methods for transmitted-light microscopy 
Journal of Microscopy  2014;257(1):8-22.
Phase contrast microscopy allows the study of highly transparent yet detail-rich specimens by producing intensity contrast from phase objects within the sample. Presented here is a generalized phase contrast illumination schema in which condenser optics are entirely abrogated, yielding a condenser-free yet highly effective method of obtaining phase contrast in transmitted-light microscopy. A ring of light emitting diodes (LEDs) is positioned within the light-path such that observation of the objective back focal plane places the illuminating ring in appropriate conjunction with the phase ring. It is demonstrated that true Zernike phase contrast is obtained, whose geometry can be flexibly manipulated to provide an arbitrary working distance between illuminator and sample. Condenser-free phase contrast is demonstrated across a range of magnifications (4–100×), numerical apertures (0.13–1.65NA) and conventional phase positions. Also demonstrated is condenser-free darkfield microscopy as well as combinatorial contrast including Rheinberg illumination and simultaneous, colour-contrasted, brightfield, darkfield and Zernike phase contrast. By providing enhanced and arbitrary working space above the preparation, a range of concurrent imaging and electrophysiological techniques will be technically facilitated. Condenser-free phase contrast is demonstrated in conjunction with scanning ion conductance microscopy (SICM), using a notched ring to admit the scanned probe. The compact, versatile LED illumination schema will further lend itself to novel next-generation transmitted-light microscopy designs. The condenser-free illumination method, using rings of independent or radially-scanned emitters, may be exploited in future in other electromagnetic wavebands, including X-rays or the infrared.
PMCID: PMC4277858  PMID: 25226859
Condenser-free contrast enhancement; darkfield microscopy; LED illumination; Rheinberg illumination; scanning probe microscopy; Zernike phase contrast microscopy
14.  Piezo-thermal Probe Array for High Throughput Applications 
Microcantilevers are used in a number of applications including atomic-force microscopy (AFM). In this work, deflection-sensing elements along with heating elements are integrated onto micromachined cantilever arrays to increase sensitivity, and reduce complexity and cost. An array of probes with 5–10 nm gold ultrathin film sensors on silicon substrates for high throughput scanning probe microscopy is developed. The deflection sensitivity is 0.2 ppm/nm. Plots of the change in resistance of the sensing element with displacement are used to calibrate the probes and determine probe contact with the substrate. Topographical scans demonstrate high throughput and nanometer resolution. The heating elements are calibrated and the thermal coefficient of resistance (TCR) is 655 ppm/K. The melting temperature of a material is measured by locally heating the material with the heating element of the cantilever while monitoring the bending with the deflection sensing element. The melting point value measured with this method is in close agreement with the reported value in literature.
PMCID: PMC3638734  PMID: 23641125
Microcantilevers; Scanning probe microscopy; Piezoresistive sensing; Parallel imaging; Elastography; Mechanical characterization; Melting point; High throughput
15.  Fluorescence In Situ Hybridization Using 16S rRNA-Targeted Oligonucleotides Reveals Localization of Methanogens and Selected Uncultured Bacteria in Mesophilic and Thermophilic Sludge Granules 
16S rRNA-targeted in situ hybridization combined with confocal laser scanning microscopy was used to elucidate the spatial distribution of microbes within two types of methanogenic granular sludge, mesophilic (35°C) and thermophilic (55°C), in upflow anaerobic sludge blanket reactors fed with sucrose-, acetate-, and propionate-based artificial wastewater. The spatial organization of the microbes was visualized in thin sections of the granules by using fluorescent oligonucleotide probes specific to several phylogenetic groups of microbes. In situ hybridization with archaeal- and bacterial-domain probes within granule sections clearly showed that both mesophilic and thermophilic granules had layered structures and that the outer layer harbored mainly bacterial cells while the inner layer consisted mainly of archaeal cells. Methanosaeta-, Methanobacterium-, Methanospirillum-, and Methanosarcina-like cells were detected with oligonucleotide probes specific for the different groups of methanogens, and they were found to be localized inside the granules, in both types of which dominant methanogens were members of the genus Methanosaeta. For specific detection of bacteria which were previously detected by whole-microbial-community 16S ribosomal DNA (rDNA)-cloning analysis (Y. Sekiguchi, Y. Kamagata, K. Syutsubo, A. Ohashi, H. Harada, and K. Nakamura, Microbiology 144:2655–2665, 1998) we designed probes specific for clonal 16S rDNAs related to unidentified green nonsulfur bacteria and clones related to Syntrophobacter species. The probe designed for the cluster closely related to Syntrophobacter species hybridized with coccoid cells in the inner layer of the mesophilic granule sections. The probe for the unidentified bacteria which were clustered with the green nonsulfur bacteria detected filamentous cells in the outermost layer of the thermophilic sludge granule sections. These results revealed the spatial organizations of methanogens and uncultivated bacteria and their in situ morphologies and metabolic functions in both mesophilic and thermophilic granular sludges.
PMCID: PMC91175  PMID: 10049894
16.  Comprehensive volumetric confocal microscopy with adaptive focusing 
Biomedical Optics Express  2011;2(6):1412-1422.
Comprehensive microscopy of distal esophagus could greatly improve the screening and surveillance of esophageal diseases such as Barrett’s esophagus by providing histomorphologic information over the entire region at risk. Spectrally encoded confocal microscopy (SECM) is a high-speed reflectance confocal microscopy technology that can be configured to image the entire distal esophagus by helically scanning the beam using optics within a balloon-centering probe. It is challenging to image the human esophagus in vivo with balloon-based SECM, however, because patient motion and anatomic tissue surface irregularities decenter the optics, making it difficult to keep the focus at a predetermined location within the tissue as the beam is scanned. In this paper, we present a SECM probe equipped with an adaptive focusing mechanism that can compensate for tissue surface irregularity and dynamic focal variation. A tilted arrangement of the objective lens is employed in the SECM probe to provide feedback signals to an adaptive focusing mechanism. The tilted configuration also allows the probe to obtain reflectance confocal data from multiple depth levels, enabling the acquisition of three-dimensional volumetric data during a single scan of the probe. A tissue phantom with a surface area of 12.6 cm2 was imaged using the new SECM probe, and 8 large-area reflectance confocal microscopy images were acquired over the depth range of 56 μm in 20 minutes. Large-area SECM images of excised swine small intestine tissue were also acquired, enabling the visualization of villous architecture, epithelium, and lamina propria. The adaptive focusing mechanism was demonstrated to enable acquisition of in-focus images even when the probe was not centered and the tissue surface was irregular.
PMCID: PMC3114210  PMID: 21698005
(170.1790) Confocal microscopy; (170.2150) Endoscopic imaging; (170.2680) Gastrointestinal
17.  Dipole characterization of single neurons from their extracellular action potentials 
The spatial variation of the extracellular action potentials (EAP) of a single neuron contains information about the size and location of the dominant current source of its action potential generator, which is typically in the vicinity of the soma. Using this dependence in reverse in a three-component realistic probe + brain + source model, we solved the inverse problem of characterizing the equivalent current source of an isolated neuron from the EAP data sampled by an extracellular probe at multiple independent recording locations. We used a dipole for the model source because there is extensive evidence it accurately captures the spatial roll-off of the EAP amplitude, and because, as we show, dipole localization, beyond a minimum cell-probe distance, is a more accurate alternative to approaches based on monopole source models. Dipole characterization is separable into a linear dipole moment optimization where the dipole location is fixed, and a second, nonlinear, global optimization of the source location. We solved the linear optimization on a discrete grid via the lead fields of the probe, which can be calculated for any realistic probe + brain model by the finite element method. The global source location was optimized by means of Tikhonov regularization that jointly minimizes model error and dipole size. The particular strategy chosen reflects the fact that the dipole model is used in the near field, in contrast to the typical prior applications of dipole models to EKG and EEG source analysis. We applied dipole localization to data collected with stepped tetrodes whose detailed geometry was measured via scanning electron microscopy. The optimal dipole could account for 96% of the power in the spatial variation of the EAP amplitude. Among various model error contributions to the residual, we address especially the error in probe geometry, and the extent to which it biases estimates of dipole parameters. This dipole characterization method can be applied to any recording technique that has the capabilities of taking multiple independent measurements of the same single units.
PMCID: PMC3274615  PMID: 21667156
Multisite recording; Inverse problem; Passive conductor model; Lead field theory; Finite element method (FEM)
18.  In Situ Detection of Novel Bacterial Endosymbionts of Acanthamoeba spp. Phylogenetically Related to Members of the Order Rickettsiales 
Acanthamoebae are ubiquitous soil and water bactivores which may serve as amplification vehicles for a variety of pathogenic facultative bacteria and as hosts to other, presently uncultured bacterial endosymbionts. The spectrum of uncultured endosymbionts includes gram-negative rods and gram-variable cocci, the latter recently shown to be members of the Chlamydiales. We report here the isolation from corneal scrapings of two Acanthamoeba strains that harbor gram-negative rod endosymbionts that could not be cultured by standard techniques. These bacteria were phylogenetically characterized following amplification and sequencing of the near-full-length 16S rRNA gene. We used two fluorescently labelled oligonucleotide probes targeting signature regions within the retrieved sequences to detect these organisms in situ. Phylogenetic analyses demonstrated that they displayed 99.6% sequence similarity and formed an independent and well-separated lineage within the Rickettsiales branch of the alpha subdivision of the Proteobacteria. Nearest relatives included members of the genus Rickettsia, with sequence similarities of approximately 85 to 86%, suggesting that these symbionts are representatives of a new genus and, perhaps, family. Distance matrix, parsimony, and maximum-likelihood tree-generating methods all consistently supported deep branching of the 16S rDNA sequences within the Rickettsiales. The oligonucleotide probes displayed at least three mismatches to all other available 16S rDNA sequences, and they both readily permitted the unambiguous detection of rod-shaped bacteria within intact acanthamoebae by confocal laser-scanning microscopy. Considering the long-standing relationship of most Rickettsiales with arthropods, the finding of a related lineage of endosymbionts in protozoan hosts was unexpected and may have implications for the preadaptation and/or recruitment of rickettsia-like bacteria to metazoan hosts.
PMCID: PMC91004  PMID: 9872781
19.  Research on Double-Probe, Double- and Triple-Tip Effects during Atomic Force Microscopy Scanning 
Scanning  2004;26(4):155-161.
Information obtained by atomic force microscopy (AFM) depends strongly on the kind of probe or tip used; therefore, probe and tip effects have to be taken into account when verifying or interpreting the data acquired. In many papers, double-tip effects have been mentioned while other research was done; however, there are only a few special reports on double- or triple-tip effects, especially double-probe effects. In our paper, metaphase chromosomes of Chinese hamster ovary (CHO) cells, aggregates of pectin molecules, membrane surface of mouse embryonic stem cells, and R-phycoerythrin-conjugated immunoglobulin G complexes were imaged by AFM with high-quality probes, double-probe cantilever, and double-tip and triple-tip probes, respectively, in order to determine double-probe, double-tip, and triple-tip effects during AFM scanning. We found that the double-probe, double-tip, and triple-tip effects share the same principle, and that these effects correlate with distance and height differences between probes of double-probe cantilever or tips of double-tip or multiple-tip probes. Since many other factors influence double-probe or double-tip effects, more in-depth studies must be undertaken. However, this initial research will make all users of AFM techniques aware of double-probe and double-tip or triple-tip effects during AFM scanning and aid in verifying or interpreting the data acquired.
PMCID: PMC2863299  PMID: 15473266
double-probe effects; double-tip effects; triple-tip effects; atomic force microscopy; tip artifacts; chromosome; pectin; phycoerythrin conjugated immunoglobulin G
20.  The Probe Profile and Lateral Resolution of Scanning Transmission Electron Microscopy of Thick Specimens 
Microscopy and Microanalysis  2012;18(3):582-590.
Lateral profiles of the electron probe of scanning transmission electron microscopy (STEM) were simulated at different vertical positions in a micrometers-thick carbon sample. The simulations were carried out using the Monte Carlo method in the CASINO software. A model was developed to fit the probe profiles. The model consisted of the sum of a Gaussian function describing the central peak of the profile, and two exponential decay functions describing the tail of the profile. Calculations were performed to investigate the fraction of unscattered electrons as function of the vertical position of the probe in the sample. Line scans were also simulated over gold nanoparticles at the bottom of a carbon film to calculate the achievable resolution as function of the sample thickness and the number of electrons. The resolution was shown to be noise limited for film thicknesses less than 1 μm. Probe broadening limited the resolution for thicker films. The validity of the simulation method was verified by comparing simulated data with experimental data. The simulation method can be used as quantitative method to predict STEM performance or to interpret STEM images of thick specimens.
PMCID: PMC3389604  PMID: 22564444
Electron probe broadening; Monte Carlo simulations; nanoparticles; noise-limited resolution; STEM; spatial resolution; thick specimen
21.  The Power of Correlative Microscopy: Multi-modal, Multi-scale, Multi-dimensional 
Correlative microscopy is a sophisticated approach that combines the capabilities of typically separate, but powerful microscopy platforms: often including, but not limited, to conventional light, confocal and super-resolution microscopy, atomic force microscopy, transmission and scanning electron microscopy, magnetic resonance imaging and micro/nanoCT (computed tomography). When targeting rare or specific events within large populations or tissues, correlative microscopy is increasingly being recognized as the method of choice. Furthermore, this multi-modal assimilation of technologies provides complementary and often unique information, such as internal and external spatial, structural, biochemical and biophysical details from the same targeted sample. The development of a continuous stream of cutting-edge applications, probes, preparation methodologies, hardware and software developments will enable realization of the full potential of correlative microscopy.
PMCID: PMC3189301  PMID: 21782417
22.  Points to Be Considered When Applying FibroScan S Probe in Children With Biliary Atresia 
With the introduction of smaller probes (S1, S2), the use of transient elastography has been expanded to children. Accordingly, we aimed to address points of consideration in probe choice and interpretation of measured liver stiffness by applying and comparing FibroScan S and M probes in biliary atresia.
Using S1, S2, and M probes, 3 liver stiffness measurements, success rates, and interquartile ranges were obtained from 100 patients. Patients were assigned to 2 groups according to thoracic perimeter (≤45 cm vs >45 cm). In both groups, obtained values were compared and the relation between liver stiffness measurement and aspartate aminotransferase-to-platelet ratio index was analyzed.
In the small-thorax group, the success rate was highest with the S1 probe and the intraclass correlation coefficient (ICC) was highest for S1 versus S2 (0.98), compared with that for S1 versus M (0.69) and S2 versus M (0.77). In the large-thorax group, ICC was the highest for S2 versus M (0.88), compared with that for S1 versus S2 (0.69) and S1 versus M (0.51). In the small-thorax group, correlations between aspartate aminotransferase-to-platelet ratio index and liver stiffness measurement were stronger for S1 (0.65) and S2 (0.64) than for M (0.49). In the large-thorax group, all probes showed good correlation, S1 (0.68), S2 (0.62), and M (0.62).
We recommend that the S1 probe is more appropriate for use in small children, especially those with a thorax perimeter of <45 cm. If no S probe is available, the M probe may be acceptable in children whose thorax perimeter is >45 cm.
PMCID: PMC4222704  PMID: 25003372
biliary atresia; children; liver fibrosis; transient elastography
23.  Development and application of 16S rRNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples. 
Comparative sequence analysis of the 16S rRNA genes from several Leptothrix and Sphaerotilus strains led to the design of an oligonucleotide probe (PS-1) based on a sequence within the hypervariable region 1 specific for four Leptothrix strains and for one of the four Sphaerotilus natans strains examined. Another probe (PSP-6) was based on a sequence within the hypervariable region 2. PSP-6 was specific for one of the two evolutionary lineages previously described for Leptothrix spp. (P. L. Siering and W. C. Ghiorse, Int. J. Syst. Bacteriol. 46:173-182, 1996). Fluorescein-labeled oligonucleotide probes were synthesized, and their specificity for fluorescence in situ hybridization identification was confirmed by a laser scanning microscopy technique (W. C. Ghiorse, D. N. Miller, R. L. Sandoli, and P. L. Siering, Microsc. Res. Tech. 33:73-86, 1996) to compare whole-cell hybridizations of closely related bacteria. Probe specificity was also tested in dot blot against total RNA isolated from four Leptothrix strains, four Sphaerotilus strains, and 15 other members of the class Proteobacteria. When the probes were tested on samples from the Sapsucker Woods wetland habitat where Leptothrix spp. are thought to play a role in manganese and iron oxidation, positive signals were obtained from several sheathed filamentous bacteria including some that were morphologically similar to previously isolated strains of "Leptothrix discophora." Other unknown filamentous sheathed bacteria also gave strong positive signals. This work provides a foundation for future studies correlating the presence of members of the Leptothrix-Sphaerotilus group of sheathed bacteria with manganese and iron oxidation activity in habitats where biological iron and manganese oxidation are important environmental processes.
PMCID: PMC168354  PMID: 9023942
24.  Improving the Lateral Resolution of Quartz Tuning Fork-Based Sensors in Liquid by Integrating Commercial AFM Tips into the Fiber End 
Sensors (Basel, Switzerland)  2015;15(1):1601-1610.
The use of quartz tuning fork sensors as probes for scanning probe microscopy is growing in popularity. Working in shear mode, some methods achieve a lateral resolution comparable with that obtained with standard cantilevered probes, but only in experiments conducted in air or vacuum. Here, we report a method to produce and use commercial AFM tips in electrically driven quartz tuning fork sensors operating in shear mode in a liquid environment. The process is based on attaching a standard AFM tip to the end of a fiber probe which has previously been sharpened. Only the end of the probe is immersed in the buffer solution during imaging. The lateral resolution achieved is about 6 times higher than that of the etched microfiber on its own.
PMCID: PMC4327093  PMID: 25594596
atomic force microscopy; scanning probe microscopy; quartz tuning fork; self-sensing probe; shear force microscopy; nanotip
25.  Detection of a microbial biofilm in intra-amniotic infection 
Microbial biofilms are communities of sessile microorganisms formed by cells that are attached irreversibly to a substratum or interface or to each other and embedded in a hydrated matrix of extracellular polymeric substances. Microbial biofilms have been implicated in >80% of human infections such as periodontitis, urethritis, endocarditis, and device-associated infections. Thus far, intra-amniotic infection has been attributed to planktonic (free-floating) bacteria. A case is presented in which “amniotic fluid sludge” was found to contain microbial biofilms. This represents the first report of a microbial biofilm in the amniotic cavity.
Study Design
“Amniotic fluid sludge” was detected by transvaginal sonography, and retrieved by transvaginal amniotomy. Bacteria were identified using scanning electron microscope and fluorescence in situ hybridization for conserved regions of the microbial genome; and the exopolymeric matrix was identified by histochemistry using the wheat germ agglutinin lectin method. The structure of the biofilm was imaged with confocal laser scanning microscopy.
“Amniotic fluid sludge” was imaged with scanning electron microscopy, which allowed identification of bacteria embedded in an amorphous material and inflammatory cells. Bacteria were demonstrated using fluorescent in situ hybredization using a eubacteria probe. Extracellular matrix was identified with the wheat germ agglutinin lectin stain. Confocal microscopy allowed three-dimensional visualization of the microbial biofilm.
Microbial biofilms have been identified in a case of intra-amniotic infection with “amniotic fluid sludge.”
PMCID: PMC2614390  PMID: 18166328
amniocentesis; amniotic fluid sludge; chorioamnionitis; intra-amniotic infection; microbial invasion of the amniotic cavity; preterm labor

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