• Volume 9, 2019
  • Volume 8, 2018
  • Volume 7, 2017
  • Volume 6, 2016
  • Volume 5, 2015
  • Volume 4, 2014
  • Volume 3, 2013
  • Volume 2, 2012
  • Volume 1, 2011

Past Issues in 2019

Volume: 9 Issue: 16

Biochemistry

A Radioactive in vitro ERK3 Kinase Assay Authors:  Lobna Elkhadragy and Weiwen Long, date: 08/20/2019, view: 235, Q&A: 0
Mitogen-activated protein kinases (MAPKs) are serine/threonine kinases that have an important role in signal transduction. Extracellular signal-regulated kinase 3 (ERK3), also known as MAPK6, is an atypical MAPK. Here, we describe in detail an in vitro assay for the kinase activity of ERK3 using myelin basic protein (MBP) or steroid ...
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Cell-based Assay for Recruitment of DDR1 to Collagen-coated Beads Authors:  Victoria Juskaite and Birgit Leitinger, date: 08/20/2019, view: 260, Q&A: 0
The discoidin domain receptors, DDR1 and DDR2, are key signaling receptors for the extracellular matrix protein collagen. The interactions of cells with collagen are difficult to study because of the difficulty to obtain native collagen fibers for in vitro studies. Thus, in vitro studies often use acid-soluble collagens in the ...
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Cancer Biology

Three-dimensional Reconstruction and Quantification of Proteins and mRNAs at the Single-cell Level in Cultured Cells Authors:  Xueer Jiang, Ingrid Brust-Mascher and Li-En Jao, date: 08/20/2019, view: 506, Q&A: 0
Gene expression is often regulated by the abundance, localization, and translation of mRNAs in both space and time. Being able to visualize mRNAs and protein products in single cells is critical to understand this regulatory process. The development of single-molecule RNA fluorescence in situ hybridization (smFISH) allows the detection of ...
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Cell Biology

Fibroblast Gap-closure Assay-Microscopy-based in vitro Assay Measuring the Migration of Murine Fibroblasts Authors:  Agnieszka P. Looney and Mallar Bhattacharya, date: 08/20/2019, view: 344, Q&A: 0
Pulmonary fibrosis is characterized by pathological scaring of the lung. Similar to other fibrotic diseases, scar formation is driven by excessive extracellular matrix deposition by activated, proliferative, and migratory fibroblasts.

Currently, the two most widely used chemotaxis and cell migration assays are the scratch assay and the ...
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A Novel Technique for Imaging and Analysis of Hair Cells in the Organ of Corti Using Modified Sca/eS and Machine Learning Authors:  Shinji Urata, Tadatsune Iida, Yuri Suzuki, Shiou-Yuh Lin, Yu Mizushima, Chisato Fujimoto, Yu Matsumoto and Tatsuya Yamasoba, date: 08/20/2019, view: 361, Q&A: 0
Here, we describe a sorbitol-based optical clearing method, called modified Sca/eS that can be used to image all hair cells (HCs) in the mouse cochlea. This modification of Sca/eS is defined by three steps: decalcification, de-lipidation, and refractive index matching, which can all be completed within 72 h. Furthermore, we established automated ...
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Developmental Biology

Ex vivo Drosophila Wing Imaginal Disc Culture and Furin Inhibitor Assay Authors:  Alex Sohr, Lijuan Du and Sougata Roy, date: 08/20/2019, view: 218, Q&A: 0
Furin is an evolutionarily conserved proprotein convertase (PC) family enzyme with a broad range of substrates that are essential for developmental, homeostatic, and disease pathways. Classical genetic approaches and in vitro biochemical or cell biological assays identified that precursor forms of most growth factor family proteins are ...
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Immunology

In vitro Differentiation of Thymic Treg Cell Progenitors to Mature Thymic Treg Cells Authors:  David L. Owen and Michael A. Farrar, date: 08/20/2019, view: 215, Q&A: 0
Thymic Treg cell differentiation occurs via a two-step process. Step one generates Treg cell progenitors (TregP) and is driven by strong TCR interactions with antigens presented in the thymus. Step two is initiated by activation of STAT5 via IL-2, or IL-15, leading to mature Treg cells capable of ...
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Microbiology

Measurement of the Length of the Integrated Donor DNA during Bacillus subtilis Natural Chromosomal Transformation Authors:  Ester Serrano and Begoña Carrasco, date: 08/20/2019, view: 235, Q&A: 0
For natural transformation to occur, bacterial cells must first develop a programmed physiological state called competence. Competence in Bacillus subtilis, which occurs only in a fraction of cells, is a transient stress response that allows cells to take up DNA from the environment. During natural chromosomal transformation, the ...
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Assessment of Metacaspase Activity in Phytoplankton Authors:  Dina Spungin and Ilana Berman-Frank, date: 08/20/2019, view: 148, Q&A: 0
Programmed cell death (PCD) is an irreversible, genetically-controlled form of cell suicide in which an endogenous biochemical pathway leads to morphological changes and ultimately, cellular demise. PCD is accompanied by de-novo protein synthesis of a family of proteases-"caspases" that are often used as a diagnostic marker of PCD. ...
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Non-invasive Quantification of Cell Wall Porosity by Fluorescence Quenching Microscopy Authors:  Xiaohui Liu, Thomas Günther Pomorski and Johannes Liesche, date: 08/20/2019, view: 200, Q&A: 0
All bacteria, fungi and plant cells are surrounded by a cell wall. This complex network of polysaccharides and glycoproteins provides mechanical support, defines cell shape, controls cell growth and influences the exchange of substances between the cell and its surroundings. Despite its name, the cell wall is a flexible, dynamic structure. ...
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Molecular Biology

Genotyping of the OATP1B1 c. 521 T>C Polymorphism from the Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Specimens: An Optimized Protocol Authors:  Alexandra R Crowe, Jonathan Miller and Wei Yue, date: 08/20/2019, view: 180, Q&A: 0
Organic anion transporting polypeptide (OATP) 1B1 is a liver-specific transport protein that plays an important role in hepatic drug disposition. It transports many drugs from the blood into the liver, including lipid-lowering statins. The c. 521 T>C polymorphism of OATP1B1 has reduced transport activity and is associated with statin-induced ...
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Application of a Modified Smart-seq2 Sample Preparation Protocol for Rare Cell Full-length Single-cell mRNA Sequencing to Mouse Oocytes Authors:  Rebecca S. Treger, Scott D. Pope, Xiaojun Xing and Akiko Iwasaki, date: 08/20/2019, view: 252, Q&A: 0
Endogenous retroviruses (ERV) are transposable retroelements that form ~10% of the murine genome and whose family members are differentially expressed throughout embryogenesis. However, precise regulation of ERV in germ cells remains unclear. To investigate ERV expression in oocytes, we adapted a single-cell mRNA-sequencing library preparation ...
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Neuroscience

Whisker Nuisance Test: A Valuable Tool to Assess Tactile Hypersensitivity in Mice Authors:  Luigi Balasco, Gabriele Chelini, Yuri Bozzi and Giovanni Provenzano, date: 08/20/2019, view: 243, Q&A: 0
Abnormal response to tactile stimulation, described as both hyper- and hypo-reactivity, is a common sensory impairment in multiple neuropsychiatric disorders. The neural bases of tactile sensitivity remain so far unknown. In the last years, animal studies have proven to be useful for shedding light on the cellular and molecular mechanism ...
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Construction of Viral Vectors for Cell Type-specific CRISPR Gene Editing in the Adult Mouse Brain Authors:  Hiroshi Yamaguchi and Luis de Lecea, date: 08/20/2019, view: 425, Q&A: 0
Recently developed gene editing technologies based on engineered CRISPR/Cas9 systems enables researchers to disrupt genes in a cell type-specific manner in the adult mouse brain. Using these technologies, we recently showed that the dopamine beta-hydroxylase gene in Locus Coeruleus (LC) norepinephrine neurons plays a vital role in the maintenance ...
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Cylinder Test to Assess Sensory-motor Function in a Mouse Model of Parkinson’s Disease Authors:  Luiz Alexandre Viana Magno, Mélcar Collodetti, Helia Tenza-Ferrer and Marco Aurélio Romano-Silva, date: 08/20/2019, view: 269, Q&A: 0
Parkinson’s disease is a progressive neurodegenerative movement disorder that happens due to the loss of dopaminergic neurons in the substantia nigra. The deficiency of dopamine in the basal nuclei drives cardinal motor symptoms such as bradykinesia and hypokinesia. The current protocol describes the cylinder test, which is a relatively simple ...
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