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High throughput microscopy

Mustafa Ugur Daloglu, Aydogan Ozcan
Not only essential for scientific research, but also in the analysis of male fertility and for animal husbandry, sperm tracking and characterization techniques have been greatly benefiting from computational imaging. Digital image sensors, in combination with optical microscopy tools and powerful computers, have enabled the use of advanced detection and tracking algorithms that automatically map sperm trajectories and calculate various motility parameters across large data sets. Computational techniques are driving the field even further, facilitating the development of unconventional sperm imaging and tracking methods that do not rely on standard optical microscopes and objective lenses, which limit the field of view and volume of the semen sample that can be imaged...
August 1, 2017: Biology of Reproduction
Brenda N Nakagaki, Maria A Freitas-Lopes, Érika Carvalho, Raquel Carvalho-Gontijo, Hortência M Castro-Oliveira, Rafael M Rezende, Denise C Cara, Mônica M Santos, Rodrigo Pestana Lopes, Bruna A David, Gustavo B Menezes
Resident and circulating immune cells have been extensively studied due to their almost ubiquitous role in cell biology. Despite their classification under the "immune cell department", it is becoming increasingly clear that these cells are involved in many different non-immune related phenomena, including fetus development, vascular formation, memory, social behavior and many other phenotypes. There is a huge potential in combining high-throughput assays - including flow cytometry and gene analysis - with in vivo imaging...
October 16, 2017: Anais da Academia Brasileira de Ciências
Chang Liu, Ya-Huei Chang, Jianan Chen, Shien-Ping Feng
High-index faceted nano/microcrystals exhibit enhanced catalytic activity and can thus serve as new-generation catalysts as their high density of low-coordinated atoms leads to significantly enhanced catalytic activity. In this study, an effective electrochemical approach termed cyclic scanning electrodeposition (CSE) was developed to convert a thin Cu film into Cu2O concave octahedrons enclosed by 24 {344} high-index facets at room temperature with high yield and high throughput. The formation mechanism and the role of each ion in the electrolyte were systematically studied, which facilitated the design of a high-index faceted metal/metal oxide through CSE...
October 17, 2017: ACS Applied Materials & Interfaces
Baoshan Guo, Cheng Lei, Yi Wu, Hirofumi Kobayashi, Takuro Ito, Yaxiaer Yalikun, Sangwook Lee, Akihiro Isozaki, Ming Li, Yiyue Jiang, Atsushi Yasumoto, Dino Di Carlo, Yo Tanaka, Yutaka Yatomi, Yasuyuki Ozeki, Keisuke Goda
Innovations in optical microscopy have opened new windows onto scientific research, industrial quality control, and medical practice over the last few decades. One of such innovations is optofluidic time-stretch quantitative phase microscopy - an emerging method for high-throughput quantitative phase imaging that builds on the interference between temporally stretched signal and reference pulses by using dispersive properties of light in both spatial and temporal domains in an interferometric configuration on a microfluidic platform...
October 12, 2017: Methods: a Companion to Methods in Enzymology
Maxime Bombrun, Hui Gao, Petter Ranefall, Niklas Mejhert, Peter Arner, Carolina Wählby
Neutral lipids packed in lipid droplets (LDs) are essential as a source of fuel for organisms, and specialized storing cells, the adipocytes, provide a buffer for energy variations. Many modern-society-disorders are connected with excess accumulation or deficiency of LDs in adipose tissue. Intracellular LD number and size distribution reflect the tissue conditions, while the associated mechanisms and genes rs are still poorly understood. Large-scale genetic screens using human in vitro differentiated primary adipocytes require cell samples donated from many patients...
October 14, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Per Niklas Hedde, Leonel Malacrida, Siavash Ahrar, Albert Siryaporn, Enrico Gratton
Previously described selective plane illumination microscopy techniques typically offset ease of use and sample handling for maximum imaging performance or vice versa. Also, to reduce cost and complexity while maximizing flexibility, it is highly desirable to implement light sheet microscopy such that it can be added to a standard research microscope instead of setting up a dedicated system. We devised a new approach termed sideSPIM that provides uncompromised imaging performance and easy sample handling while, at the same time, offering new applications of plane illumination towards fluidics and high throughput 3D imaging of multiple specimen...
September 1, 2017: Biomedical Optics Express
Alba Boix-Amorós, Cecilia Martinez-Costa, Amparo Querol, Maria Carmen Collado, Alex Mira
Human breastmilk contains a variety of bacteria that are transmitted to the infant and have been suggested to contribute to gut microbiota development and immune maturation. However, the characterization of fungal organisms in milk from healthy mothers is currently unknown although their presence has been reported in the infant gut and also in milk from other mammals. Breastmilk samples from healthy lactating mothers (n = 65) within 1 month after birth were analyzed. Fungal presence was assessed by different techniques, including microscopy, growth and identification of cultured isolates, fungal load estimation by qPCR, and fungal composition using 28S rRNA gene high-throughput sequencing...
October 12, 2017: Scientific Reports
Yong Yu, Ayse Sena Mutlu, Harrison Liu, Meng C Wang
High-throughput screens at microscopic resolution can uncover molecular mechanisms of cellular dynamics, but remain technically challenging in live multicellular organisms. Here we present a genetic screening method using photo-highlighting for candidate selection on microscopes. We apply this method to stimulated Raman scattering (SRS) microscopy and systematically identify 57 Caenorhabditis elegans mutants with altered lipid distribution. Four of these mutants target the components of the Bone Morphogenetic Protein (BMP) signaling pathway, revealing that BMP signaling inactivation causes exhaustion of lipid reserves in somatic tissues...
October 11, 2017: Nature Communications
Lee Erik Korshoj, Sepideh Afsari, Anushree Chatterjee, Prashant Nagpal
Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups, and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements...
October 10, 2017: Journal of the American Chemical Society
Francesco Paolo Schena, Ionut Nistor, Claudia Curci
Background: The diagnosis of glomerular diseases is based on the evaluation of histological lesions in renal tissue by means of light and electronic microscopy, and immunofluorescence technique. Frozen and archival formalin-fixed paraffin-embedded kidney biopsies represent a stored resource for high-throughput technologies. Transcriptomics makes it possible to study the whole gene-expression profile of cells and tissues in a specific period and/or condition. The results, whether considered alone or integrated with other omics data, could help to improve existing knowledge about the pathogenetic mechanisms of glomerulopathies...
August 1, 2017: Nephrology, Dialysis, Transplantation
Braulio Gutiérrez-Medina, Manuel de Jesús Sánchez Miranda
Bright field (BF) optical microscopy is regarded as a poor method to observe unstained biological samples due to intrinsic low image contrast. We introduce quantitative image restoration in bright field (QRBF), a digital image processing method that restores out-of-focus BF images of unstained cells. Our procedure is based on deconvolution, using a point spread function modeled from theory. By comparing with reference images of bacteria observed in fluorescence, we show that QRBF faithfully recovers shape and enables quantify size of individual cells, even from a single input image...
October 4, 2017: Biophysical Journal
Young Joon Kwon, Sujay Guha, Florin Tuluc, Marni J Falk
Mitochondrial respiratory chain disease is caused by a wide range of individually rare genetic disorders that impair cellular energy metabolism. While fluorescence microscopy analysis of nematodes fed MitoTracker Green (MTG) and tetramethylrhodamine ethyl ester (TMRE) can reliably quantify relative mitochondrial density and membrane potential, respectively, in C. elegans, it is a tedious process with limitations in the number and age of animals that can be studied. A novel, large particle, flow cytometry-based method reported here accelerates and automates the relative quantitation of mitochondrial physiology in nematode populations...
October 3, 2017: Mitochondrion
Erik T Hernandez, Jagannath Swaminathan, Edward M Marcotte, Eric V Anslyn
Single-molecule protein sequencing is regarded as a promising new method in the field of proteomics. It potentially offers orders of magnitude improvements in sensitivitiy and throughput for protein detection when compared to mass spectrometry. However, the development of such a technology faces significant barriers, especially in the need to chemically derivatize specific amino-acid types with unique labels. For example, fluorescent dyes would be suitable for single-molecule microscopy or nanopore-based sequencing...
January 21, 2017: New Journal of Chemistry, Nouveau Journal de Chimie
Katie Giger Seu, Julien Papoin, Rose Fessler, Jimmy Hom, Gang Huang, Narla Mohandas, Lionel Blanc, Theodosia A Kalfa
Mammalian erythropoiesis occurs within erythroblastic islands (EBIs), niches where maturing erythroblasts interact closely with a central macrophage. While it is generally accepted that EBI macrophages play an important role in erythropoiesis, thorough investigation of the mechanisms by which they support erythropoiesis is limited largely by inability to identify and isolate the specific macrophage sub-population that constitute the EBI. Early studies utilized immunohistochemistry or immunofluorescence to study EBI morphology and structure, while more recent efforts have used flow cytometry for high-throughput quantitative characterization of EBIs and their central macrophages...
2017: Frontiers in Immunology
Xixia Li, Gang Ji, Xi Chen, Wei Ding, Lei Sun, Wei Xu, Hua Han, Fei Sun
Large scale, high resolution three dimensional (3D) ultrastructural reconstruction of cells and tissues has become increasingly important to our understanding of complex biological systems. There have been a few partial 3D ultra-structures of Caenorhabditis elegans (C. elegans) reported, however 3D reconstruction of a whole nematode has never been achieved. Here, we independently developed a technique called automatic collector of ultrathin sections scanning electron microscopy and using this methodology, generated a 3D reconstruction of an entire C...
October 1, 2017: Journal of Structural Biology
Catherine C Bannon, Douglas A Campbell
Diatoms are marine primary producers that sink in part due to the density of their silica frustules. Sinking of these phytoplankters is crucial for both the biological pump that sequesters carbon to the deep ocean and for the life strategy of the organism. Sinking rates have been previously measured through settling columns, or with fluorimeters or video microscopy arranged perpendicularly to the direction of sinking. These side-view techniques require large volumes of culture, specialized equipment and are difficult to scale up to multiple simultaneous measures for screening...
2017: PloS One
Jianglai Wu, Anson H L Tang, Aaron T Y Mok, Wenwei Yan, Godfrey C F Chan, Kenneth K Y Wong, Kevin K Tsia
Apart from the spatial resolution enhancement, scaling of temporal resolution, equivalently the imaging throughput, of fluorescence microscopy is of equal importance in advancing cell biology and clinical diagnostics. Yet, this attribute has mostly been overlooked because of the inherent speed limitation of existing imaging strategies. To address the challenge, we employ an all-optical laser-scanning mechanism, enabled by an array of reconfigurable spatiotemporally-encoded virtual sources, to demonstrate ultrafast fluorescence microscopy at line-scan rate as high as 8 MHz...
September 1, 2017: Biomedical Optics Express
Navid Farahani, Alex Braun, Dylan Jutt, Todd Huffman, Nick Reder, Zheng Liu, Yukako Yagi, Liron Pantanowitz
Imaging is vital for the assessment of physiologic and phenotypic details. In the past, biomedical imaging was heavily reliant on analog, low-throughput methods, which would produce two-dimensional images. However, newer, digital, and high-throughput three-dimensional (3D) imaging methods, which rely on computer vision and computer graphics, are transforming the way biomedical professionals practice. 3D imaging has been useful in diagnostic, prognostic, and therapeutic decision-making for the medical and biomedical professions...
2017: Journal of Pathology Informatics
Hirofumi Kobayashi, Cheng Lei, Yi Wu, Ailin Mao, Yiyue Jiang, Baoshan Guo, Yasuyuki Ozeki, Keisuke Goda
In the last decade, high-content screening based on multivariate single-cell imaging has been proven effective in drug discovery to evaluate drug-induced phenotypic variations. Unfortunately, this method inherently requires fluorescent labeling which has several drawbacks. Here we present a label-free method for evaluating cellular drug responses only by high-throughput bright-field imaging with the aid of machine learning algorithms. Specifically, we performed high-throughput bright-field imaging of numerous drug-treated and -untreated cells (N = ~240,000) by optofluidic time-stretch microscopy with high throughput up to 10,000 cells/s and applied machine learning to the cell images to identify their morphological variations which are too subtle for human eyes to detect...
September 29, 2017: Scientific Reports
Nicholas S Eyre, Stephen M Johnson, Auda A Eltahla, Maria Aloi, Amanda L Aloia, Christopher A McDevitt, Rowena A Bull, Michael R Beard
Dengue virus (DENV) is a major global pathogen that causes significant morbidity and mortality in tropical and sub-tropical areas worldwide. An improved understanding of the regions within the DENV genome and its encoded proteins that are required for the virus replication cycle will expedite development of urgently required therapeutics and vaccines. We subjected an infectious DENV genome to unbiased insertional mutagenesis and employed next-generation sequencing to identify sites that tolerate 15-nucleotide insertions during the virus replication cycle in hepatic cell culture...
September 27, 2017: Journal of Virology
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