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https://www.readbyqxmd.com/read/28198806/arrays-of-individual-dna-molecules-on-nanopatterned-substrates
#1
Roland Hager, Alma Halilovic, Jonathan R Burns, Friedrich Schäffler, Stefan Howorka
Arrays of individual molecules can combine the advantages of microarrays and single-molecule studies. They miniaturize assays to reduce sample and reagent consumption and increase throughput, and additionally uncover static and dynamic heterogeneity usually masked in molecular ensembles. However, realizing single-DNA arrays must tackle the challenge of capturing structurally highly dynamic strands onto defined substrate positions. Here, we create single-molecule arrays by electrostatically adhering single-stranded DNA of gene-like length onto positively charged carbon nanoislands...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198734/new-frontiers-in-intravital-microscopy-of-the-kidney
#2
Andrew M Hall, Claus D Schuh, Dominik Haenni
PURPOSE OF REVIEW: Intravital imaging with multiphoton microscopy enables the detailed study of dynamic cellular processes within functioning organs in living animals, in ways that would not otherwise be possible. It therefore represents a powerful tool in translational kidney research. In this article, we will discuss several new technical developments that have significantly increased the capabilities of kidney imaging. RECENT FINDINGS: Important contemporary advances in biomedical imaging technology include longer wavelength excitation lasers, far-red emitting fluorescent reporters, highly sensitive detectors, fluorescence lifetime measurements, adaptive optics, microendoscopes, high-throughput automated analysis algorithms and tissue clearing techniques...
February 13, 2017: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/28194956/direct-imaging-of-single-plasmonic-metal-nanoparticles-in-capillary-with-laser-light-sheet-scattering-imaging
#3
Xuan Cao, Jingjing Feng, Qi Pan, Bin Xiong, Yan He, Edward S Yeung
Understanding the heterogeneous distribution of the physical and chemical properties of plasmonic metal nanoparticles is fundamentally important to their basic and applied research. Traditionally, they are obtained either indirectly via bulk spectroscopic measurements plus electron microscopic characterizations, or through single molecule/particle imaging of nanoparticles immobilized on planar substrates. In this study, by using light-sheet scattering microscopy with a supercontinuum white laser, highly sensitive imaging of individual MNPs flowing inside a capillary, driven by either pressure or electric field, was achieved for the first time...
February 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28194949/single-cell-profiling-using-ionic-liquid-matrix-enhanced-secondary-ion-mass-spectrometry-for-neuronal-cell-type-differentiation
#4
Thanh D Do, Troy J Comi, Sage J B Dunham, Stanislav S Rubakhin, Jonathan V Sweedler
A high-throughput single cell profiling method has been developed for matrix-enhanced-secondary ion mass spectrometry (ME-SIMS) to investigate the lipid profiles of neuronal cells. Populations of cells are dispersed onto the substrate, their locations determined using optical microscopy, and the cell locations used to guide the acquisition of SIMS spectra from the cells. Up to 2,000 cells can be assayed in one experiment at a rate of 6 s per cell. Multiple saturated and unsaturated phosphatidylcholines (PCs) and their fragments are detected and verified with tandem mass spectrometry from individual cells when ionic liquids are employed as a matrix...
February 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28194225/net-a-new-framework-for-the-vectorization-and-examination-of-network-data
#5
Jana Lasser, Eleni Katifori
BACKGROUND: The analysis of complex networks both in general and in particular as pertaining to real biological systems has been the focus of intense scientific attention in the past and present. In this paper we introduce two tools that provide fast and efficient means for the processing and quantification of biological networks like Drosophila tracheoles or leaf venation patterns: the Network Extraction Tool (NET) to extract data and the Graph-edit-GUI (GeGUI) to visualize and modify networks...
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/28186188/all-in-one-3d-printed-microscopy-chamber-for-multidimensional-imaging-the-universlide
#6
Kevin Alessandri, Laetitia Andrique, Maxime Feyeux, Andreas Bikfalvi, Pierre Nassoy, Gaëlle Recher
While live 3D high resolution microscopy techniques are developing rapidly, their use for biological applications is partially hampered by practical difficulties such as the lack of a versatile sample chamber. Here, we propose the design of a multi-usage observation chamber adapted for live 3D bio-imaging. We show the usefulness and practicality of this chamber, which we named the UniverSlide, for live imaging of two case examples, namely multicellular systems encapsulated in sub-millimeter hydrogel shells and zebrafish larvae...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28181485/high-throughput-single-cell-analysis-for-the-proteomic-dynamics-study-of-the-yeast-osmotic-stress-response
#7
Rongfei Zhang, Haiyu Yuan, Shujing Wang, Qi Ouyang, Yong Chen, Nan Hao, Chunxiong Luo
Motorized fluorescence microscopy combined with high-throughput microfluidic chips is a powerful method to obtain information about different biological processes in cell biology studies. Generally, to observe different strains under different environments, high-throughput microfluidic chips require complex preparatory work. In this study, we designed a novel and easily operated high-throughput microfluidic system to observe 96 different GFP-tagged yeast strains in one switchable culture condition or 24 different GFP-tagged yeast strains in four parallel switchable culture conditions...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28174601/development-of-a-genetically-programed-vanillin-sensing-bacterium-for-high-throughput-screening-of-lignin-degrading-enzyme-libraries
#8
Barindra Sana, Kuan Hui Burton Chia, Sarada S Raghavan, Balamurugan Ramalingam, Niranjan Nagarajan, Jayasree Seayad, Farid J Ghadessy
BACKGROUND: Lignin is a potential biorefinery feedstock for the production of value-added chemicals including vanillin. A huge amount of lignin is produced as a by-product of the paper industry, while cellulosic components of plant biomass are utilized for the production of paper pulp. In spite of vast potential, lignin remains the least exploited component of plant biomass due to its extremely complex and heterogenous structure. Several enzymes have been reported to have lignin-degrading properties and could be potentially used in lignin biorefining if their catalytic properties could be improved by enzyme engineering...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28166742/analysis-of-small-rnas-revealed-differential-expressions-during-pollen-and-embryo-sac-development-in-autotetraploid-rice
#9
Xiang Li, Muhammad Qasim Shahid, Juan Xia, Zijun Lu, Na Fang, Lan Wang, Jinwen Wu, Zhixiong Chen, Xiangdong Liu
BACKGROUND: Partial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28165060/novel-flow-cytometry-approach-to-identify-bronchial-epithelial-cells-from-healthy-human-airways
#10
Danay Maestre-Batlle, Olga M Pena, Jeremy A Hirota, Evelyn Gunawan, Christopher F Rider, Darren Sutherland, Neil E Alexis, Chris Carlsten
Sampling various compartments within the lower airways to examine human bronchial epithelial cells (HBEC) is essential for understanding numerous lung diseases. Conventional methods to identify HBEC in bronchoalveolar lavage (BAL) and wash (BW) have throughput limitations in terms of efficiency and ensuring adequate cell numbers for quantification. Flow cytometry can provide high-throughput quantification of cell number and function in BAL and BW samples, while requiring low cell numbers. To date, a flow cytometric method to identify HBEC recovered from lower human airway samples is unavailable...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28161665/lipid-nanoparticles-assessment-by-flow-cytometry
#11
Anna Bryła, Wojciech Juzwa, Marek Weiss, Grażyna Lewandowicz
BACKGROUND: Liposomes are promising carriers for drugs and bioactive compounds. Size and structure are their crucial parameters. Thus, it is essential to assess individual vesicles as prepared. Currently available techniques fail to measure liposome's size and structure simultaneously, with a high throughput. To solve this problem, we have developed a novel, flow cytometric method quantifying liposomes. METHODS: Firstly, the following fluorescent staining combinations were tested: DiD/TO, Rh123/DiD, Syto9/DiD...
February 1, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28143748/a-three-dimensional-neural-spheroid-model-for-capillary-like-network-formation
#12
Molly E Boutin, Liana L Kramer, Liane L Livi, Tyler Brown, Christopher Moore, Diane Hoffman-Kim
BACKGROUND: In vitro three-dimensional neural spheroid models have an in vivo-like cell density, and have the potential to reduce animal usage and increase experimental throughput. The aim of this study was to establish a spheroid model to study the formation of capillary-like networks in a three-dimensional environment that incorporates both neuronal and glial cell types, and does not require exogenous vasculogenic growth factors. NEW METHOD: We created self-assembled, scaffold-free cellular spheroids using primary-derived postnatal rodent cortex as a cell source...
January 28, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28129584/bone-natural-autofluorescence-and-confocal-laser-scanning-microscopy-preliminary-results-of-a-novel-useful-tool-to-distinguish-between-forensic-and-ancient-human-skeletal-remains
#13
Luigi Capasso, Ruggero D'Anastasio, Simone Guarnieri, Joan Viciano, Maria Mariggiò
The fast, high-throughput distinction between palaeoanthropological/archaeological remains and recent forensic/clinical bone samples is of vital importance in the field of medico-legal science. In this paper, a novel dating method was developed using the autofluorescence of human bones and the confocal laser scanning microscope as the means to distinguish between archaeological and forensic anthropological skeletal findings. Human bones exhibit fluorescence, typically induced by natural antibiotics that are absorbed by collagen, and provide secondary, exogenous fluorophores...
January 22, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28125106/strain-library-imaging-protocol-for-high-throughput-automated-single-cell-microscopy-of-large-bacterial-collections-arrayed-on-multiwell-plates
#14
Handuo Shi, Alexandre Colavin, Timothy K Lee, Kerwyn Casey Huang
Single-cell microscopy is a powerful tool for studying gene functions using strain libraries, but it suffers from throughput limitations. Here we describe the Strain Library Imaging Protocol (SLIP), which is a high-throughput, automated microscopy workflow for large strain collections that requires minimal user involvement. SLIP involves transferring arrayed bacterial cultures from multiwell plates onto large agar pads using inexpensive replicator pins and automatically imaging the resulting single cells. The acquired images are subsequently reviewed and analyzed by custom MATLAB scripts that segment single-cell contours and extract quantitative metrics...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28106532/rotational-scanning-atomic-force-microscopy
#15
A Ulčinas, Š Vaitekonis
A non-raster scanning technique for atomic force microscopy (AFM) imaging which combines rotational and translational motion is presented. The use of rotational motion for the fast scan axis allows us to significantly increase the scanning speed while imaging a large area (diameter > 30 μm). An image reconstruction algorithm and the factors influencing the resolution of the technique are discussed. The experimental results show the potential of the rotational scanning technique for high-throughput large area AFM investigation...
March 10, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28098273/high-definition-infrared-chemical-imaging-of-colorectal-tissue-using-a-spero-qcl-microscope
#16
B Bird, J Rowlette
Mid-infrared microscopy has become a key technique in the field of biomedical science and spectroscopy. This label-free, non-destructive technique permits the visualisation of a wide range of intrinsic biochemical markers in tissues, cells and biofluids by detection of the vibrational modes of the constituent molecules. Together, infrared microscopy and chemometrics is a widely accepted method that can distinguish healthy and diseased states with high accuracy. However, despite the exponential growth of the field and its research world-wide, several barriers currently exist for its full translation into the clinical sphere, namely sample throughput and data management...
January 18, 2017: Analyst
https://www.readbyqxmd.com/read/28096363/an-rna-based-signature-enables-high-specificity-detection-of-circulating-tumor-cells-in-hepatocellular-carcinoma
#17
Mark Kalinich, Irun Bhan, Tanya T Kwan, David T Miyamoto, Sarah Javaid, Joseph A LiCausi, John D Milner, Xin Hong, Lipika Goyal, Srinjoy Sil, Melissa Choz, Uyen Ho, Ravi Kapur, Alona Muzikansky, Huidan Zhang, David A Weitz, Lecia V Sequist, David P Ryan, Raymond T Chung, Andrew X Zhu, Kurt J Isselbacher, David T Ting, Mehmet Toner, Shyamala Maheswaran, Daniel A Haber
Circulating tumor cells (CTCs) are shed into the bloodstream by invasive cancers, but the difficulty inherent in identifying these rare cells by microscopy has precluded their routine use in monitoring or screening for cancer. We recently described a high-throughput microfluidic CTC-iChip, which efficiently depletes hematopoietic cells from blood specimens and enriches for CTCs with well-preserved RNA. Application of RNA-based digital PCR to detect CTC-derived signatures may thus enable highly accurate tissue lineage-based cancer detection in blood specimens...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095175/evaluation-of-the-droplet-microarray-platform-for-high-throughput-screening-of-suspension-cells
#18
Anna A Popova, Claire Depew, Katya Manuella Permana, Alexander Trubitsyn, Ravindra Peravali, Jorge Ángel González Ordiano, Markus Reischl, Pavel A Levkin
Phenotypic cell-based high-throughput screenings play a central role in drug discovery and toxicology. The main tendency in cell screenings is the increase of the throughput and decrease of reaction volume in order to accelerate the experiments, reduce the costs, and enable screenings of rare cells. Conventionally, cell-based assays are performed in microtiter plates, which exist in 96- to 1536-wells formats and cannot be further miniaturized. In addition, performing screenings of suspension cells is associated with risk of losing cell content during the staining procedures and incompatibility with high-content microscopy...
November 1, 2016: Journal of Laboratory Automation
https://www.readbyqxmd.com/read/28079286/design-synthesis-biological-evaluation-and-3d-qsar-analysis-of-podophyllotoxin-dioxazole-combination-as-tubulin-targeting-anticancer-agents
#19
Zi-Zhen Wang, Wen-Xue Sun, Xue Wang, Ya-Han Zhang, Han-Yue Qiu, Jin-Liang Qi, Yan-Jun Pang, Gui-Hua Lu, Xiao-Ming Wang, Fu-Gen Yu, Yong-Hua Yang
The advancement of cancer fighting drugs has never been a simple linear process. Those drugs design professionals begin to find inspiration from the nature after failing to find the ideal products by creative drugs design and high-throughput screening. To obtain new molecules for inhibiting tubulin, podophyllotoxin was adopted as the leading compound and 1,3,4-oxadiazole was brought in to the C-4 site of podophyllotoxin in this research. A series of seventeen podophyllotoxin derived esters have been achieved and then evaluated their antitumor activities against four different cancer cell lines: A549, MCF-7, HepG2 and HeLa...
January 12, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28075531/three-dimensional-imaging-flow-cytometry-through-light-sheet-fluorescence-microscopy
#20
REVIEW
Emilio J Gualda, Hugo Pereira, Gabriel G Martins, Rui Gardner, Nuno Moreno
Flow cytometry is the tool of choice for high-speed acquisition and analysis of large cell populations, with the tradeoff of lacking intracellular spatial information. Although in the last decades flow cytometry systems that can actually acquire two-dimensional spatial information were developed, some of the limitations remained though, namely constrains related to sample size and lack of depth or dynamic information. The combination of fluidics and light-sheet illumination has the potential to address these limitations...
January 11, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
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