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High throughput microscopy

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https://www.readbyqxmd.com/read/28430778/a-no-film-slot-blot-for-the-detection-of-developing-p-falciparum-oocysts-in-mosquitoes
#1
Bryan Grabias, Nitin Verma, Hong Zheng, Abhai K Tripathi, Godfree Mlambo, Merribeth J Morin, Emily Locke, Sanjai Kumar
Non-microscopy-based assays for sensitive and rapid detection of Plasmodium infection in mosquitoes are needed to allow rapid and high throughput measurement of transmission intensity and malaria control program effectiveness. Here, we report on a modified enhanced chemiluminescence-based slot blot assay for detection of Plasmodium falciparum (Pf) circumsporozite protein (PfCSP) expressed on parasite oocysts developing inside the mosquito midgut. This modified assay has several novel features that include eliminating the need for exposure to autoradiography (AR) film, as well as utilizing a novel high affinity anti-CSP antibody, and optimizing assay procedures resulting in significant reduction in the time required to perform the assay...
2017: PloS One
https://www.readbyqxmd.com/read/28429122/quantifying-golgi-structure-using-em-combining-volume-sem-and-stereology-for-higher-throughput
#2
REVIEW
Sophie Ferguson, Anna M Steyer, Terry M Mayhew, Yannick Schwab, John Milton Lucocq
Investigating organelles such as the Golgi complex depends increasingly on high-throughput quantitative morphological analyses from multiple experimental or genetic conditions. Light microscopy (LM) has been an effective tool for screening but fails to reveal fine details of Golgi structures such as vesicles, tubules and cisternae. Electron microscopy (EM) has sufficient resolution but traditional transmission EM (TEM) methods are slow and inefficient. Newer volume scanning EM (volume-SEM) methods now have the potential to speed up 3D analysis by automated sectioning and imaging...
April 20, 2017: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/28427455/comparison-of-methods-for-detecting-asymptomatic-malaria-infections-in-the-china-myanmar-border-area
#3
Yonghong Zhao, Yan Zhao, Yanmin Lv, Fei Liu, Qinghui Wang, Peipei Li, Zhenjun Zhao, Yingjie Liu, Liwang Cui, Qi Fan, Yaming Cao
BACKGROUND: Sensitive methods for detecting asymptomatic malaria infections are essential for identifying potential transmission reservoirs and obtaining an accurate assessment of malaria epidemiology in low-endemicity areas aiming to eliminate malaria. PCR techniques to detect parasite nucleic acids (DNA or RNA) are among the most commonly used molecular methods. However, most of these methods are of low throughput and cannot be used for large-scale molecular epidemiological studies...
April 20, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28414801/probabilistic-fluorescence-based-synapse-detection
#4
Anish K Simhal, Cecilia Aguerrebere, Forrest Collman, Joshua T Vogelstein, Kristina D Micheva, Richard J Weinberg, Stephen J Smith, Guillermo Sapiro
Deeper exploration of the brain's vast synaptic networks will require new tools for high-throughput structural and molecular profiling of the diverse populations of synapses that compose those networks. Fluorescence microscopy (FM) and electron microscopy (EM) offer complementary advantages and disadvantages for single-synapse analysis. FM combines exquisite molecular discrimination capacities with high speed and low cost, but rigorous discrimination between synaptic and non-synaptic fluorescence signals is challenging...
April 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28407595/proteo-lipobeads-to-encapsulate-cytochrome-c-oxidase-from-paracoccus-denitrificans
#5
Andreas F Geiss, Christina Bliem, Pinar Frank, Ciril Reiner-Rozman, Justin Kewney, Michael Boersch, Renate L C Naumann
Proteo-lipobeads (PLBs) are investigated as cell-free model systems to encapsulate membrane proteins such as ion channels and transporters. PLBs are based on nickel nitrile tri-acetic acid (Ni-NTA)-functionalized agarose beads, onto which membrane proteins (MP) are bound via histidine(his)-tag. Composite beads thus obtained (subsequently called proteobeads) are dialyzed in the presence of lipid micelles to form PLBs. As an example we employed cytochrome c oxidase from P. denitrificans with a his-tag fused to the C-terminus of subunitI...
April 5, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28402718/prions-on-the-run-how-extracellular-vesicles-serve-as-delivery-vehicles-for-self-templating-protein-aggregates
#6
Shu Liu, André Hossinger, Sarah Göbbels, Ina M Vorberg
Extracellular vesicles (EVs) are actively secreted, membrane-bound communication vehicles that exchange biomolecules between cells. EVs also serve as dissemination vehicles for pathogens, including prions, proteinaceous infectious agents that cause transmissible spongiform encephalopathies (TSEs) in mammals. Increasing evidence accumulates that diverse protein aggregates associated with common neurodegenerative diseases are packaged into EVs as well. Vesicle-mediated intercellular transmission of protein aggregates can induce aggregation of homotypic proteins in acceptor cells and might thereby contribute to disease progression...
March 4, 2017: Prion
https://www.readbyqxmd.com/read/28399328/high-throughput-label-free-single-cell-microalgal-lipid-screening-by-machine-learning-equipped-optofluidic-time-stretch-quantitative-phase-microscopy
#7
Baoshan Guo, Cheng Lei, Hirofumi Kobayashi, Takuro Ito, Yaxiaer Yalikun, Yiyue Jiang, Yo Tanaka, Yasuyuki Ozeki, Keisuke Goda
The development of reliable, sustainable, and economical sources of alternative fuels to petroleum is required to tackle the global energy crisis. One such alternative is microalgal biofuel, which is expected to play a key role in reducing the detrimental effects of global warming as microalgae absorb atmospheric CO2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid amounts and fail to characterize a diverse population of microalgal cells with single-cell resolution in a non-invasive and interference-free manner...
April 11, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28393906/demonstration-of-nanoimprinted-hyperlens-array-for-high-throughput-sub-diffraction-imaging
#8
Minsueop Byun, Dasol Lee, Minkyung Kim, Yangdoo Kim, Kwan Kim, Jong G Ok, Junsuk Rho, Heon Lee
Overcoming the resolution limit of conventional optics is regarded as the most important issue in optical imaging science and technology. Although hyperlenses, super-resolution imaging devices based on highly anisotropic dispersion relations that allow the access of high-wavevector components, have recently achieved far-field sub-diffraction imaging in real-time, the previously demonstrated devices have suffered from the extreme difficulties of both the fabrication process and the non-artificial objects placement...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28392532/high-throughput-screening-of-erratic-cell-volume-regulation-using-a-hydrogel-based-single-cell-microwell-array
#9
Casey L Brown, Valerie Fleischauer, Jinseok Heo
Here, we report that a single-cell microwell array based on photocrosslinked hydrogel can be used to screen cells exhibiting a defective regulatory volume decrease (RVD) in high-throughput. The RVD is a regulatory function of cells that maintains cell volume homeostasis in a hypotonic medium. Single Madin-Darby canine kidney (MDCK) cells grown in the microwells were loaded with a volume-sensitive fluorescence dye. Changes in the volume of discrete single cells were traced for 20 min in a hypotonic solution using a wide-field fluorescence microscopy...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28391243/accurate-classification-of-protein-subcellular-localization-from-high-throughput-microscopy-images-using-deep-learning
#10
Tanel Pärnamaa, Leopold Parts
High throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held out images...
April 8, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28386390/acute-lymphoblastic-leukaemia-cells-produce-large-extracellular-vesicles-containing-organelles-and-an-active-cytoskeleton
#11
Suzanne M Johnson, Clare Dempsey, Catriona Parker, Aleksandr Mironov, Helen Bradley, Vaskar Saha
Extracellular vesicles have been described in non-paracrine cellular interactions in cancer. We report a similar phenomenon in B-cell precursor (BCP) acute lymphoblastic leukaemia (ALL). Using advanced microscopy and high throughput screening, we further characterise a subset of large vesicles (LEVs) identified in cell lines, murine models of human BCP-ALL and clinical samples. Primary ALL blasts and cell lines released heterogeneous anucleate vesicles <6 micron into extracellular fluids. Larger LEVs were enclosed in continuous membranes, contained intact organelles and demonstrated an organised cytoskeleton...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28386206/high-throughput-automated-image-processing-for-large-scale-fluorescence-microscopy-experiments
#12
Allen Goodman, Anne E Carpenter
No abstract text is available yet for this article.
July 2016: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28379412/deepem3d-approaching-human-level-performance-on-3d-anisotropic-em-image-segmentation
#13
Tao Zeng, Bian Wu, Shuiwang Ji
Motivation: Progress in 3D electron microscopy (EM) imaging has greatly facilitated neuroscience research in high-throughput data acquisition. Correspondingly, high-throughput automated image analysis methods are necessary to work on par with the speed of data being produced. One such example is the need for automated EM image segmentation for neurite reconstruction. However, the efficiency and reliability of current methods are still lagging far behind human performance. Results: Here, we propose DeepEM3D, a deep learning method for segmenting 3D anisotropic brain electron microscopy images...
March 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28378146/use-of-a-highly-parallel-microfluidic-flow-cell-array-to-determine-therapeutic-drug-dose-response-curves
#14
Jesús A Arellano, Taylor A Howell, James Gammon, Sungpil Cho, Margit M Janát-Amsbury, Bruce Gale
A high-throughput, microfluidic flow cell array (MFCA) system has been modified to enable drug screening against small-volume cell-, and tissue cultures. The MFCA is composed of a 3D channel network that simultaneously flows fluids through forty-eight 830 μm by 500 μm flow cells, which physically divide and fluidically seal an existing culture into multiple compartments when docked onto the surface of a cell or tissue culture dish. The modified system provides temperature (37 °C) and CO2/pH level controls, while continuously flowing solutions (media or other liquid such as drug suspensions) over the cells/tissues...
June 2017: Biomedical Microdevices
https://www.readbyqxmd.com/read/28376782/image-analysis-driven-single-cell-analytics-for-systems-microbiology
#15
Athanasios D Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P Tampakaki, Konstantinos P Koutsoumanis, Elias S Manolakos
BACKGROUND: Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology. RESULTS: BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view...
April 4, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28374851/claudin-expression-in-the-rat-endolymphatic-duct-and-sac-first-insights-into-regulation-of-the-paracellular-barrier-by-vasopressin
#16
Daniel Runggaldier, Lidia Garcia Pradas, Peter H Neckel, Andreas F Mack, Bernhard Hirt, Corinna Gleiser
Hearing and balance functions of the inner ear rely on the homeostasis of the endolymphatic fluid. When disturbed, pathologic endolymphatic hydrops evolves as observed in Menière's disease. The molecular basis of inner ear fluid regulation across the endolymphatic epithelium is largely unknown. In this study we identified the specific expression of the tight junction (TJ) molecules Claudin 3, 4, 6, 7, 8, 10, and 16 in epithelial preparations of the rat inner ear endolymphatic duct (ED) and endolymphatic sac (ES) by high-throughput qPCR and immunofluorescence confocal microscopy...
April 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28374061/spatio-temporal-variations-of-marine-biofilm-communities-colonizing-artificial-substrata-including-antifouling-coatings-in-contrasted-french-coastal-environments
#17
Jean-François Briand, Aude Barani, Cédric Garnier, Karine Réhel, Félix Urvois, Christophe LePoupon, Agnès Bouchez, Didier Debroas, Christine Bressy
Surface colonization in seawater first corresponds to the selection of specific microbial biofilm communities. By coupling flow cytometry, microscopy and high throughput sequencing (HTS, 454 pyrosequencing) with artificial surfaces and environmental analyses, we intend to identify the contribution of biofilm community drivers at two contrasted French sites, one temperate and eutrophic (Lorient, Atlantic coast) and the other at a mesotrophic but highly contaminated bay (Toulon, North-Western Mediterranean Sea)...
April 3, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28372370/high-throughput-atomic-force-microscopes-operating-in-parallel
#18
Hamed Sadeghian, Rodolf Herfst, Bert Dekker, Jasper Winters, Tom Bijnagte, Ramon Rijnbeek
Atomic force microscopy (AFM) is an essential nanoinstrument technique for several applications such as cell biology and nanoelectronics metrology and inspection. The need for statistically significant sample sizes means that data collection can be an extremely lengthy process in AFM. The use of a single AFM instrument is known for its very low speed and not being suitable for scanning large areas, resulting in a very-low-throughput measurement. We address this challenge by parallelizing AFM instruments. The parallelization is achieved by miniaturizing the AFM instrument and operating many of them simultaneously...
March 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28366666/a-high-content-microscopy-assay-to-determine-drug-activity-against-intracellular-mycobacterium-tuberculosis
#19
Alyssa J Manning, Yulia Ovechkina, Amanda McGillivray, Lindsay Flint, David M Roberts, Tanya Parish
Tuberculosis is one of the infectious diseases with the greatest global burden, affecting millions of people. The rise of multi- and extensively-drug resistant forms of Mycobacterium tuberculosis over the last few decades has highlighted the urgent need for development of new drugs to treat the disease. Many drug development pipelines are based on in vitro assays examining a compound's effect on M. tuberculosis alone. These do not account for the effect of a compound on mammalian cells nor the interaction between host and pathogen...
March 31, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28360088/vegf-a-regulates-cellular-localization-of-sr-bi-as-well-as-transendothelial-transport-of-hdl-but-not-ldl
#20
Srividya Velagapudi, Mustafa Yalcinkaya, Antonio Piemontese, Roger Meier, Simon Flyvbjerg Nørrelykke, Damir Perisa, Andrzej Rzepiela, Michael Stebler, Szymon Stoma, Paolo Zanoni, Lucia Rohrer, Arnold von Eckardstein
OBJECTIVE: Low- and high-density lipoproteins (LDL and HDL) must pass the endothelial layer to exert pro- and antiatherogenic activities, respectively, within the vascular wall. However, the rate-limiting factors that mediate transendothelial transport of lipoproteins are yet little known. Therefore, we performed a high-throughput screen with kinase drug inhibitors to identify modulators of transendothelial LDL and HDL transport. APPROACH AND RESULTS: Microscopy-based high-content screening was performed by incubating human aortic endothelial cells with 141 kinase-inhibiting drugs and fluorescent-labeled LDL or HDL...
March 30, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
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