New in Bio-protocol: November 2025 Updates

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Latest Issue: Nov 20, 2025 Articles published in November Articles in Press Archive

Bio-protocol: November 5 and November 20 issues

Volume: 15, Issue: 22 Nov 20, 2025

Biochemistry

Quantifying Intestinal Glucose Absorption Using Isolated Vascularly Perfused Rat Small Intestine

Authors: Cecilie Bæch-Laursen, Sabine Bæch-Laursen, Jens Juul Holst

Bioinformatics and Computational Biology

Click-qPCR: A Simple Tool for Interactive qPCR Data Analysis

Authors: Azusa Kubota, Atsushi Tajima

A Computational Workflow for Membrane Protein–Ligand Interaction Studies: Focus on α5-Containing GABA (A) Receptors

Authors: Syarifah Maisarah Sayed Mohamad, Khairul Bariyyah Abd Halim, Azzmer Azzar Abdul Hamid, Ahmad Tarmizi Che Has

A Step-by-Step Computational Protocol for Functional Annotation and Structural Modelling of Insect Chemosensory Proteins

Authors: Rajeswari Kalepu, Azzmer Azzar Abdul Hamid, Maizom Hassan, Norfarhan Mohd-Assaad, Nor Azlan Nor Muhammad

Biological Engineering

Spheroid Sheets: A Scalable Platform for Producing Tissue Membrane Constructs

Authors: Quang Bach Le, Hariharan Ezhilarasu, Weng Wan Chan, Deepak Choudhury

Cancer Biology

Improved Immunohistochemistry of Mouse Eye Sections Using Davidson's Fixative and Melanin Bleaching

Authors: Anne Nathalie Longakit, Chloe Hess, Christina Zhang, Catherine D. Van Raamsdonk

Immunopeptidomics Workflow for Isolation and LC-MS/MS Analysis of MHC Class I-Bound Peptides Under Hypoxic Conditions

Authors: Hala Estephan, Ester M. Hammond, Eleni Adamopoulou

Cell Biology

Monitoring Endocytosis of Integral Membrane Proteins Using Western Blot-Based Detection of Biotinylated Antibody Uptake

Authors: Alexandra Graninger, Prasanna Satpute-Krishnan

Rapid and solvent-free, 2-hydroxyethyl methacrylate (HEMA)-acrylamide (AAm) copolymer-based optical clearing of tissue for fluorescent imaging

Authors: Yanran Wang, Siying Feng, Xiaoqi Zhou, Qiufeng Yao, Hui Ma, Kefeng Wu

Environmental science

A Comparative Protocol for Preserving Deep-Water Marine Invertebrate Tissues: DNA/RNA Shield vs. Liquid Nitrogen for Dual Extraction of High-Quality Nucleic Acids

Authors: Ana S. Gomes, Eduarda M. Guerreiro, Xavier Pochon, Nigel Keeley, Olivier Laroche

Immunology

Dual Phospho-CyTOF Workflows for Comparative JAK/STAT Signaling Analysis in Human Cryopreserved PBMCs and Whole Blood

Authors: Ilyssa E. Ramos, Brynja Matthiasardottir, Teresa S. Hawley, Kyu Lee Han, Michal Toborek, Iyadh Douagi, Georgette N. Jones, James M. Cherry

Medicine

In Vivo Retroviral Transduction of Cardiac Myofibroblasts Using Intramyocardial Injection Immediately Post-myocardial Infarction

Authors: Satsuki Ono, Hayato Watanabe, Yuma Horii, Michio Nakaya

Neuroscience

Characterizing Tissue Oxygen Tension During Neurogenesis in Human Cerebral Organoids

Authors: Yuan-Hsuan Liu, Hsiao-Mei Wu

Intracerebral Cannula Implantation in Mouse: A Proposed Method to Assess Glioblastoma Invasiveness and Serial Locoregional Treatment

Authors: Aurélie Henry, Philippe Stordeur, Andrée Lapierre, Chloé Buttenaers, Marc Lefevre, Maëlle Noelanders, Cathy Mottart, Lucie Delincé, Simon Destiné, Quentin Etienne, Caroline Nijskens, Patrice Filee, Gaëtan Thirion

Mouse Vestibulo-Ocular Reflex Testing for Otolith Organs and Horizontal Semicircular Canal

Authors: Tong Zhao, Shijie Xiao, Qingsong Liu, Jinxuan Liu, Fangyi Chen

Selective Enrichment and Identification of Cerebrospinal Fluid-Contacting Neurons In Vitro via PKD2L1 Promoter-Driven Lentiviral System

Authors: Wei Tan, Zeyu Shangguan, Shuwen Jing, Xuexing Shi, Qizhe Li, Hao Li, Haodong Zhang, Zhangrong Luo, Chunqing Wang, Xiaowei Dou, Qing Li

Plant Science

Quantitative Analysis of the Arabidopsis Leaf Secretory Proteome via TMT-Based Mass Spectrometry

Authors: Sakharam Waghmare, Lingfeng Xia, Suzanne McGill, Richard Burchmore, Rucha Karnik

Volume: 15, Issue: 21 Nov 5, 2025

Biochemistry

Lipid-Mediated Sequential Recruitment of Proteins Via Dual SLIPT and Dual SLIPT^NVOC in Live Cells

Authors: Kristina V. Bayer, Richard Wombacher

Cluster FLISA—A Method to Compare Protein Expression Efficiency Between Cell Lines and Subunit Clustering of Proteins

Authors: Sabrina Brockmöller, Lara Maria Molitor

Bioinformatics and Computational Biology

Computational Workflow for Genome-Wide DNA Methylation Profiling and Differential Methylation Analysis

Authors: Pei-Yu Lin, Guan-Jun Lin, Kuan-Lin Chen, Shiang-Chin Huang, Pao-Yang Chen

In Silico Prediction and In Vitro Validation of Bacterial Interactions in the Plant Rhizosphere Using a Synthetic Bacterial Community

Authors: Arijit Mukherjee, Boon H. Tan, Sanjay Swarup

Biological Engineering

Production of Genetically Engineered Extracellular Vesicles for Targeted Protein Delivery

Authors: Leyla A. Ovchinnikova, Evgeniy G. Evtushenko, Dmitriy V. Bagrov, Anton O. Goncharov, Alexander G. Gabibov, Yakov A. Lomakin

Cell Biology

Protocol for the Isolation and Analysis of Extracellular Vesicles From Peripheral Blood: Red Cell, Endothelial, and Platelet-Derived Extracellular Vesicles

Authors: Bhawani Yasassri Alvitigala, Eranga Sanjeewa Wijewickrama, Laura Denney, Praveen Weeratunga, Pradeep Kaluarachchi, Ariaranee Gnanathasan, Lallindra Viranjan Gooneratne

Medicine

A Quantitative Spectrophotometric Assay Matched With Environmental Scanning Electron Microscopy to Measure Calcium Crystals in Human Osteoarthritic Synovial Fluid

Authors: Michela Battistelli, Laura Valentini, Eleonora Olivotto

Microbiology

A Practical CRISPR-Based Method for Rapid Genome Editing in Caulobacter crescentus

Authors: Xuezhou Yuan, Xin Yu, Wei Zhao, Jingxian Sun

Optimized Protocol for the Collection, Cryopreservation, and In Vitro Cultivation of Human Gut Microbiota for Toxicomicrobiomics Applications

Authors: Paulina Średnicka, Paulina Emanowicz, Michał Wójcicki

Molecular Biology

Examining the Roles of m⁶A Sites in mRNA Using the Luciferase Gene Fused With Mutated RRACH Motifs

Authors: Nobuko Katoku-Kikyo, Nobuaki Kikyo

Library Preparation for Genome-Wide DNA Methylation Profiling

Authors: Fei-Man Hsu, Matteo Pellegrini, Pao-Yang Chen

Neuroscience

Generation of 3D Human iPSC-Derived Multi-Cell Type Neurospheres for Studying Neuron, Astrocyte, and Microglia Crosstalk

Authors: Stefan Wendt, Christopher Lee, Wenji Cai, Ada J. Lin, Jessica Huang, V. Poon, Xianyuan Xiang, Wei Hong, Brian A. MacVicar, Haakon B. Nygaard

Optogenetic Approach for Investigating Descending Control of Nociception in Ex Vivo Spinal Cord Preparation

Authors: Volodymyr Krotov, Ivan Blashchak, Jayden Moore, Anastasia Moore, Sergii Romanenko, Nana Voitenko, Pavel Belan

Labeling Postsynaptic Densities for Super-Resolution Microscopy With Minimal Signal-Loss and Offset

Authors: Sheng-Yang Ho, Christiane Huhn, Adam Skeens, Martin Hruska, Hans M. Maric, Johannes W. Hell

Colocalizing Telomeres With PML or γH2AX Foci by IF-FISH in Mouse Brain Neurons

Author: Anna Konopka

Plant Science

Live-Cell Monitoring of Piecemeal Chloroplast Autophagy

Authors: Masanori Izumi, Sakuya Nakamura, Shinya Hagihara

A Reliable In Planta Inoculation and Antifungal Screening Protocol for Rhizoctonia solani-Induced Sheath Blight in Rice

Authors: Alinaj Yasin, Anurag Kashyap, Bhaskar Dowarah, Jyotishmoi Dey, Sangita Bharali, Bharat Chandra Nath, Pranaba Nanda Bhattacharyya, Supriya Sharma, Parinda Barua, Palash Deb Nath

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Prashanth N Suravajhala, Ph.D.

Professor, Systems Genomics Group

Department of Biosciences, Room # 323D, AB-3 

Manipal University Jaipur, Dehmi Kalan 303007,  India.

Founder, Bioclues.org

Group page: http://www.bioinformatics.org/wiki/Prash 

Twitter: @prashbio

"One rule is important in science- only courageous people win "   ~ Max Planck