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Journal Methods Mol Biol

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Measurement of Lung Vessel and Epithelial Permeability In Vivo with Evans Blue.

Prestina Smith, Lauren A Jeffers, Michael Koval,

Lung fluid balance is maintained in part by the barriers formed by the pulmonary microvasculature and alveolar epithelium. Failure of either of these barriers leads to pulmonary edema, which limits lung function and exacerbates the severity of acute lung injury. Here we describe a method using Evans Blue dye to ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, :]

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Ultrastructural Analysis of Cell-Cell Interactions in Drosophila Ovary.

Matthew Antel, Valentina Baena, Mark Terasaki, Mayu Inaba,

The Drosophila ovary is an exceptional model for studying cell-cell interactions in vivo. Cells communicate with each other in a highly coordinated manner. Accurate spatiotemporal regulation of cell-cell interaction is critical for the development of eggs. Ultrastructural analysis using electron microscopy (EM) permits the visualization of both cells and subcellular ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, :]

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Experimental Modeling of Eosinophil-Associated Diseases.

Sathisha Upparahalli Venkateshaiah, Murli Manohar, Hemanth Kumar Kandikattu, Anil Mishra,

Eosinophils are an important subtype of leukocytes derived from bone marrow multipotent hematopoietic stem cells and represent about 1% of leukocytes in circulating blood. In homeostatic conditions, eosinophils reside in the intestine to maintain the balance of immune responses by communicating with gut microbes without causing inflammation. However, under the ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2241:275-291]

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Detection of Eosinophil Extracellular DNA Traps.

Marina Valente Barroso, Josiane Sabbadini Neves,

The process of extracellular DNA trap release by leukocytes, including eosinophils, has been considered as an important cell-mediated immune response to different inflammatory stimuli helping to understand the physiopathology of many diseases. Here we describe in detail two useful and simple protocols for a semiquantitative and a qualitative analysis of ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2241:193-198]

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In Vivo Eosinophil Expansion Using Gene Transfer by Electroporation.

Emi Hamaguchi-Tsuru, Masataka Korenaga, Fabrizio Bruschi,

Eosinophils are differentiated in the bone marrow and transit through the blood circulation to home into tissues primarily under the regulation of IL-5. Because the number of eosinophils in the peripheral blood is relatively low under normal conditions, in vivo functional studies of eosinophils remain extremely difficult. Increasing their numbers ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2241:133-137]

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Mutant Mice and Animal Models of Airway Allergic Disease.

Julyanne Brassard, David Marsolais, Marie-Renee Blanchet,

Eosinophilia is a hallmark of allergic airway inflammation, and eosinophils represent an integral effector leukocyte through their release of various granule-stored cytokines and proteins. Numerous mouse models have been developed to mimic clinical disease and they have been instrumental in furthering our understanding of the role of eosinophils in disease. ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2241:59-74]

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Molecular Biology of Eosinophils: Introduction.

Paige Lacy, Helene F Rosenberg, Garry M Walsh,

The eosinophil is an enigmatic cell with a continuing ability to fascinate. A considerable history of research endeavor on eosinophil biology stretches from the present time back to the nineteenth century. Perhaps one of the most fascinating aspects of the eosinophil is how accumulating knowledge has changed the perception of ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2241:1-14]

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Fluorescence Assays to Study Membrane Penetration of Proteins.

Yosuke Senju, Hongxia Zhao,

Phosphoinositides play important roles in the regulation of protein recruitment at specialized membrane domains, protein activity, and membrane dynamics. Phosphoinositide-protein interplay occurs via multiple mechanisms and proteins associate with membranes through different binding patterns. Determinations of membrane-binding mode and membrane penetration depth of proteins in lipid bilayer are thus important ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2251:215-223]

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A Real-Time Phosphatidylinositol 4-Phosphate 5-Kinase Assay Using Fluorescence Spectroscopy.

Taki Nishimura,

Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) is an enzyme that converts phosphatidylinositol 4-phosphate [PI4P] to phosphatidylinositol 4,5-bisphosphate [PI(4,5)P<sub>2</sub>]. PIP5K plays a key role in the regulation of vesicular transport, cytoskeleton reorganization, and cell division. In general, to investigate an enzymatic activity of PIP5K, the amount of incorporated [P<sup>32</sup>] ATP into PI(4,5)P<sub>2</sub> fraction ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2251:121-132]

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Label-Free Quantification of Phosphoinositides in Drosophila by Mass Spectrometry.

Avishek Ghosh, Padinjat Raghu,

Phosphoinositides (PIs), the seven phosphorylated derivatives of phosphatidylinositol, are recognized as key molecules in the control of multiple molecular events in eukaryotic cells. Within cells, PIs are low-abundance lipids making their detection and quantification challenging. While many methods that allow radiolabeling and quantification of PIs in the context of cultured ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2251:19-37]

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Purification and Immunophenotypic Characterization of Human CD24hiCD38hi and CD24hiCD27+ Regulatory B Cells in Transplantation.

Rowa Y Alhabbab, Giovanna Lombardi,

Transplantation is still the treatment of choice for organ failure; however, allograft induces inflammatory immune responses that require immunosuppressive treatment. The role of regulatory B cells (Bregs) in downregulating inflammation has been reported to be significant in several diseases including transplant rejection. Many reports have analyzed different B-cell subpopulations, including ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2270:451-467]

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B-Cell Commitment to IL-10 Production: The VertX Il10egfp Mouse.

Akihiko Oka, Bo Liu, Jeremy W Herzog, R Balfour Sartor,

Although the inflammatory cytokine IL-10 is pivotal in regulatory B-cell function, detecting IL-10-producing B cells by intracellular IL-10 staining requires multiple steps and tedious preparation. In contrast, the Il10-eGFP reporter mouse model (VertX), generated in 2009, allows easier and quicker detection of IL-10-producing B cells with the possibility of sorting ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2270:341-358]

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Use of Toll-Like Receptor (TLR) Ligation to Characterize Human Regulatory B-Cells Subsets.

Mathilde A M Chayé, Chiara Tontini, Arifa Ozir-Fazalalikhan, Astrid L Voskamp, Hermelijn H Smits,

Toll-like receptors (TLRs) are pattern recognition receptors (PRRs), which constitute key components in the recognition of pathogens, thereby initiating innate immune responses and promoting adaptive immune responses. In B cells, TLR ligation is important for their activation and, together with CD40, for their differentiation. TLR ligands are also strong promoters ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2270:235-261]

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Characterization and Activity of TIM-1 and IL-10-Reporter Expressing Regulatory B Cells.

Kanishka Mohib, David M Rothstein, Qing Ding,

In addition to their role in humoral immunity, B cells can exhibit regulatory activity. Such B cells have been termed regulatory B cells (Bregs). Bregs have been shown to inhibit inflammatory immune responses in a variety of autoimmune, alloimmune, and infectious settings. Breg activity is frequently IL-10-dependent, although a number ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2270:179-202]

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Purification of Murine and Human IL-10-Producing B Cells from Different Anatomical Compartments.

Francesca Mion, Eleonora Martinis, Carlo E M Pucillo, Silvia Tonon,

IL-10 is the best known and most studied anti-inflammatory cytokine and, in the last 20 years, it has acquired even greater fame as it has been associated with the regulatory phenotype of B cells. Indeed, although great efforts have been made to find a unique marker, to date IL-10 remains ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2270:61-76]

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Data Preparation Protocol for Low Signal-to-Noise Ratio Fluorine-19 MRI.

Ludger Starke, Thoralf Niendorf, Sonia Waiczies,

Fluorine-19 MRI shows great promise for a wide range of applications including renal imaging, yet the typically low signal-to-noise ratios and sparse signal distribution necessitate a thorough data preparation.This chapter describes a general data preparation workflow for fluorine MRI experiments. The main processing steps are: (1) estimation of noise level, ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:711-722]

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Analysis Protocol for Dynamic Contrast Enhanced (DCE) MRI of Renal Perfusion and Filtration.

Frank G Zöllner, Walter Dastrù, Pietro Irrera, Dario Livio Longo, Kevin M Bennett, Scott C Beeman, G Larry Bretthorst, Joel R Garbow,

Here we present an analysis protocol for dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data of the kidneys. It covers comprehensive steps to facilitate signal to contrast agent concentration mapping via T<sub>1</sub> mapping and the calculation of renal perfusion and filtration parametric maps using model-free approaches, model free analysis using ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:637-653]

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Subsegmentation of the Kidney in Experimental MR Images Using Morphology-Based Regions-of-Interest or Multiple-Layer Concentric Objects.

Leili Riazy, Bastien Milani, João S Periquito, Kathleen Cantow, Thoralf Niendorf, Menno Pruijm, Erdmann Seeliger, Andreas Pohlmann,

Functional renal MRI promises access to a wide range of physiologically relevant parameters such as blood oxygenation, perfusion, tissue microstructure, pH, and sodium concentration. For quantitative comparison of results, representative values must be extracted from the parametric maps obtained with these different MRI techniques. To improve reproducibility of results this ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:549-564]

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Sodium (23Na) MRI of the Kidney: Experimental Protocol.

James T Grist, Esben Søvsø Hansen, Frank G Zöllner, Christoffer Laustsen,

Sodium handling is a key physiological hallmark of renal function. Alterations are generally considered a pathophysiologic event associated with kidney injury, with disturbances in the corticomedullary sodium gradient being indicative of a number of conditions. This experimental protocol review describes the individual steps needed to perform <sup>23</sup>Na MRI; allowing accurate ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:473-480]

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Experimental Protocol for MRI Mapping of the Blood Oxygenation-Sensitive Parameters T2* and T2 in the Kidney.

Andreas Pohlmann, Kaixuan Zhao, Sean B Fain, Pottumarthi V Prasad, Thoralf Niendorf,

Renal hypoxia is generally accepted as a key pathophysiologic event in acute kidney injury of various origins, and has also been suggested to play a role in the development of chronic kidney disease. Here we describe a step-by-step experimental protocol for indirect monitoring of renal blood oxygenation in rodents via ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:403-417]

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Essential Practical Steps for MRI of the Kidney in Experimental Research.

Andreas Pohlmann, João S Periquito, Thoralf Niendorf,

Magnetic resonance imaging (MRI) is an emerging method to obtain valuable functional and structural information about the kidney noninvasively. Before performing specialized MR measurements for probing tissue structure and function, some essential practical steps are needed, which are common for most applications. Here we describe in a step-by-step manner how ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:349-367]

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Dynamic Contrast Enhancement (DCE) MRI-Derived Renal Perfusion and Filtration: Basic Concepts.

Michael Pedersen, Pietro Irrera, Walter Dastrù, Frank G Zöllner, Kevin M Bennett, Scott C Beeman, G Larry Bretthorst, Joel R Garbow, Dario Livio Longo,

Dynamic contrast-enhanced (DCE) MRI monitors the transit of contrast agents, typically gadolinium chelates, through the intrarenal regions, the renal cortex, the medulla, and the collecting system. In this way, DCE-MRI reveals the renal uptake and excretion of the contrast agent. An optimal DCE-MRI acquisition protocol involves finding a good compromise ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:205-227]

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Hardware Considerations for Preclinical Magnetic Resonance of the Kidney.

Paula Ramos Delgado, Ekkehard Küstermann, André Kühne, Jason M Millward, Thoralf Niendorf, Andreas Pohlmann, Martin Meier,

Magnetic resonance imaging (MRI) is a noninvasive imaging technology that offers unparalleled anatomical and functional detail, along with diagnostic sensitivity. MRI is suitable for longitudinal studies due to the lack of exposure to ionizing radiation. Before undertaking preclinical MRI investigations of the kidney, the appropriate MRI hardware should be carefully ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:131-155]

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Preparation and Monitoring of Small Animals in Renal MRI.

Tamas Kaucsar, Adam Hosszu, Erdmann Seeliger, Henning M Reimann, Andrea Fekete,

Renal diseases remain devastating illnesses with unacceptably high rates of mortality and morbidity worldwide. Animal models are essential tools to better understand the pathomechanism of kidney-related illnesses and to develop new, successful therapeutic strategies. Magnetic resonance imaging (MRI) has been actively explored in the last decades for assessing renal function, ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2216:45-55]

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Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach.

Stepan Pachganov, Khalimat Murtazalieva, Alexei Zarubin, Tatiana Taran, Duane Chartier, Tatiana V Tatarinova,

As the interest in genetic resequencing increases, so does the need for effective mathematical, computational, and statistical approaches. One of the difficult problems in genome annotation is determination of precise positions of transcription start sites. In this paper, we present TransPrise-an efficient deep learning tool for predicting positions of eukaryotic ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2021, 2238:261-274]

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