Published in Bio-protocol September Issues

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Bio-protocol: Sep 5 and Sep 20 issues

Volume:13 Issue:18 Sep 20, 2023

Biochemistry

Computational Analysis of Plasma Lipidomics from Mice Fed Standard Chow and Ketogenic Diet Authors: Amy L. Seufert, James W. Hickman, Jaewoo Choi, Brooke A. Napier DOI: 10.21769/BioProtoc.4819

Fractionation of Native Protein Complexes from Mammalian Cells to Determine the Differential Proteasome Activity and Abundance Authors: Ana Paula Zen Petisco Fiore, Christine Vogel DOI: 10.21769/BioProtoc.4822

Identification of Matriglycan by Dual Exoglycosidase Digestion of α-Dystroglycan Authors: Ishita Chandel, Kevin P. Campbell DOI: 10.21769/BioProtoc.4827

Biological Engineering

Quantitative Analysis of Clot Deposition on Extracorporeal Life Support Membrane Oxygenators Using Digital and Scanning Electron Microscopy Imaging Techniques Authors: Yanyi Zang, Teryn R. Roberts, George T. Harea, Brendan M. Beely, Leonardo J. Olivera Perez, Sreedevi Ande, Maria Batchinsky, Ji H. Lee, Marianne A. Thrailkill, Melissa M. Reynolds, Andriy I. Batchinsky DOI: 10.21769/BioProtoc.4814

Biological Sciences

Intraperitoneal Injection of Neonatal Mice Authors: Amanda M. Pocratsky, James N. Sleigh DOI: 10.21769/BioProtoc.4826

Cell Biology

Isolation of Epithelial and Stromal Cells from Colon Tissues in Homeostasis and Under Inflammatory Conditions Authors: Clara Morral, Reem Ghinnagow, Tatiana Karakasheva, Yusen Zhou, Anusha Thadi, Ning Li, Benjamin Yoshor, Gloria E. Soto, Chia-Hui Chen, Daniel Aleynick, Sarah Weinbrom, MaryKate Fulton, Yasin Uzun, Meenakshi Bewtra, Judith R. Kelsen, Christopher J. Lengner, Kai Tan, Andy J. Minn, Kathryn E. Hamilton DOI: 10.21769/BioProtoc.4825

Immunology

Double Staining with Fluorescent Tracers to Determine Myeloid Cell Migration of Leishmania-infected Cells from Mouse Skin to Lymphatic Tissues by Flow Cytometry Authors: Ashanti C. Uscanga-Palomeque, E. Yaneth Osorio, Peter C. Melby DOI: 10.21769/BioProtoc.4817

Functional Phenotyping of Lung Mouse CD4+ T Cells Using Multiparametric Flow Cytometry Analysis Authors: Céline M. Maquet, Laurent Gillet, Bénédicte D. Machiels DOI: 10.21769/BioProtoc.4815

Differentiation of Bone Marrow Monocytes into Alveolar Macrophages-like Cells through Co-culture with Lung Epithelial Cells and Group 2 Innate Lymphoid Cells Authors: Pauline Loos, Thomas Marichal, Bénédicte Machiels, Laurent Gillet DOI: 10.21769/BioProtoc.4818

Molecular Biology

A Post-translational Modification–enhanced Pull-down Method to Study Degron Domains and the Associated Protein Degradation Complexes Authors: Pierluigi Scalia, Stephen J. Williams DOI: 10.21769/BioProtoc.4816

Controlled Level of Contamination Coupled to Deep Sequencing (CoLoC-seq) Probes the Global Localisation Topology of Organelle Transcriptomes Authors: Anna Smirnova, Damien Jeandard, Alexandre Smirnov DOI: 10.21769/BioProtoc.4820

Fluorescence in situ Localization of Pri-miRNAs in Isolated Arabidopsis thaliana Nuclei Authors: Tomasz Gulanicz, Agnieszka Zienkiewicz, Krzysztof Zienkiewicz, Anna Kasprowicz-Maluski, Zofia Szweykowska-Kulinska, Artur Jarmolowski DOI: 10.21769/BioProtoc.4824

Immunoprecipitation of Reporter Nascent Chains from Active Ribosomes to Study Translation Efficiency Authors: Roberta Cacioppo, Catherine Lindon DOI: 10.21769/BioProtoc.4821

Successful Transfection of MicroRNA Mimics or Inhibitors in a Regular Cell Line and in Primary Cells Derived from Patients with Rheumatoid Arthritis Authors: Si Wang, Jing Xu, Yuanxu Guo, Yongsong Cai, Wenhua Zhu, Liesu Meng, Congshan Jiang, Shemin Lu DOI: 10.21769/BioProtoc.4823

Genome-wide Mapping of 5′-monophosphorylated Ends of Mammalian Nascent RNA Transcripts Authors: Michael A. Cortázar, Nova Fong, David L. Bentley DOI: 10.21769/BioProtoc.4828

Retraction

Retraction Notice: Paper Lateral Flow Biosensor for Nodavirus Reverse Transcribed RNA Detection doi: 10.21769/BioProtoc.3711 Authors: Dimitra K. Toubanaki, Evdokia Karagouni DOI: 10.21769/BioProtoc.4864

Volume:13 Issue:17 Sep 5, 2023

Biochemistry

An in vitro Assay to Probe the Formation of Biomolecular Condensates Authors: Yu Zhang, Shen Lisha DOI: 10.21769/BioProtoc.4813

Use of Open Surface Plasmon Resonance (OpenSPR) to Characterize the Binding Affinity of Protein–Protein Interactions Authors: Cassie Shu Zhu, Jianhua Li, Haichao Wang DOI: 10.21769/BioProtoc.4795

Cell Biology

Methods to Quantify the Dynamic Recycling of Plasma Membrane Channels Authors: Rawad Hodeify, Khaled Machaca DOI: 10.21769/BioProtoc.4800

Endoplasmic Reticulum Isolation: An Optimized Approach into Cells and Mouse Liver Fractionation Authors: Marc Leiro, Raúl Ventura, Nil Rojo-Querol, María Isabel Hernández-Alvarez DOI: 10.21769/BioProtoc.4803

Isolation, Purification, and Culture of Embryonic Melanoblasts from Green Fluorescent Protein–expressing Reporter Mice Authors: Melissa Crawford, Kevin Barr, Lina Dagnino DOI: 10.21769/BioProtoc.4805

A Large-format Polyacrylamide Gel with Controllable Matrix Mechanics for Mammalian Cell Culture and Conditioned Media Production Authors: Catherine S. Millar-Haskell, Jason P. Gleghorn DOI: 10.21769/BioProtoc.4807

Developmental Biology

Isolation of Embryonic Cardiomyocytes and Cell Proliferation Assay Using Genetically Engineered Reporter Mouse Model Authors: Maren Beall, Deqiang Li, Jihyun Jang DOI: 10.21769/BioProtoc.4802

Immunology

Determination of Antibody Activity by Platelet Aggregation Authors: Halina H.L. Leung, Jose Perdomo, Zohra Ahmadi, Beng H. Chong DOI: 10.21769/BioProtoc.4804

Microbiology

Gene Replacement by a Selectable Marker in the Filamentous Fungus Magnaporthe oryzae Authors: Nalleli Garcia, Alexa N. Farmer, Richmond Baptiste, Jessie Fernandez DOI: 10.21769/BioProtoc.4809

Functional Assay for Measuring Bacterial Degradation of Gemcitabine Chemotherapy Authors: Serkan Sayin, Amir Mitchell DOI: 10.21769/BioProtoc.4797

Molecular Biology

Detection of Cytoplasmic and Nuclear Circular RNA via RT-qPCR Authors: Ke-En Tan, Wei Lun Ng, Chee-Kwee Ea, Yat-Yuen Lim DOI: 10.21769/BioProtoc.4798

Fast and Sustainable Thermo-osmotic DNA Extraction Protocol for Trans-spectrum Contingency and Field Use Authors: Stavroula Goudoudaki, Manousos E. Kambouris, Marianna Manoussopoulou, George P. Patrinos, Aristea Velegraki, Yiannis Manoussopoulos DOI: 10.21769/BioProtoc.4796

Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package Authors: Patrick H.D. Petersen, Joanna Lopacinska-Jørgensen, Claus K. Høgdall, Estrid Vilma Høgdall DOI: 10.21769/BioProtoc.4801

Neuroscience

Confocal Imaging and 3D Reconstruction to Determine How Genetic Perturbations Impact Presynaptic Morphology at the Mouse Calyx of Held Authors: Christian Keine, Tamara Radulovic, Mohammed Al-Yaari, Samuel M. Young Jr. DOI: 10.21769/BioProtoc.4799

Spatial Centrosome Proteomic Profiling of Human iPSC-derived Neural Cells Authors: Fatma Uzbas, Adam C. O’Neill DOI: 10.21769/BioProtoc.4812

The Effects of Whole-body Cold-water Immersion on Brain Connectivity Related to the Affective State in Adults Using fMRI: A Protocol of a Pre-post Experimental Design Authors: Ala Yankouskaya, Heather Massey, John James Totman, Lin Hui Lai, Ruth Williamson DOI: 10.21769/BioProtoc.4794

Plant Science

An In-depth Guide to the Ultrastructural Expansion Microscopy (U-ExM) of Chlamydomonas reinhardtii Authors: Nikolai Klena, Giovanni Maltinti, Umut Batman, Gaia Pigino, Paul Guichard, Virginie Hamel DOI: 10.21769/BioProtoc.4792

A Protocol for Mitotic Metaphase Chromosome Count Using Shoot Meristematic Tissues of Mulberry Tree Species Authors: Raju Mondal, Sreya Antony, Belaghihalli N. Gnanesh, G. Thanavendan, G. Ravikumar, B. T. Sreenivasa, S. Gandhi Doss, K. Vijayan DOI: 10.21769/BioProtoc.4643

13CO2-labelling and Sampling in Algae for Flux Analysis of Photosynthetic and Central Carbon Metabolism Authors: Or Geffen, David Achaintre, Haim Treves DOI: 10.21769/BioProtoc.4808

An Optimized Protocol for Detecting Guard Cell–specific Gene Expression by in situ RT-PCR in Brassica rapa Authors: Yingying Song, Xinlei Guo, Jian Wu, Jianli Liang, Runmao Lin, Zifu Yan, Xiaowu Wang DOI: 10.21769/BioProtoc.4810

Stem Cell

Absolute Quantification of mRNA Isoforms in Adult Stem Cells Using Microfluidic Digital PCR Authors: Shubhangi Das Barman, Zofija Frimand, Antoine de Morree DOI: 10.21769/BioProtoc.4811

Correction

Update Notice: Site-specific Incorporation of Phosphoserine into Recombinant Proteins in Escherichia coli Authors: Phillip Zhu, Ryan A. Mehl, Richard B. Cooley DOI: 10.21769/BioProtoc.4860