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Journal of Visualized Experiments: JoVE

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https://www.readbyqxmd.com/read/27911419/methods-of-soil-resampling-to-monitor-changes-in-the-chemical-concentrations-of-forest-soils
#1
Gregory B Lawrence, Ivan J Fernandez, Paul W Hazlett, Scott W Bailey, Donald S Ross, Thomas R Villars, Angelica Quintana, Rock Ouimet, Michael R McHale, Chris E Johnson, Russell D Briggs, Robert A Colter, Jason Siemion, Olivia L Bartlett, Olga Vargas, Michael R Antidormi, Mary M Koppers
Recent soils research has shown that important chemical soil characteristics can change in less than a decade, often the result of broad environmental changes. Repeated sampling to monitor these changes in forest soils is a relatively new practice that is not well documented in the literature and has only recently been broadly embraced by the scientific community. The objective of this protocol is therefore to synthesize the latest information on methods of soil resampling in a format that can be used to design and implement a soil monitoring program...
November 25, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911387/use-of-a-filter-cartridge-for-filtration-of-water-samples-and-extraction-of-environmental-dna
#2
Masaki Miya, Toshifumi Minamoto, Hiroki Yamanaka, Shin-Ichiro Oka, Keiichi Sato, Satoshi Yamamoto, Tetsuya Sado, Hideyuki Doi
Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies employed disk fiber filters to collect eDNA from water samples, although a number of microbial studies in aquatic environments have employed filter cartridges, because the cartridge has the advantage of accommodating large water volumes and of overall ease of use. Here we provide a protocol for filtration of water samples using the filter cartridge and extraction of eDNA from the filter without having to cut open the housing...
November 25, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911369/field-experiments-of-pollination-ecology-the-case-of-lycoris-sanguinea-var-sanguinea
#3
Futa Yamaji, Takeshi A Ohsawa
Plant-pollinator interactions have been studied for approximately one hundred years. During that time, many field methods have been developed to clarify the pollination effectiveness of each pollinator for visited flowers. Pollinator observations have been one of the most common methods to identify pollinators, and bagging and cage experiments have been conducted to show the effectiveness of specific pollinators. In a previous study of Lycoris sanguinea var. sanguinea, its effective pollinators, the visitation frequencies of each floral visitor, and its reproductive strategies were not identified...
November 25, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911417/plasma-assisted-molecular-beam-epitaxy-of-n-polar-inaln-barrier-high-electron-mobility-transistors
#4
Matthew T Hardy, David F Storm, D Scott Katzer, Brian P Downey, Neeraj Nepal, David J Meyer
Plasma-assisted molecular beam epitaxy is well suited for the epitaxial growth of III-nitride thin films and heterostructures with smooth, abrupt interfaces required for high-quality high-electron-mobility transistors (HEMTs). A procedure is presented for the growth of N-polar InAlN HEMTs, including wafer preparation and growth of buffer layers, the InAlN barrier layer, AlN and GaN interlayers and the GaN channel. Critical issues at each step of the process are identified, such as avoiding Ga accumulation in the GaN buffer, the role of temperature on InAlN compositional homogeneity, and the use of Ga flux during the AlN interlayer and the interrupt prior to GaN channel growth...
November 24, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911412/reproducible-arterial-denudation-injury-by-infrarenal-abdominal-aortic-clamping-in-a-murine-model
#5
Aditya S Shirali, Austin I McDonald, Julia J Mack, M Luisa Iruela-Arispe
Percutaneous vascular interventions uniformly result in arterial denudation injuries that subsequently lead to thrombosis and restenosis. These complications can be attributed to impairments in re-endothelialization within the wound margins. Yet, the cellular and molecular mechanisms of re-endothelialization remain to be defined. While several animal models to study re-endothelialization after arterial denudation are available, few are performed in the mouse because of surgical limitations. This undermines the opportunity to exploit transgenic mouse lines and investigate the contribution of specific genes to the process of re-endothelialization...
November 24, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911394/confirmation-of-myocardial-ischemia-and-reperfusion-injury-in-mice-using-surface-pad-electrocardiography
#6
Stephanie L C Scofield, Krishna Singh
Many animal models have been established for the study of myocardial remodeling and heart failure due to its status as the number one cause of mortality worldwide. In humans, a pathologic occlusion forms in a coronary artery and reperfusion of that occluded artery is considered essential to maintain viability of the myocardium at risk. Although essential for myocardial recovery, reperfusion of the ischemic myocardium creates its own tissue injury. The physiologic response and healing of an ischemia/reperfusion injury is different from a chronic occlusion injury...
November 24, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911393/a-detailed-protocol-for-perspiration-monitoring-using-a-novel-small-wireless-device
#7
Kazuhiro Ogai, Masakazu Fukuoka, Kei-Ichiro Kitamura, Kiyoshi Uchide, Tetsu Nemoto
Perspiration monitoring can be utilized for the detection of certain diseases, such as thermoregulation and mental disorders, particularly when the patients are unaware of such disorders or are having difficulty expressing their symptoms. Until now, several devices for perspiration monitoring have been developed; however, such devices tend to have a relatively large exterior, considerable power consumption, and/or less sensitivity. Recently, we developed a small, wireless device for perspiration monitoring...
November 24, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911411/preparation-and-in-vivo-use-of-an-activity-based-probe-for-n-acylethanolamine-acid-amidase
#8
Elisa Romeo, Silvia Pontis, Stefano Ponzano, Fabiola Bonezzi, Marco Migliore, Simona Di Martino, Maria Summa, Daniele Piomelli
Activity-based protein profiling (ABPP) is a method for the identification of an enzyme of interest in a complex proteome through the use of a chemical probe that targets the enzyme's active sites. A reporter tag introduced into the probe allows for the detection of the labeled enzyme by in-gel fluorescence scanning, protein blot, fluorescence microscopy, or liquid chromatography-mass spectrometry. Here, we describe the preparation and use of the compound ARN14686, a click chemistry activity-based probe (CC-ABP) that selectively recognizes the enzyme N-acylethanolamine acid amidase (NAAA)...
November 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911408/defining-substrate-specificities-for-lipase-and-phospholipase-candidates
#9
Diana X Sahonero-Canavesi, Maritza Zavaleta-Pastor, Lourdes Martínez-Aguilar, Isabel M López-Lara, Otto Geiger
Microorganisms produce a wide spectrum of (phospho)lipases that are secreted in order to make external substrates available for the organism. Alternatively, other (phospho)lipases may be physically associated with the producing organism causing a turnover of intrinsic lipids and frequently giving rise to a remodeling of the cellular membranes. Although potential (phospho)lipases can be predicted with a number of algorithms when the gene/protein sequence is available, experimental proof of the enzyme activities, substrate specificities, and potential physiological functions has frequently not been obtained...
November 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911400/visualizing-stromule-frequency-with-fluorescence-microscopy
#10
Jacob O Brunkard, Anne M Runkel, Patricia Zambryski
Stromules, or "stroma-filled tubules", are narrow, tubular extensions from the surface of the chloroplast that are universally observed in plant cells but whose functions remain mysterious. Alongside growing attention on the role of chloroplasts in coordinating plant responses to stress, interest in stromules and their relationship to chloroplast signaling dynamics has increased in recent years, aided by advances in fluorescence microscopy and protein fluorophores that allow for rapid, accurate visualization of stromule dynamics...
November 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911377/hybrid-cut-an-improved-sectioning-method-for-recalcitrant-plant-tissue-samples
#11
Tien-Kuan Chen, Hui-Ting Yang, Su-Chiung Fang, Yi-Chen Lien, Ting-Ting Yang, Swee-Suak Ko
Maintaining plant section integrity is essential for studying detailed anatomical structures at the cellular, tissue, or even organ level. However, some plant cells have rigid cell walls, tough fibers and crystals (calcium oxalate, silica, etc.), and high water content that often disrupt tissue integrity during plant tissue sectioning. This study establishes a simple Hybrid-Cut tissue sectioning method. This protocol modifies a paraffin-based sectioning technique and improves the integrity of tissue sections from different plants...
November 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911403/preparation-and-reactivity-of-a-triphosphenium-bromide-salt-a-convenient-and-stable-source-of-phosphorus-i
#12
Stephanie C Kosnik, Justin F Binder, Maxemilian C Nascimento, Charles L B Macdonald
We present herein the optimized synthesis of a triphosphenium bromide salt. Apart from being a versatile metathesis reagent, this unusually stable low-valent-phosphorus-containing compound acts as a useful P(+) transfer agent. Unlike traditional methods employed to access low-coordinate phosphorus species which usually require pyrophoric phosphorus-containing precursors (white phosphorus, Tris(trimethylsilyl)phosphine, etc.), or harsh reducing agents (alkali metals, potassium graphite, etc.), the current approach does not involve pyrophoric or explosive reagents and can be done on large scales (>20 g) in excellent yields by undergraduates with basic air-free synthetic training...
November 22, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911389/testing-of-nanoparticle-release-from-a-composite-containing-nanomaterial-using-a-chamber-system
#13
Gun Ho Lee, Kang-Ho Ahn, Il Je Yu
With the rapid development of nanotechnology as one of the most important technologies in the 21(st) century, interest in the safety of consumer products containing nanomaterials is also increasing. Evaluating the nanomaterial release from products containing nanomaterials is a crucial step in assessing the safety of these products, and has resulted in several international efforts to develop consistent and reliable technologies for standardizing the evaluation of nanomaterial release. In this study, the release of nanomaterials from products containing nanomaterials is evaluated using a chamber system that includes a condensation particle counter, optical particle counter, and sampling ports to collect filter samples for electron microscopy analysis...
November 22, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911378/iridium-oxide-reduced-graphene-oxide-nanohybrid-thin-film-modified-screen-printed-electrodes-as-disposable-electrochemical-paper-microfluidic-ph-sensors
#14
Jiang Yang, Tae-Joon Kwak, Xiaodong Zhang, Robert McClain, Woo-Jin Chang, Sundaram Gunasekaran
A facile, controllable, inexpensive and green electrochemical synthesis of IrO2-graphene nanohybrid thin films is developed to fabricate an easy-to-use integrated paper microfluidic electrochemical pH sensor for resource-limited settings. Taking advantages from both pH meters and strips, the pH sensing platform is composed of hydrophobic barrier-patterned paper micropad (µPAD) using polydimethylsiloxane (PDMS), screen-printed electrode (SPE) modified with IrO2-graphene films and molded acrylonitrile butadiene styrene (ABS) plastic holder...
November 22, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911372/quantitative-hardness-measurement-by-instrumented-afm-indentation
#15
Arnaud Caron
In this work, a combination of amplitude-modulated non-contact atomic force microscopy and atomic force spectroscopy is applied for instrumented hardness measurements on an Au(111) surface with atomistic resolution of single plasticity events. A careful experimental procedure is described that includes the force sensor selection, its calibration, the calibration of the cantilever deflection detection system, and the minimization of instrumental drift for accurate and reproducible force-distance measurements...
November 22, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911401/an-optimized-protocol-to-analyze-glycolysis-and-mitochondrial-respiration-in-lymphocytes
#16
Javier Traba, Pietro Miozzo, Billur Akkaya, Susan K Pierce, Munir Akkaya
Lymphocytes respond to a variety of stimuli by activating intracellular signaling pathways, which in turn leads to rapid cellular proliferation, migration and differentiation, and cytokine production. All of these events are tightly linked to the energy status of the cell, and therefore studying the energy-producing pathways may give clues about the overall functionality of these cells. The extracellular flux analyzer is a commonly used device for evaluating the performance of glycolysis and mitochondrial respiration in many cell types...
November 21, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911379/rapid-acquisition-of-3d-images-using-high-resolution-episcopic-microscopy
#17
Haochuan Zhang, JunGang Huang, Xin Liu, Ping Zhu, Zhongrong Li, Xue Li
High-resolution episcopic microscopic (HREM) technology enables rapid acquisition of high-resolution digital volumetric and three-dimensional (3D) morphometric data. Here, we describe the detailed protocol to image the entire mouse embryo. The protocol consists of four major sections: sample preparation, embedding, image acquisition and finally, 3D visualization. The technology requires specimens to be stained with a fluorescent dye, which can be problematic for large or dense specimens. To overcome this limitation, we have improved the existing protocol to enhance tissue penetration of the dye by pretreating the specimen with a solution containing urea and sodium dodecyl sulfate...
November 21, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911367/a-simple-fluorescence-assay-for-quantification-of-canine-neutrophil-extracellular-trap-release
#18
Unity Jeffery, Robert D Gray, Dana N LeVine
Neutrophil extracellular traps are networks of DNA, histones and neutrophil proteins released in response to infectious and inflammatory stimuli. Although a component of the innate immune response, NETs are implicated in a range of disease processes including autoimmunity and thrombosis. This protocol describes a simple method for canine neutrophil isolation and quantification of NETs using a microplate fluorescence assay. Blood is collected using conventional venipuncture techniques. Neutrophils are isolated using dextran sedimentation and a density gradient using conditions optimized for dog blood...
November 21, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911376/rapid-and-efficient-generation-of-recombinant-human-pluripotent-stem-cells-by-recombinase-mediated-cassette-exchange-in-the-aavs1-locus
#19
Laura Ordovás, Ruben Boon, Mariaelena Pistoni, Yemiao Chen, Rangarajan Sambathkumar, Nicky Helsen, Jolien Vanhove, Pieter Berckmans, Qing Cai, Kim Vanuytsel, Susanna Raitano, Catherine M Verfaillie
Even with the revolution of gene-targeting technologies led by CRISPR-Cas9, genetic modification of human pluripotent stem cells (hPSCs) is still time consuming. Comparative studies that use recombinant lines with transgenes integrated into safe harbor loci could benefit from approaches that use site-specific targeted recombinases, like Cre or FLPe, which are more rapid and less prone to off-target effects. Such methods have been described, although they do not significantly outperform gene targeting in most aspects...
November 20, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911370/integrated-compensatory-responses-in-a-human-model-of-hemorrhage
#20
Victor A Convertino, Carmen Hinojosa-Laborde, Gary W Muniz, Robert Carter
Hemorrhage is the leading cause of trauma-related deaths, partly because early diagnosis of the severity of blood loss is difficult. Assessment of hemorrhaging patients is difficult because current clinical tools provide measures of vital signs that remain stable during the early stages of bleeding due to compensatory mechanisms. Consequently, there is a need to understand and measure the total integration of mechanisms that compensate for reduced circulating blood volume and how they change during ongoing progressive hemorrhage...
November 20, 2016: Journal of Visualized Experiments: JoVE
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