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High throughput microscopy

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https://www.readbyqxmd.com/read/29666607/exploring-biogeochemistry-and-microbial-diversity-of-extant-microbialites-in-mexico-and-cuba
#1
Patricia M Valdespino-Castillo, Ping Hu, Martín Merino-Ibarra, Luz M López-Gómez, Daniel Cerqueda-García, Roberto González-De Zayas, Teresa Pi-Puig, Julio A Lestayo, Hoi-Ying Holman, Luisa I Falcón
Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29660691/proteomic-analysis-of-liquid-biopsy-from-tumor-draining-vein-indicates-that-high-expression-of-exosomal-ecm1-is-associated-with-relapse-in-stage-i-iii-colon-cancer
#2
Sandra Santasusagna, Isabel Moreno, Alfons Navarro, Joan J Castellano, Francisco Martinez, Raquel Hernández, Carmen Muñoz, Mariano Monzo
BACKGROUND: The analysis of exosomes in blood obtained from the tumor-draining mesenteric vein (MV) can identify tumor biomarkers before they reach target organs and form the premetastatic niche where circulating tumor cells can anchor. Our group has recently shown that microRNAs in plasma from the MV-but not the peripheral vein (PV)-have been related to liver metastases in colon cancer (CC) patients. Here we examine the exosomal protein cargo in plasma from the MV and paired PV in 31 CC patients...
April 13, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29659610/dna-metabarcoding-and-microscopic-analyses-of-sea-turtles-biofilms-complementary-to-understand-turtle-behavior
#3
Sinziana F Rivera, Valentin Vasselon, Katia Ballorain, Alice Carpentier, Carlos E Wetzel, Luc Ector, Agnès Bouchez, Frédéric Rimet
Sea turtles are distributed in tropical and subtropical seas worldwide. They play several ecological roles and are considered important indicators of the health of marine ecosystems. Studying epibiotic diatoms living on turtle shells suggestively has great potential in the study of turtle behavior because diatoms are always there. However, diatom identification at the species level is time consuming, requires well-trained specialists, and there is a high probability of finding new taxa growing on turtle shells, which makes identification tricky...
2018: PloS One
https://www.readbyqxmd.com/read/29658943/deep-learning-massively-accelerates-super-resolution-localization-microscopy
#4
Wei Ouyang, Andrey Aristov, Mickaël Lelek, Xian Hao, Christophe Zimmer
The speed of super-resolution microscopy methods based on single-molecule localization, for example, PALM and STORM, is limited by the need to record many thousands of frames with a small number of observed molecules in each. Here, we present ANNA-PALM, a computational strategy that uses artificial neural networks to reconstruct super-resolution views from sparse, rapidly acquired localization images and/or widefield images. Simulations and experimental imaging of microtubules, nuclear pores, and mitochondria show that high-quality, super-resolution images can be reconstructed from up to two orders of magnitude fewer frames than usually needed, without compromising spatial resolution...
April 16, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29656514/microbial-diversity-and-biomarker-analysis-of-modern-freshwater-microbialites-from-laguna-bacalar-mexico
#5
D B Johnson, P A Beddows, T M Flynn, M R Osburn
Laguna Bacalar is a sulfate-rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three-pronged geobiological approach of microscopy, high-throughput DNA sequencing, and lipid biomarker analyses...
April 15, 2018: Geobiology
https://www.readbyqxmd.com/read/29644261/detection-and-analysis-of-circular-rnas-by-rt-pcr
#6
Amaresh C Panda, Myriam Gorospe
Gene expression in eukaryotic cells is tightly regulated at the transcriptional and posttranscriptional levels. Posttranscriptional processes, including pre-mRNA splicing, mRNA export, mRNA turnover, and mRNA translation, are controlled by RNA-binding proteins (RBPs) and noncoding (nc)RNAs. The vast family of ncRNAs comprises diverse regulatory RNAs, such as microRNAs and long noncoding (lnc)RNAs, but also the poorly explored class of circular (circ)RNAs. Although first discovered more than three decades ago by electron microscopy, only the advent of high-throughput RNA-sequencing (RNA-seq) and the development of innovative bioinformatic pipelines have begun to allow the systematic identification of circRNAs (Szabo and Salzman, 2016; Panda et al ...
March 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/29630095/pathogenicity-of-high-risk-hpv-infection-in-pseudocondyloma-of-vulvae-and-its-carcinogenicity-in-inducing-cervical-lesions
#7
P-F Song, J-Y Chen, Q He, J Wang, J Xu
OBJECTIVE: To identify high-risk human papillomavirus (HPV) infection in pseudocondyloma of vulvae (PV) and the causal relationship between high-risk HPV infection and cervical cancer. PATIENTS AND METHODS: The patients were divided into condyloma acuminatum group, PV groups and PV high-risk HPV infection group according to the clinical data and morphological features. Condyloma acuminatum group and PV group were two control groups. The exfoliated cells were detected and typed by human HPV nucleic acid typing kit...
March 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29629087/3d-chemical-imaging-of-the-brain-using-quantitative-ir-spectro-microscopy
#8
Abiodun Ogunleke, Benoit Recur, Hugo Balacey, Hsiang-Hsin Chen, Maylis Delugin, Yeukuang Hwu, Sophie Javerzat, Cyril Petibois
Three-dimensional (3D) histology is the next frontier for modern anatomo-pathology. Characterizing abnormal parameters in a tissue is essential to understand the rationale of pathology development. However, there is no analytical technique, in vivo or histological, that is able to discover such abnormal features and provide a 3D distribution at microscopic resolution. Here, we introduce a unique high-throughput infrared (IR) microscopy method that combines automated image correction and subsequent spectral data analysis for 3D-IR image reconstruction...
January 7, 2018: Chemical Science
https://www.readbyqxmd.com/read/29622579/high-throughput-non-perturbing-quantification-of-lipid-droplets-with-digital-holographic-microscopy
#9
Vasco Campos, Benjamin Rappaz, Fabien Kuttler, Gerardo Turcatti, Olaia Naveiras
In vitro differentiating adipocytes are sensitive to liquid manipulations and have the tendency to float. Assessing adipocyte differentiation using current microscopy techniques involves cell staining and washing, while using flow cytometry involves cell retrieval in suspension. These methods induce biases, are difficult to reproduce and involve tedious optimizations. In this study we present Digital Holographic Microscopy (DHM) as a label-free, non-perturbing means to quantify lipid droplets in differentiating adipocytes in a robust medium- to high-throughput manner...
April 5, 2018: Journal of Lipid Research
https://www.readbyqxmd.com/read/29620521/integrating-images-from-multiple-microscopy-screens-reveals-diverse-patterns-of-protein-subcellular-localization-change
#10
Alex X Lu, Yolanda T Chong, Ian Shen Hsu, Bob Strome, Louis-Francois Handfield, Oren Kraus, Brenda J Andrews, Alan M Moses
Evaluating protein localization changes on a systematic level is a powerful tool for understanding how cells respond to environmental, chemical, or genetic perturbations. To date, work in understanding these proteomic responses through high-throughput imaging has catalogued localization changes independently for each perturbation. To distinguish changes that are targeted responses to the specific perturbation and more generalized programs, we developed a scalable approach to visualize the localization behavior of proteins across multiple experiments as a quantitative pattern...
April 5, 2018: ELife
https://www.readbyqxmd.com/read/29617990/structure-and-dynamics-of-microbiomes-associated-with-the-marine-sponge-tedania-sp-during-its-life-cycle
#11
Shufei Wu, Huilong Ou, Tan Liu, Dexiang Wang, Jing Zhao
Tedania sp. is a dominant sponge that is ubiquitous along the southeast coast of China. High-throughput sequencing and transmission electron microscopy were used to describe a detailed profile of sponge-associated microbiomes at 7 life stages: adult, embryo-containing spawning adult, embryo, pre-competent larval at 2 h, 4 h and competent larvae at 8 h, post-larva within 1-2 h after settlement, as well as the surrounding seawater. Among a total of 15098 operational taxonomic units (OTUs), 13 were present exclusively in all stages of the sponge life cycle and could thus be identified as sponge-specific bacteria...
March 30, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29613769/protein-protein-interactions-in-the-molecular-chaperone-network
#12
Rebecca Freilich, Taylor Arhar, Jennifer L Abrams, Jason E Gestwicki
Molecular chaperones play a central role in protein homeostasis (a.k.a. proteostasis) by balancing protein folding, quality control, and turnover. To perform these diverse tasks, chaperones need the malleability to bind nearly any "client" protein and the fidelity to detect when it is misfolded. Remarkably, these activities are carried out by only ∼180 dedicated chaperones in humans. How do a relatively small number of chaperones maintain cellular and organismal proteostasis for an entire proteome? Furthermore, once a chaperone binds a client, how does it "decide" what to do with it? One clue comes from observations that individual chaperones engage in protein-protein interactions (PPIs)-both with each other and with their clients...
April 3, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29610320/label-free-and-charge-sensitive-dynamic-imaging-of-lipid-membrane-hydration-on-millisecond-time-scales
#13
Orly B Tarun, Christof Hannesschläger, Peter Pohl, Sylvie Roke
Biological membranes are highly dynamic and complex lipid bilayers, responsible for the fate of living cells. To achieve this function, the hydrating environment is crucial. However, membrane imaging typically neglects water, focusing on the insertion of probes, resonant responses of lipids, or the hydrophobic core. Owing to a recent improvement of second-harmonic (SH) imaging throughput by three orders of magnitude, we show here that we can use SH microscopy to follow membrane hydration of freestanding lipid bilayers on millisecond time scales...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29598825/combined-flow-cytometry-and-high-throughput-image-analysis-for-the-study-of-essential-genes-in-caenorhabditis-elegans
#14
Blanca Hernando-Rodríguez, Annmary Paul Erinjeri, María Jesús Rodríguez-Palero, Val Millar, Sara González-Hernández, María Olmedo, Bettina Schulze, Ralf Baumeister, Manuel J Muñoz, Peter Askjaer, Marta Artal-Sanz
BACKGROUND: Advances in automated image-based microscopy platforms coupled with high-throughput liquid workflows have facilitated the design of large-scale screens utilising multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high-throughput approaches, and a systematic way to analyse genetic interactions of essential genes in multicellular organisms has been lacking...
March 29, 2018: BMC Biology
https://www.readbyqxmd.com/read/29573365/fundamental-drivers-for-endolithic-microbial-community-assemblies-in-the-hyper-arid-atacama-desert
#15
Victoria Meslier, Maria Cristina Casero, Micah Dailey, Jacek Wierzchos, Carmen Ascaso, Octavio Artieda, P R McCullough, Jocelyne DiRuggiero
In hyper-arid deserts, endolithic microbial communities colonize the rocks' interior as a survival strategy. Yet, the composition of these communities and the drivers promoting their assembly are still poorly understood. We analyzed the diversity and community composition of endoliths from four different lithic substrates - calcite, gypsum, ignimbrite and granite - collected in the hyper-arid zone of the Atacama Desert, Chile. By combining microscopy, mineralogy, spectroscopy, and high throughput sequencing, we found these communities to be highly specific to their lithic substrate, although they were all dominated by the same four main phyla, Cyanobacteria, Actinobacteria, Chloroflexi and Proteobacteria...
March 24, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29558527/dna-metabarcoding-uncovers-fungal-diversity-of-mixed-airborne-samples-in-italy
#16
Elisa Banchi, Claudio Gennaro Ametrano, David Stanković, Pierluigi Verardo, Olga Moretti, Francesca Gabrielli, Stefania Lazzarin, Maria Francesca Borney, Francesca Tassan, Mauro Tretiach, Alberto Pallavicini, Lucia Muggia
Fungal spores and mycelium fragments are particles which become and remain airborne and have been subjects of aerobiological studies. The presence and the abundance of taxa in aerobiological samples can be very variable and impaired by changeable climatic conditions. Because many fungi produce mycotoxins and both their mycelium fragments and spores are potential allergens, monitoring the presence of these taxa is of key importance. So far data on exposure and sensitization to fungal allergens are mainly based on the assessment of few, easily identifiable taxa and focused only on certain environments...
2018: PloS One
https://www.readbyqxmd.com/read/29553519/quantification-of-lipid-abundance-and-evaluation-of-lipid-distribution-in-caenorhabditis-elegans-by-nile-red-and-oil-red-o-staining
#17
Wilber Escorcia, Dana L Ruter, James Nhan, Sean P Curran
Caenorhabditis elegans is an exceptional model organism in which to study lipid metabolism and energy homeostasis. Many of its lipid genes are conserved in humans and are associated with metabolic syndrome or other diseases. Examination of lipid accumulation in this organism can be carried out by fixative dyes or label-free methods. Fixative stains like Nile red and oil red O are inexpensive, reliable ways to quantitatively measure lipid levels and to qualitatively observe lipid distribution across tissues, respectively...
March 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29550673/high-speed-low-dose-analytical-electron-microscopy-with-dynamic-sampling
#18
Karl A Hujsak, Eric W Roth, William Kellogg, Yue Li, Vinayak P Dravid
Technological advances in electron microscopy, particularly improved detectors and aberration correctors, have led to higher throughput and less invasive imaging of materials and biological structures by enhancing signal-to-noise ratios at lower electron exposures. Analytical methods, such as electron energy loss spectroscopy (EELS) and energy dispersive x-ray spectrometry (EDS), have also benefitted and offer a rich set of local elemental and bonding information with nano-or atomic resolution. However, spatially resolved spectrum imaging with EELS and EDS continue to be difficult to scale due to limited detector collection angles or high signal background, requiring hours or even days for full maps...
March 10, 2018: Micron: the International Research and Review Journal for Microscopy
https://www.readbyqxmd.com/read/29550602/effects-of-dietary-lactobacillus-rhamnosus-jcm1136-and-lactococcus-lactis-subsp-lactis-jcm5805-on-the-growth-intestinal-microbiota-morphology-immune-response-and-disease-resistance-of-juvenile-nile-tilapia-oreochromis-niloticus
#19
Yun Xia, Maixin Lu, Gang Chen, Jianmeng Cao, Fengying Gao, Miao Wang, Zhigang Liu, Defeng Zhang, Huaping Zhu, Mengmeng Yi
The present study aimed to evaluate the individual and combined effects of Lactobacillus rhamnosus (LR) JCM1136 and Lactococcus lactis subsp. lactis (LL) JCM5805 on the growth, intestinal microbiota, intestinal morphology, immune response and disease resistance of juvenile Nile tilapia (Oreochromis niloticus). A total of 720 apparently healthy juvenile Nile tilapia (0.20 ± 0.05 g) were randomly divided into four equal groups. Fish were fed with a basal diet (CK) supplemented with JCM1136 (LR), JCM5805 (LL), and JCM1136 + JCM5805 (LR+LL) at 1 × 108  CFU/g basal diet for 6 weeks, followed by a basal diet for 1 week...
March 14, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29546734/high-throughput-ultraviolet-photoacoustic-microscopy-with-multifocal-excitation
#20
Toru Imai, Junhui Shi, Terence T W Wong, Lei Li, Liren Zhu, Lihong V Wang
Ultraviolet photoacoustic microscopy (UV-PAM) is a promising intraoperative tool for surgical margin assessment (SMA), one that can provide label-free histology-like images with high resolution. In this study, using a microlens array and a one-dimensional (1-D) array ultrasonic transducer, we developed a high-throughput multifocal UV-PAM (MF-UV-PAM). Our new system achieved a 1.6  ±  0.2  μm lateral resolution and produced images 40 times faster than the previously developed point-by-point scanning UV-PAM...
March 2018: Journal of Biomedical Optics
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