Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo.

Owing to their unique abilities to manipulate, label, and image individual molecules in vitro and in cellulo, single-molecule techniques provide previously unattainable access to elementary biological processes. In imaging, single-molecule fluorescence resonance energy transfer (smFRET) and protein-induced fluorescence enhancement in vitro can report on conformational changes and molecular interactions, single-molecule pull-down (SiMPull) can capture and analyze the composition and function of native protein complexes, and single-molecule tracking (SMT) in live cells reveals cellular structures and dynamics. In labeling, the abilities to specifically label genomic loci, mRNA, and nascent polypeptides in cells have uncovered chromosome organization and dynamics, transcription and translation dynamics, and gene expression regulation. In manipulation, optical tweezers, integration of single-molecule fluorescence with force measurements, and single-molecule force probes in live cells have transformed our mechanistic understanding of diverse biological processes, ranging from protein folding, nucleic acids-protein interactions to cell surface receptor function.

A 25 micron-thin microscope for imaging upconverting nanoparticles with NIR-I and NIR-II illumination.

Rationale: Intraoperative visualization in small surgical cavities and hard-to-access areas are essential requirements for modern, minimally invasive surgeries and demand significant miniaturization. However, current optical imagers require multiple hard-to-miniaturize components including lenses, filters and optical fibers. These components restrict both the form-factor and maneuverability of these imagers, and imagers largely remain stand-alone devices with centimeter-scale dimensions. Methods: We have engineered INSITE (Immunotargeted Nanoparticle Single-Chip Imaging Technology), which integrates the unique optical properties of lanthanide-based alloyed upconverting nanoparticles (aUCNPs) with the time-resolved imaging of a 25-micron thin CMOS-based (complementary metal oxide semiconductor) imager. We have synthesized core/shell aUCNPs of different compositions and imaged their visible emission with INSITE under either NIR-I and NIR-II photoexcitation. We characterized aUCNP imaging with INSITE across both varying aUCNP composition and 980 nm and 1550 nm excitation wavelengths. To demonstrate clinical experimental validity, we also conducted an intratumoral injection into LNCaP prostate tumors in a male nude mouse that was subsequently excised and imaged with INSITE. Results: Under the low illumination fluences compatible with live animal imaging, we measure aUCNP radiative lifetimes of 600 µs - 1.3 ms, which provides strong signal for time-resolved INSITE imaging. Core/shell NaEr0.6Yb0.4F4 aUCNPs show the highest INSITE signal when illuminated at either 980 nm or 1550 nm, with signal from NIR-I excitation about an order of magnitude brighter than from NIR-II excitation. The 55 µm spatial resolution achievable with this approach is demonstrated through imaging of aUCNPs in PDMS (polydimethylsiloxane) micro-wells, showing resolution of micrometer-scale targets with single-pixel precision. INSITE imaging of intratumoral NaEr0.8Yb0.2F4 aUCNPs shows a signal-to-background ratio of 9, limited only by photodiode dark current and electronic noise. Conclusion: This work demonstrates INSITE imaging of aUCNPs in tumors, achieving an imaging platform that is thinned to just a 25 µm-thin, planar form-factor, with both NIR-I and NIR-II excitation. Based on a highly paralleled array structure INSITE is scalable, enabling direct coupling with a wide array of surgical and robotic tools for seamless integration with tissue actuation, resection or ablation.

GOING WITH THE FLOW.

From bacteria to circulating tumor cells, advances in flow cytometry technology are pushing the boundaries of cell biology research.

Nuclear and optical dual-labelled imaging agents. Design and challenges.

Over the last two decades, molecular imaging has been established as a valuable technology, aiming at visualization and characterization of biochemical processes on a molecular level in isolated cells, tissues and higher organisms. Within the wide scope of the various imaging techniques, dual-labelled modalities for nuclear (PET, SPECT) and near-infrared fluorescence (NIRF) imaging show promise owing to their comparable detection sensitivity. Novel materials offer excellent prospects for the development of new non-invasive strategies of early diagnosis and efficient monitoring of therapeutic treatments. In the field of cancer medicine, the combination of different imaging techniques such as PET/SPECT and OI for tracking down tumours and metastases, and subsequent image-guided surgery for tumour resection is particularly attractive. This review focuses on the development of promising dual-labelled agents to be applied in bimodal nuclear/optical imaging, combining radionuclides and fluorescent dyes. The discussion encompasses modular ligands as well as nanoscale systems, including antibodies and their fragments.

Advanced methods in fluorescence microscopy.

It requires a good deal of will power to resist hyperbole in considering the advances that have been achieved in fluorescence microscopy in the last 25 years. Our effort has been to survey the modalities of microscopic fluorescence imaging available to cell biologists and perhaps useful for diagnostic pathologists. The gamut extends from established confocal laser scanning through multiphoton and TIRF to the emerging technologies of super-resolution microscopy that breech the Abbé limit of resolution. Also considered are the recent innovations in structured and light sheet illumination, the use of FRET and molecular beacons that exploit specific characteristics of designer fluorescent proteins, fluorescence speckles, and second harmonic generation for native anisometric structures like collagen, microtubules and sarcomeres.

Imaging of protease functions--current guide to spotting cysteine cathepsins in classical and novel scenes of action in mammalian epithelial cells and tissues.

The human genome encodes some hundreds of proteases. Many of these are well studied and understood with respect to their biochemistry, molecular mechanisms of proteolytic cleavage, expression patterns, molecular structure, substrate preferences and regulatory mechanisms, including their endogenous inhibitors. Moreover, precise determination of protease localisation within subcellular compartments, peri- and extracellular spaces has been extremely useful in elucidating biological functions of peptidases. This can be achieved by refined methodology as will be demonstrated herein for the cysteine cathepsins. Besides localisation, it is now feasible to study in situ enzymatic activity at the various levels of subcellular compartments, cells, tissues, and even whole organisms including mouse.

Intravital microscopy: a novel tool to study cell biology in living animals.

Intravital microscopy encompasses various optical microscopy techniques aimed at visualizing biological processes in live animals. In the last decade, the development of non-linear optical microscopy resulted in an enormous increase of in vivo studies, which have addressed key biological questions in fields such as neurobiology, immunology and tumor biology. Recently, few studies have shown that subcellular processes can be imaged dynamically in the live animal at a resolution comparable to that achieved in cell cultures, providing new opportunities to study cell biology under physiological conditions. The overall aim of this review is to give the reader a general idea of the potential applications of intravital microscopy with a particular emphasis on subcellular imaging. An overview of some of the most exciting studies in this field will be presented using resolution as a main organizing criterion. Indeed, first we will focus on those studies in which organs were imaged at the tissue level, then on those focusing on single cells imaging, and finally on those imaging subcellular organelles and structures.

Quantitative real-time imaging of molecular dynamics during cancer cell invasion and metastasis in vivo.

Despite our advanced understanding of primary cancer development and progression, metastasis and the systemic spread of the disease to secondary sites remains the leading cause of cancer-associated death. The metastatic process is therefore a major potential therapeutic target area for cancer researchers and elucidating the key steps that are susceptible to therapeutic intervention will be critical to improve our treatment strategies. Recent advances in intravital imaging are rapidly improving our insight into this process and are helping in the design of stage-specific drug regimes for the treatment of metastatic cancer. Here we discuss current developments in intravital imaging and our recent use of photobleaching and photoactivation in the analysis of dynamic biomarkers in living animals to assess the efficacy of therapeutic intervention on early stages of tumor cell metastasis.

Dendritic cells: therapy and imaging.

BACKGROUND: Dendritic cells (DCs) play a major role in cell-mediated immunotherapy. In this approach, DCs are isolated from cancer patients and pulsed with exogenous and specific tumor antigens in vitro, and the antigen-loaded DCs are then transferred to the hosts to enhance the immune response against tumor targets. Clinical observations and animal studies have shown that tumors can elicit immune responses caused by tumor infiltration of T-lymphocytes. Several pilot clinical trials have been recently conducted using this strategy for treating several types of cancers. OBJECTIVE: To optimize DC-based therapy with emerging molecular imaging techniques. METHODS: A review of the most current literature on DCs and imaging work. RESULTS/CONCLUSION: The translational application of DC-based therapy can be supported greatly through molecular imaging. New discoveries on DC migration and behavior in vivo will lead to new advances in the treatment of a broad range of cancers.

Concept of a selective tumour therapy and its evaluation by near-infrared fluorescence imaging and flat-panel volume computed tomography in mice.

Conventional chemotherapy of cancer has its limitations, especially in advanced and disseminated disease and suffers from lack of specificity. This results in a poor therapeutic index and considerable toxicity to normal organs. Therefore, many efforts are made to develop novel therapeutic tools against cancer with the aim of selectively targeting the drug to the tumour site. Drug delivery strategies fundamentally rely on the identification of good-quality biomarkers, allowing unequivocal discrimination between cancer and healthy tissue. At present, antibodies or antibody fragments have clearly proven their value as carrier molecules specific for a tumour-associated molecular marker. This present review draws attention to the use of near-infrared fluorescence (NIRF) imaging to investigate binding specificity and kinetics of carrier molecules such as monoclonal antibodies. In addition, flat-panel volume computed tomography (fpVCT) will be presented to monitor anatomical structures in tumour mouse models over time in a non-invasive manner. Each imaging device sheds light on a different aspect; functional imaging is applied to optimise the dose schedule and the concept of selective tumour therapies, whereas anatomical imaging assesses preclinically the efficacy of novel tumour therapies. Both imaging techniques in combination allow the visualisation of functional information obtained by NIRF imaging within an adequate anatomic framework.

[Fluorescence cystoscopy. Perspective in clinical practice and research]. / Fluoreszenzzystoskopie. Perspektiven in Klinik und Forschung.

Many studies confirm the clinical interest of photodynamic diagnostics (PDD) in non-muscle invasive bladder cancer management. PDD or fluorescence cystoscopy is not only of great value in occult urothelial cancer detection, but may have a positive impact on disease-free survival and prognosis. Yet, its specificity is found to be highly variable between studies mainly in relation to different disease profiles. New imaging techniques aimed at enhancing visualization to assess the bladder wall are under development.

Fluorescence photodiagnosis in clinical practice.

Fluorescence diagnosis has become an important method of investigation in clinical practice particularly in identification and localisation of pre and early cancerous lesions as well as image guided therapy. The method relies on the principle of differential fluorescence emission between abnormal and normal tissues in response to excitation by a specific wavelength of light within the visible spectrum range. In clinical practice two types of fluorescence diagnostic methods are used, namely autofluorescence and drug-induced fluorescence. The former relies on the differential fluorescence of "native" fluorophores whereas the latter requires a photosensitiser which enhances the differential fluorescence emission of the normal versus the abnormal tissues. Development and advances in fibreoptic, endoscopic instrumentation currently permit fluorescence endoscopy to be carried out in a number of situations.

Current indications and future perspective of fluorescence bronchoscopy: a review study.

BACKGROUND: Autofluorescence bronchoscopy (AFB) was introduced into clinical practice early in the 1990s for identification and localisation of intra-epithelial pre-neoplastic (dysplastic mucosa) and early neoplastic (carcinoma in situ) endobronchial lesions. OBJECTIVES: to determine the current range of indications of AFB through review of published literature and to compare sensitivity and specificity of AFB with those of WLB for identification of pre- and early neoplastic lesions in each of the indications. METHOD: Search of the literature produced 62 eligible articles for the review. These were "empirically" classified into five categories: 1. AFB for identification and localisation of early neoplastic changes. 2. AFB for identification and localisation of bronchial neoplastic changes in smokers. 3. AFB for monitoring treatment and surveillance of early neoplastic changes. 4. AFB for identification and localisation of synchronous and multi-focal lesions. 5. AFB used as a tool for lung cancer screening. RESULTS: In all categories the sensitivity of AFB was several times greater than WLB in identifying pre-neoplastic and early neoplastic lesions and the specificity of WLB was higher than that of AFB. When AFB was used for identification and localisation of dysplasia and carcinoma in situ its sensitivity was 25-47% (mean 33%) higher than that of WLB. Its specificity was 7-18% (mean 11%) lower than WLB. The ratio of sensitivity of AFB/WLB was highest in every category when the population tested comprised a higher proportion of pre- and early neoplastic lesions than invasive cancer. In such cases there was relatively lower specificity for AFB compared to WLB. CONCLUSION: The review suggests that AFB should be included in routine investigations of patients suspected of having lung cancer, those undergoing lung cancer surgery and in post-treatment follow-up to discover early cancer and/or recurrence. Also, it has to be included in any screening programme protocol.

Photodiagnosis for cutaneous malignancy: a brief clinical and technical review.

Photodiagnosis (PD) for cutaneous malignancy attempts to differentiate between normal and diseased skin without the need for histological evaluation. This technique exploits natural or induced differences in fluorescent signatures between these tissues. The technique may be as simple as using ultraviolet light in combination with clinical exam to as complex as optical tomography. While the need is great due to the enormous number of skin lesions currently requiring physical biopsy, the results so far generated are not as specific or sensitive as is required in the clinic. This brief review outlines the value of PD, its potential applications and shortcomings as well as a short primer on the most common technique employed in clinical practice.

Recent improvements in the detection and treatment of nonmuscle-invasive bladder cancer.

In total, 70-80% of newly diagnosed bladder cancers are confined to the mucosa and staged as Ta, T1 or carcinoma in situ according to the 2002 tumor, lymph nodes and metastasis classification. The standard treatment for these nonmuscle-invasive bladder cancers is transurethral tumor resection with or without adjuvant intravesical chemotherapy or intravesical immunotherapy and subsequent follow-up. Diagnosis and follow-up of nonmuscle-invasive bladder cancer offers two main problems. First, approximately 10-20% of all tumors are not seen in standard cystoscopy. Additionally, frequently repeated follow-up cystoscopies are bothersome for the patient. As an adjunct to standard cystoscopy, fluorescence-guided cystoscopy has demonstrated significantly higher tumor detection rates and optimized patient treatment in recent Phase III studies. Second, routinely performed urine cytology is characterized by high specificity but low sensitivity. Today, several urine tests are available that may increase diagnostic accuracy and potentially prolong intervals of follow-up cystocopy. Owing to rather high recurrence rates after transurethral tumor resection in most tumors and high progression rates in poorly differentiated tumors, adjuvant intravesical chemotherapy or intravesical immunotherapy has gained widespread use in patients with nonmuscle-invasive bladder cancer. Only a few further immunomodulatory drugs, such as recombinant cytokines, have shown significant clinical effectiveness. Additional approaches, such as photodynamic therapy with different photosensitizers and thermotherapy in combination with intravesical chemotherapy, have been evaluated in Phase III studies.

Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.

BACKGROUND: Detailed knowledge of the subcellular location of each expressed protein is critical to a full understanding of its function. Fluorescence microscopy, in combination with methods for fluorescent tagging, is the most suitable current method for proteome-wide determination of subcellular location. Previous work has shown that neural network classifiers can distinguish all major protein subcellular location patterns in both 2D and 3D fluorescence microscope images. Building on these results, we evaluate here new classifiers and features to improve the recognition of protein subcellular location patterns in both 2D and 3D fluorescence microscope images. RESULTS: We report here a thorough comparison of the performance on this problem of eight different state-of-the-art classification methods, including neural networks, support vector machines with linear, polynomial, radial basis, and exponential radial basis kernel functions, and ensemble methods such as AdaBoost, Bagging, and Mixtures-of-Experts. Ten-fold cross validation was used to evaluate each classifier with various parameters on different Subcellular Location Feature sets representing both 2D and 3D fluorescence microscope images, including new feature sets incorporating features derived from Gabor and Daubechies wavelet transforms. After optimal parameters were chosen for each of the eight classifiers, optimal majority-voting ensemble classifiers were formed for each feature set. Comparison of results for each image for all eight classifiers permits estimation of the lower bound classification error rate for each subcellular pattern, which we interpret to reflect the fraction of cells whose patterns are distorted by mitosis, cell death or acquisition errors. Overall, we obtained statistically significant improvements in classification accuracy over the best previously published results, with the overall error rate being reduced by one-third to one-half and with the average accuracy for single 2D images being higher than 90% for the first time. In particular, the classification accuracy for the easily confused endomembrane compartments (endoplasmic reticulum, Golgi, endosomes, lysosomes) was improved by 5-15%. We achieved further improvements when classification was conducted on image sets rather than on individual cell images. CONCLUSIONS: The availability of accurate, fast, automated classification systems for protein location patterns in conjunction with high throughput fluorescence microscope imaging techniques enables a new subfield of proteomics, location proteomics. The accuracy and sensitivity of this approach represents an important alternative to low-resolution assignments by curation or sequence-based prediction.