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High throughput microscopy

Eugen Widmeier, Weizhen Tan, Merlin Airik, Friedhelm Hildebrandt
INTRODUCTION: Steroid-resistant nephrotic syndrome (SRNS) inevitably progresses to end-stage kidney disease, requiring dialysis or transplantation for survival. However, treatment modalities and drug discovery remain limited. Mutations in over 30 genes have been discovered as monogenic causes of SRNS. Most of these genes are predominantly expressed in the glomerular epithelial cell, the podocyte, placing it at the center of the pathogenesis of SRNS. Podocyte migration rate (PMR) represents a relevant intermediate phenotype of disease in monogenic causes of SRNS...
October 19, 2016: American Journal of Physiology. Renal Physiology
Jochen F Eisele, Florian Fäßler, Patrick F Bürgel, Christina Chaban
There are two major methodical approaches with which changes of status in stomatal pores are addressed: indirectly by measurement of leaf transpiration, and directly by measurement of stomatal apertures. Application of the former method requires special equipment, whereas microscopic images are utilized for the direct measurements. Due to obscure visualization of cell boundaries in intact leaves, a certain degree of invasive leaf manipulation is often required. Our aim was to develop a protocol based on the minimization of leaf manipulation and the reduction of analysis completion time, while still producing consistent results...
2016: PloS One
Liliana R Cisneros Castillo, Andrei-Dumitru Oancea, Christian Stüllein, Anne Régnier-Vigouroux
Multicellular tumor spheroids (MCTSs) embedded in a matrix are re-emerging as a powerful alternative to monolayer-based cultures. The primary information gained from a three-dimensional model is the invasiveness of treatment-exposed MCTSs through the acquisition of light microscopy images. The amount and complexity of the acquired data and the bias arisen by their manual analysis are disadvantages calling for an automated, high-throughput analysis. We present a universal algorithm we developed with the scope of being robust enough to handle images of various qualities and various invasion profiles...
October 12, 2016: Scientific Reports
Amy T Shah, Taylor M Cannon, James N Higginbotham, Robert J Coffey, Melissa C Skala
Clinical cancer treatment aims to target all cell subpopulations within a tumor. Autofluorescence microscopy of the metabolic cofactors NAD(P)H and FAD has shown sensitivity to anti-cancer treatment response. Alternatively, flow cytometry is attractive for high throughput analysis and flow sorting. This study measures cellular autofluorescence in three flow cytometry channels and applies cellular autofluorescence to sort a heterogeneous mixture of breast cancer cells into subpopulations enriched for each phenotype...
October 12, 2016: Journal of Biophotonics
Maximilian Billmann, Michael Boutros
RNA interference (RNAi) is a potent tool for perturbation of gene function in model organisms and human cells. In Drosophila, efficient RNAi enables screening approaches for components of cellular processes in vivo and in vitro. In cultured cells, measuring the effect of depleting gene products on a genome-wide scale can systematically associate gene function with diverse processes, such as cell growth and proliferation, signaling and trafficking. Here, we describe methods for RNAi experiments in cultured Drosophila cells with a focus on genome-wide loss-of-function screening...
2016: Methods in Molecular Biology
Adam S Backer, Maurice Y Lee, W E Moerner
Single-molecule orientation measurements provide unparalleled insight into a multitude of biological and polymeric systems. We report a simple, high-throughput technique for measuring the azimuthal orientation and rotational dynamics of single fluorescent molecules, which is compatible with localization microscopy. Our method involves modulating the polarization of an excitation laser, and analyzing the corresponding intensities emitted by single dye molecules and their modulation amplitudes. To demonstrate our approach, we use intercalating and groove-binding dyes to obtain super-resolved images of stretched DNA strands through binding-induced turn-on of fluorescence...
2016: Optica
Michael J Susienka, Benjamin T Wilks, Jeffrey R Morgan
Tissue fusion, whereby two or more spheroids coalesce, is a process that is fundamental to biofabrication. We have designed a quantitative, high-throughput platform to investigate the fusion of multicellular spheroids using agarose micro-molds. Spheroids of primary human chondrocytes (HCH) or human breast cancer cells (MCF-7) were self-assembled for 24 h and then brought together to form an array comprised of two spheroids (one doublet) per well. To quantify spheroid fusogenicity, we developed two assays: (1) an initial tack assay, defined as the minimum amount of time for two spheroids to form a mechanically stable tissue complex or doublet, and (2) a fusion assay, in which we defined and tracked key morphological parameters of the doublets as a function of time using wide-field fluorescence microscopy over a 24 h time-lapse...
October 10, 2016: Biofabrication
Luay M Almassalha, Greta M Bauer, John E Chandler, Scott Gladstein, Lusik Cherkezyan, Yolanda Stypula-Cyrus, Samuel Weinberg, Di Zhang, Peder Thusgaard Ruhoff, Hemant K Roy, Hariharan Subramanian, Navdeep S Chandel, Igal Szleifer, Vadim Backman
The organization of chromatin is a regulator of molecular processes including transcription, replication, and DNA repair. The structures within chromatin that regulate these processes span from the nucleosomal (10-nm) to the chromosomal (>200-nm) levels, with little known about the dynamics of chromatin structure between these scales due to a lack of quantitative imaging technique in live cells. Previous work using partial-wave spectroscopic (PWS) microscopy, a quantitative imaging technique with sensitivity to macromolecular organization between 20 and 200 nm, has shown that transformation of chromatin at these length scales is a fundamental event during carcinogenesis...
October 4, 2016: Proceedings of the National Academy of Sciences of the United States of America
Toshiko Yamazawa, Naotoshi Nakamura, Mari Sato, Chikara Sato
Exocrine glands, e.g., salivary and pancreatic glands, play an important role in digestive enzyme secretion, while endocrine glands, e.g., pancreatic islets, secrete hormones that regulate blood glucose levels. The dysfunction of these secretory organs immediately leads to various diseases, such as diabetes or Sjögren's syndrome, by poorly understood mechanisms. Gland-related diseases have been studied by optical microscopy (OM), and at higher resolution by transmission electron microscopy (TEM) of Epon embedded samples, which necessitates hydrophobic sample pretreatment...
October 2, 2016: Microscopy Research and Technique
Dara L Dickstein, Daniel R Dickstein, William G M Janssen, Patrick R Hof, Jacob R Glaser, Alfredo Rodriguez, Nate O'Connor, Paul Angstman, Susan J Tappan
Determining the density and morphology of dendritic spines is of high biological significance given the role of spines in synaptic plasticity and in neurodegenerative and neuropsychiatric disorders. Precise quantification of spines in three dimensions (3D) is essential for understanding the structural determinants of normal and pathological neuronal function. However, this quantification has been restricted to time- and labor-intensive methods such as electron microscopy and manual counting, which have limited throughput and are impractical for studies of large samples...
October 3, 2016: Current Protocols in Neuroscience
Yimin Fang, Hui Wang, Hui Yu, Xianwei Liu, Wei Wang, Hong-Yuan Chen, N J Tao
Electrochemical reactions are involved in many natural phenomena, and are responsible for various applications, including energy conversion and storage, material processing and protection, and chemical detection and analysis. An electrochemical reaction is accompanied by electron transfer between a chemical species and an electrode. For this reason, it has been studied by measuring current, charge, or related electrical quantities. This approach has led to the development of various electrochemical methods, which have played an essential role in the understanding and applications of electrochemistry...
September 23, 2016: Accounts of Chemical Research
Francesco Gregoretti, Elisa Cesarini, Chiara Lanzuolo, Gennaro Oliva, Laura Antonelli
The large amount of data generated in biological experiments that rely on advanced microscopy can be handled only with automated image analysis. Most analyses require a reliable cell image segmentation eventually capable of detecting subcellular structures.We present an automatic segmentation method to detect Polycomb group (PcG) proteins areas isolated from nuclei regions in high-resolution fluorescent cell image stacks. It combines two segmentation algorithms that use an active contour model and a classification technique serving as a tool to better understand the subcellular three-dimensional distribution of PcG proteins in live cell image sequences...
2016: Methods in Molecular Biology
Ravi Kiran Attota, Eileen Cherry Liu
Nanoparticles (NPs) are widely used in diverse application areas, such as medicine, engineering, and cosmetics. The size (or volume) of NPs is one of the most important parameters for their successful application. It is relatively straightforward to determine the volume of regular NPs such as spheres and cubes from a one-dimensional or two-dimensional measurement. However, due to the three-dimensional nature of NPs, it is challenging to determine the proper physical size of many types of regularly and irregularly-shaped quasi-spherical NPs at high-throughput using a single tool...
September 22, 2016: Analytical and Bioanalytical Chemistry
Sowmya Subramanian, Konstantinos Gerasopoulos, Min Guo, Herman O Sintim, William E Bentley, Reza Ghodssi
Bacterial biofilms are a common cause of chronic medical implant infections. Treatment and eradication of biofilms by conventional antibiotic therapy has major drawbacks including toxicity and side effects associated with high-dosage antibiotics. Additionally, administration of high doses of antibiotics may facilitate the emergence of antibiotic resistant bacteria. Thus, there is an urgent need for the development of treatments that are not based on conventional antibiotic therapies. Presented herein is a novel bacterial biofilm combination treatment independent of traditional antibiotics, by using low electric fields in combination with small molecule inhibitors of bacterial quorum sensing - autoinducer-2 analogs...
October 2016: Biomedical Microdevices
Stephan Daetwyler, Jan Huisken
In light sheet microscopy, optical sectioning by selective fluorescence excitation with a sheet of light is combined with fast full-frame acquisition. This illumination scheme provides minimal photobleaching and phototoxicity. Complemented with remote focusing and multi-view acquisition, light sheet microscopy is the method of choice for acquisition of very fast biological processes, large samples, and high-throughput applications in areas such as neuroscience, plant biology, and developmental biology. This review explains why light sheet microscopes are much faster and gentler than other established fluorescence microscopy techniques...
August 2016: Biological Bulletin
Manuel Gunkel, Holger Erfle, Vytaute Starkuviene
The Golgi complex plays a central role in a number of diverse cellular processes, and numerous regulators that control these functions and/or morphology of the Golgi complex are known by now. Many of them were identified by large-scale experiments, such as RNAi-based screening. However, high-throughput experiments frequently provide only initial information that a particular protein might play a role in regulating structure and function of the Golgi complex. Multiple follow-up experiments are necessary to functionally characterize the selected hits...
2016: Methods in Molecular Biology
Galit H Frydman, Anna Le, Felix Ellett, Julianne Jorgensen, James G Fox, Ronald G Tompkins, Daniel Irimia
Neutrophils are traditionally regarded as the "first responders" of the immune system. However, recent observations revealed that platelets often respond earlier to recruit and activate neutrophils within sites of injury and inflammation. Currently, platelet-neutrophil interactions are studied by intravital microscopy. Although such studies provide exceptional, physiologic in vivo data, they are also laborious and have low throughput. To accelerate platelet-neutrophil interaction studies, we have developed and optimized an ex vivo microfluidic platform with which the interactions between platelets and moving neutrophils are measured at single-cell level in precise conditions and with high throughput...
September 14, 2016: Journal of Leukocyte Biology
Itahisa Hernández Hidalgo, Thomas Fleming, Volker Eckstein, Stephan Herzig, Peter P Nawroth, Jens Tyedmers
Protein aggregation is both a hallmark of and a driving force for a number of diseases. It is therefore important to identify the nature of these aggregates and the mechanism(s) by which the cell counteracts their detrimental properties. Currently, the study of aggregation in vivo is performed primarily using fluorescently tagged versions of proteins and analyzing the aggregates by fluorescence microscopy. While this strategy is considered the gold standard, it has several limitations, particularly with respect to its suitability for high-throughput screening (HTS)...
2016: BioTechniques
Joris Lacroix, Sandrine Pélofy, Charline Blatché, Marie-Jeanne Pillaire, Sébastien Huet, Catherine Chapuis, Jean-Sébastien Hoffmann, Aurélien Bancaud
DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy...
September 14, 2016: Small
Jason Merritt, Seppe Kuehn
We present a high-throughput method to measure abundance dynamics in microbial communities sustained in continuous-culture. Our method uses custom epi-fluorescence microscopes to automatically image single cells drawn from a continuously-cultured population while precisely controlling culture conditions. For clonal populations of Escherichia coli our instrument reveals history-dependent resilience and growth rate dependent aggregation.
2016: Scientific Reports
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