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High throughput microscopy

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https://www.readbyqxmd.com/read/28644811/applying-pattern-recognition-to-high-resolution-images-to-determine-cellular-signaling-status
#1
Michael F Lohrer, Darrin M Hanna, Yang Liu, Kang-Hsin Wang, Fu-Tong Liu, Ted A Laurence, Gang-Yu Liu
Two frequently used tools to acquire high-resolution images of cells are scanning electron microscopy (SEM) and atomic force microscopy (AFM). The former provides a nanometer resolution view of cellular features rapidly and with high throughput, while the latter enables visualizing hydrated and living cells. In current practice, these images are viewed by eye to determine cellular status, e.g. activated versus resting. Automatic and quantitative data analysis is lacking. This work develops an algorithm of pattern recognition that works very effectively for AFM and SEM images...
June 21, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28644034/predicting-the-oxygen-binding-properties-of-platinum-nanoparticle-ensembles-by-combining-high-precision-electron-microscopy-dft
#2
Jolyon Aarons, Lewys Jones, Aakash Varambhia, Katherine E MacArthur, Dogan Ozkaya, Misbah Sarwar, Chris-Kriton Skylaris, Peter D Nellist
Many studies of heterogeneous catalysis, both experimental and computational, make use of idealised structures such as extended surfaces or regular polyhedral nanoparticles. This simplification neglects the morphological diversity in real commercial oxygen reduction reaction (ORR) catalysts used in fuel-cell cathodes. Here we introduce an approach that combines 3D nanoparticle structures obtained from high-throughput high-precision electron microscopy with density functional theory. Discrepancies between experimental observations and cuboctahedral/truncated-octahedral particles are revealed and discussed using a range of widely used descriptors, such as electron-density, d-band centres and generalised coordination numbers...
June 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28637488/a-high-throughput-colorimetric-assay-for-detection-of-schistosoma-mansoni-viability-based-on-the-tetrazolium-salt-xtt
#3
Pedro Henrique Nascimento Aguiar, Núbia Monteiro Gonçalves Soares Fernandes, Carlos Leomar Zani, Marina Moraes Mourão
BACKGROUND: Schistosoma mansoni is a trematode parasite that causes schistosomiasis, one of the most prevalent neglected tropical diseases, leading to the loss of 2.6 million disability-adjusted life years. Praziquantel is the only drug available, and new drugs are required. The most common strategy in schistosomiasis drug discovery is the use of the schistosomula larval-stage for a pre-screen in drug sensitivity assays. However, assessing schistosomula viability by microscopy has always been a limitation to the throughput of such assays...
June 21, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28636327/maldi-ms-guided-liquid-microjunction-extraction-for-ce-esi-ms-analysis-of-single-pancreatic-islet-cells
#4
Troy J Comi, Monika A Makurath, Marina C Philip, Stanislav S Rubakhin, Jonathan V Sweedler
The ability to characterize chemical heterogeneity in biological structures is essential to understanding cellular level function in both healthy and diseased states, but these variations remain difficult to assess using a single analytical technique. While mass spectrometry (MS) provides sufficient sensitivity to measure many analytes from volume-limited samples, each type of mass spectrometric analysis uncovers only a portion of the complete chemical profile of a single cell. Matrix-assisted laser desorp-tion/ionization (MALDI) MS and capillary electrophoresis electrospray ionization (CE-ESI)-MS are complementary analytical platforms frequently utilized for single cell analysis...
June 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28630898/polymeric-lithography-editor-editing-lithographic-errors-with-nanoporous-polymeric-probes
#5
Pradeep Ramiah Rajasekaran, Chuanhong Zhou, Mallika Dasari, Kay-Obbe Voss, Christina Trautmann, Punit Kohli
A new lithographic editing system with an ability to erase and rectify errors in microscale with real-time optical feedback is demonstrated. The erasing probe is a conically shaped hydrogel (tip size, ca. 500 nm) template-synthesized from track-etched conical glass wafers. The "nanosponge" hydrogel probe "erases" patterns by hydrating and absorbing molecules into a porous hydrogel matrix via diffusion analogous to a wet sponge. The presence of an interfacial liquid water layer between the hydrogel tip and the substrate during erasing enables frictionless, uninterrupted translation of the eraser on the substrate...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28628331/quantum-cascade-laser-spectral-histopathology-breast-cancer-diagnostics-using-high-throughput-chemical-imaging
#6
Michael John Pilling, Alex Henderson, Peter Gardner
Fourier Transform Infrared (FT-IR) microscopy, coupled with machine learning approaches, has been demonstrated to be a powerful technique for identifying abnormalities in human tissue. The ability to objectively identify the pre-diseased state, and diagnose cancer with high levels of accuracy, has the potential to revolutionise current histopathological practice. Despite recent technological advances in FT-IR microscopy, sample throughput and speed of acquisition are key barriers to clinical translation. Wide-field quantum cascade laser (QCL) infrared imaging systems with large focal plane array detectors and utilising discrete frequency imaging, have demonstrated that large tissue microarrays (TMA) can be imaged in a matter of minutes...
June 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28628084/long-term-imaging-of-cellular-forces-with-high-precision-by-elastic-resonator-interference-stress-microscopy
#7
Nils M Kronenberg, Philipp Liehm, Anja Steude, Johanna A Knipper, Jessica G Borger, Giuliano Scarcelli, Kristian Franze, Simon J Powis, Malte C Gather
Cellular forces are crucial for many biological processes but current methods to image them have limitations with respect to data analysis, resolution and throughput. Here, we present a robust approach to measure mechanical cell-substrate interactions in diverse biological systems by interferometrically detecting deformations of an elastic micro-cavity. Elastic resonator interference stress microscopy (ERISM) yields stress maps with exceptional precision and large dynamic range (2 nm displacement resolution over a >1 μm range, translating into 1 pN force sensitivity)...
June 19, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28627575/label-free-detection-of-aggregated-platelets-in-blood-by-machine-learning-aided-optofluidic-time-stretch-microscopy
#8
Yiyue Jiang, Cheng Lei, Atsushi Yasumoto, Hirofumi Kobayashi, Yuri Aisaka, Takuro Ito, Baoshan Guo, Nao Nitta, Natsumaro Kutsuna, Yasuyuki Ozeki, Atsuhiro Nakagawa, Yutaka Yatomi, Keisuke Goda
According to WHO, about 10 million new cases of thrombotic disorders are diagnosed worldwide every year. Thrombotic disorders, including atherothrombosis (the leading cause of death in the US and Europe), are induced by occlusion of blood vessels, due to the formation of blood clots in which aggregated platelets play an important role. The presence of aggregated platelets in blood may be related to atherothrombosis (especially acute myocardial infarction) and is, hence, useful as a potential biomarker for the disease...
June 19, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28623303/xtractb-assay-a-mycobacterium-tuberculosis-molecular-screening-test-with-sensitivity-approaching-culture
#9
Jennifer L Reed, Debby Basu, Matthew A Butzler, Sally M McFall
Nucleic acid amplification tests are increasingly used to diagnose tuberculosis (TB) due to their speed and sensitivity compared to sputum smear microscopy. However, these tests fail to equal culture's sensitivity with sputum smear microscopy negative specimens and therefore cannot be used to rule out TB disease. For molecular tests to match culture's sensitivity, they must detect ≤10 genomic copies of Mycobacterium tuberculosis (MTB) DNA, the limit of detection of culture, process ≥1 ml of sputum ensuring sufficient number of MTB are in the reaction, and efficiently remove sputum associated inhibitors from this large sample...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28621943/natural-products-discovered-in-a-high-throughput-screen-identified-as-inhibitors-of-rgs17-and-as-cytostatic-and-cytotoxic-agents-for-lung-and-prostate-cancer-cell-lines
#10
Christopher R Bodle, Duncan I Mackie, Michael P Hayes, Josephine H Schamp, Michael R Miller, Michael D Henry, Jonathan A Doorn, Jon C D Houtman, Michael A James, David L Roman
Regulator of G Protein Signaling (RGS) 17 is an overexpressed promoter of cancer survival in lung and prostate tumors, the knockdown of which results in decreased tumor cell proliferation in vitro. Identification of drug-like molecules inhibiting this protein could ameliorate the RGS17's pro-tumorigenic effect. Using high-throughput screening, a chemical library containing natural products was interrogated for inhibition of the RGS17-Gαo interaction. Initial hits were verified in control and counter screens...
June 16, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28620037/the-more-the-merrier-high-throughput-single-molecule-techniques
#11
REVIEW
Flynn R Hill, Enrico Monachino, Antoine M van Oijen
The single-molecule approach seeks to understand molecular mechanisms by observing biomolecular processes at the level of individual molecules. These methods have led to a developing understanding that for many processes, a diversity of behaviours will be observed, representing a multitude of pathways. This realisation necessitates that an adequate number of observations are recorded to fully characterise this diversity. The requirement for large numbers of observations to adequately sample distributions, subpopulations, and rare events presents a significant challenge for single-molecule techniques, which by their nature do not typically provide very high throughput...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28608904/droplet-based-light-sheet-fluorescence-microscopy-for-high-throughput-sample-preparation-3-d-imaging-and-quantitative-analysis-on-a-chip
#12
Hao Jiang, Tingting Zhu, Hao Zhang, Jun Nie, Zeyi Guan, Chi-Ming Ho, Sheng Liu, Peng Fei
We report a novel fusion of droplet microfluidics and light-sheet microscopy, to achieve high-throughput sample compartmentalization, manipulation and three-dimensional imaging on a chip. This optofluidic device characterized by orthogonal plane illumination and rapid liquid handling is compact and cost-effective, and capable of preparing sample droplets with tunable size, frequency and ingredient. Each droplet flowing through the device's imaging region is self-scanned by a laser-sheet, three-dimensionally reconstructed and quantitatively analysed...
June 13, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28594816/mrna-quantification-using-single-molecule-fish-in-drosophila-embryos
#13
Tatjana Trcek, Timothée Lionnet, Hari Shroff, Ruth Lehmann
Spatial information is critical to the interrogation of developmental and tissue-level regulation of gene expression. However, this information is usually lost when global mRNA levels from tissues are measured using reverse transcriptase PCR, microarray analysis or high-throughput sequencing. By contrast, single-molecule fluorescence in situ hybridization (smFISH) preserves the spatial information of the cellular mRNA content with subcellular resolution within tissues. Here we describe an smFISH protocol that allows for the quantification of single mRNAs in Drosophila embryos, using commercially available smFISH probes (e...
July 2017: Nature Protocols
https://www.readbyqxmd.com/read/28591707/identification-of-novel-small-molecule-beclin-1-mimetics-activating-autophagy
#14
Jia Yu, Lan Lan, Seth J Lewin, Steven A Rogers, Anuradha Roy, Xiaoqing Wu, Philip Gao, John Karanicolas, Jeffrey Aubé, Baiwang Sun, Liang Xu
Anti-apoptotic proteins Bcl-2 and Bcl-xL could block autophagy by binding to Beclin 1 protein, an essential inducer of autophagy. Compounds mimicking Beclin 1 might be able to disrupt Bcl-xL/2-Beclin 1 interaction, free out Beclin 1, and thus trigger autophagy. In order to identify small molecule Beclin 1 mimetics, a fluorescence polarization-based high-throughput screening of 50,316 compounds was carried out with a Z' score of 0.82 ± 0.05, and an outcome of 58 hits. After the structure analysis, three acridine analogues were unveiled and confirmed using the fluorescence polarization assay and the surface plasmon resonance assay...
May 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28577598/microwave-assisted-grafting-polymerization-preparation-of-strong-cation-exchange-nylon-6-capillary-channeled-polymer-fibers-and-their-chromatographic-properties
#15
Liuwei Jiang, R Kenneth Marcus
Native nylon 6 C-CP fibers were modified with 2-acrylamido-2-methylpropanesulfonic acid (AMPS) via the microwave-assisted grafting polymerization to affect a strong cation exchange stationary phase. Various concentrations of AMPS and the initiator potassium persulfate (KPS) were used in the modifications. The resultant nylon-SO3H fibers were characterized by Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), scanning electron microscopy (SEM) and acid-base titrations. The chromatographic properties, including column permeability, protein separation quality, and protein binding capacity, of the nylon-SO3H fiber columns were also studied...
July 18, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28575577/diphenylalanine-as-a-reductionist-model-for-the-mechanistic-characterization-of-%C3%AE-amyloid-modulators
#16
Sayanti Brahmachari, Zohar A Arnon, Anat Frydman-Marom, Lihi Adler-Abramovich, Ehud Gazit
The phenomenon of protein aggregation into amyloid fibrils is associated with a large number of major diseases of unrelated etiology. Unraveling the mechanism of amyloid self-assembly and identifying therapeutic directions to control this process are of utmost importance. Research in this field has been hampered by several challenges, including reproducibility, low protein purification yields and the inherent aggregation propensity of amyloidogenic proteins, making them extremely difficult to study. Herein, based on the similarity in the assembly mechanism, as well as the physical, chemical and biological characteristics, of diphenylalanine nanostructures and aromatic amino acid containing amyloid fibrils, we report a simple, yet robust peptide-based platform which could be used for screening of small molecules, potentially capable of interfering with the aggregation process, and for mechanistic exploration of their mode of action...
June 2, 2017: ACS Nano
https://www.readbyqxmd.com/read/28552967/automated-analysis-of-co-localized-protein-expression-in-histologic-sections-of-prostate-cancer
#17
Thomas A Tennill, Mitchell E Gross, Hermann B Frieboes
An automated approach based on routinely-processed, whole-slide immunohistochemistry (IHC) was implemented to study co-localized protein expression in tissue samples. Expression of two markers was chosen to represent stromal (CD31) and epithelial (Ki-67) compartments in prostate cancer. IHC was performed on whole-slide sections representing low-, intermediate-, and high-grade disease from 15 patients. The automated workflow was developed using a training set of regions-of-interest in sequential tissue sections...
2017: PloS One
https://www.readbyqxmd.com/read/28544620/phenotyping-cardiac-and-structural-birth-defects-in-fetal-and-newborn-mice
#18
REVIEW
Xiaoqin Liu, Andrew J Kim, William Reynolds, Yijen Wu, Cecilia W Lo
Mouse models are invaluable for investigating the developmental etiology and molecular pathogenesis of structural birth defects. While this has been deployed for studying a wide spectrum of birth defects, mice are particularly valuable for modeling congenital heart disease, given they have the same four-chamber cardiac anatomy as in humans. We have developed the use of noninvasive fetal ultrasound together with micro-computed tomography (micro-CT) imaging for high throughput phenotyping of mice for congenital heart defects (CHD) and other developmental anomalies...
May 22, 2017: Birth defects research
https://www.readbyqxmd.com/read/28544415/inertial-microfluidic-cell-stretcher-imcs-fully-automated-high-throughput-and-near-real-time-cell-mechanotyping
#19
Yanxiang Deng, Steven P Davis, Fan Yang, Kevin S Paulsen, Maneesh Kumar, Rebecca Sinnott DeVaux, Xianhui Wang, Douglas S Conklin, Assad Oberai, Jason I Herschkowitz, Aram J Chung
Mechanical biomarkers associated with cytoskeletal structures have been reported as powerful label-free cell state identifiers. In order to measure cell mechanical properties, traditional biophysical (e.g., atomic force microscopy, micropipette aspiration, optical stretchers) and microfluidic approaches were mainly employed; however, they critically suffer from low-throughput, low-sensitivity, and/or time-consuming and labor-intensive processes, not allowing techniques to be practically used for cell biology research applications...
May 23, 2017: Small
https://www.readbyqxmd.com/read/28540370/ultralow-friction-of-ink-jet-printed-graphene-flakes
#20
R Buzio, A Gerbi, S Uttiya, C Bernini, A E Del Rio Castillo, F Palazon, A S Siri, V Pellegrini, L Pellegrino, F Bonaccorso
We report the frictional response of few-layer graphene (FLG) flakes obtained by the liquid phase exfoliation (LPE) of pristine graphite. To this end, we inkjet print FLG on bare and hexamethyldisilazane-terminated SiO2 substrates, producing micrometric patterns with nanoscopic roughness that are investigated by atomic force microscopy. Normal force spectroscopy and atomically-resolved morphologies indicate reduced surface contamination by solvents after a vacuum annealing process. Notably, the printed FLG flakes show ultralow friction comparable to that of micromechanically exfoliated graphene flakes...
June 8, 2017: Nanoscale
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