New in Bio-protocol: December 2025 Updates

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Latest Issue: Dec 20, 2025 Articles published in December Articles in Press Archive

Bio-protocol: December 5 and December 20 issues

Volume: 15, Issue: 24 Dec 20, 2025

Bioinformatics and Computational Biology

Identifying and Characterizing Lipid-Binding Cavities in Lipid Transfer Proteins With CG-MD Simulations

Authors: Daniel Álvarez, Stefano Vanni, Sriraksha Srinivasan

Biological Engineering

Manufacturing of Living Building Materials With Calcifying Cyanobacteria

Authors: Patrick Jung, Jan Friedek, Laura Briegel-Williams, Miriam Haage-Ott, Carina Neff

In Situ Crosslinking of Bioorthogonal Nanoparticles to Restore Clot Stability in Coagulopathic Blood

Authors: Celestine Hong, Yanpu He, Angela M. Belcher, Bradley D. Olsen, Paula T. Hammond

Cell Biology

High Precision Antibody-Free Microtubule Labeling for Expansion Microscopy

Authors: Rajdeep Chowdhury, Donatus Krah, Antonios Ntolkeras, Alina Heimbrodt, Ali H. Shaib

Vascularization of Human Pancreatic Islets With Adaptive Endothelial Cells for In Vitro Analysis and In Vivo Transplantation

Authors: Ge Li, Rebecca Craig-Schapiro, Ahsan Uddin, Shahin Rafii

Developmental Biology

Whole-Mount Visualization of Primary Cilia in the Developing Mouse Brain

Authors: Oscar Torres Gutierrez, Xiaoliang Liu, Xuecai Ge

Methods for Collecting and Analyzing Post-Ejaculatory Uterine Fluid and the Uterus in Mice

Authors: Yu Matsumoto, Ban Sato, Masafumi Inui, Manato Sunamoto, Natsuko Kawano, Kenji Miyado

Immunology

An Ex Vivo Lung Histoculture Model for Studying Pulmonary Infection and Immune Response With SARS-CoV-2 as an Example of RNA Virus

Authors: Elena V. Maryukhnich, Daria M. Potashnikova, Daria A. Vorobyeva, George I. Rusakovich, Anna V. Tvorogova, Anna I. Kalinskaya, Natalia V. Pinegina, Anna V. Kovyrshina, Inna V. Dolzhikova, Alexander B. Postnikov, Fedor N. Rozov, Tatiana N. Sotnikova, Dmitry Yu. Kanner, Denis Yu. Logunov, Alexander L. Gintsburg, Elena J. Vasilieva

Microbiology

A Rapid and Cost-Effective Pipeline to Identify and Capture BGCs From Bacterial Draft Genomes

Authors: Marco A. Campos-Magaña, Vitor A. P. Martins dos Santos, Luis Garcia-Morales

Molecular Biology

Plasmid DNA Purification Using Filterprep With an Optional Endotoxin Removal Step

Authors: Yu-Qian Lin, Yung-Chun Shih, Chung-Te Chang

Neuroscience

Station Holding During Rheotaxis: A Sensitive Assay of Lateral Line Function in Larval Zebrafish

Authors: Sophie Cohen-Bodénès, Elayna I. Malak, Josef G. Trapani, Matt Gaidica, Valentin A. Militchin, Kyle C. Newton, Lavinia Sheets

Stimulation-Guided AAV Delivery and Longitudinal Assessment of Optogenetic Expression in Rat Motor Nerves

Authors: Emma M. Moravec, Jordan J. Williams

Plant Science

Chloroplast Movement Imaging Under Different Light Regimes With a Hyperspectral Camera

Authors: Paweł Hermanowicz, Anna Hebda, Justyna Łabuz

CAPS-Based SNP Genotyping for Nitrogen-Response Phenotypes in Maize Hybrids

Authors: Jannis Jacobs, Linsey Newton, Brian McSpadden Gardener, Brandon Webster, Addie Thompson, Erich Grotewold, Peter K. Lundquist

Systems Biology

Optimized Secretome Sample Preparation From High Volume Cell Culture Media for LC–MS/MS Proteomic Analysis

Authors: Basil Baby Mattamana, Raju Gajjela, Jyoti K.C., Robert A. Parish, Peter Allen Faull

Correction

Correction Notice: Identification of S-locus F-box Protein Sequences in Diploid Potato, Solanum okadae, via Degenerate PCR

Authors: Amar Hundare, Ranjan Swarup, Timothy P. Robbins

Volume: 15, Issue: 23 Dec 5, 2025

Biochemistry

Quantitative Proteomics of Nitrosylated Proteins in Melanoma Using the Biotin-Switch Technique Combined With Tandem Mass Tag Labeling

Authors: Vipin K. Yadav, Bin Fang, John M. Koomen, Jyoti Srivastava, Sanjay Premi

Bioinformatics and Computational Biology

Detailed Protocol for Segmentation and Quantification of Overlapping Prospore Membranes using DeMemSeg

Authors: Shodai Taguchi, Keita Chagi, Hiroki Kawai, Kenji Irie, Yasuyuki Suda

Biological Sciences

Room-Temperature Storage of Zebrafish and Medaka Sperm Using Lactic Acid-Stabilized L-15 Medium

Authors: Yukiko Imai, Touma Asano, Toshiya Nishimura, Kazumasa Takemoto, Akinori Kawamura, Noriyoshi Sakai

Biophysics

An Optimized Protocol for High-Quality AFM Imaging of Amyloid Fibrils

Authors: Rohith R. Kumar, Uttam Das, Patil Pranita Uttamrao, Thenmalarchelvi Rathinavelan

Immunology

Utilizing EdU to Track Leukocyte Recruitment to the Brain

Authors: Zoie K. Lipfert, Erika Arias, Ayush Batra, David P. Sullivan

Microbiology

Imaging the Entire Sexual Life Cycle of the Budding Yeast Saccharomyces cerevisiae Using a Microfluidic Platform

Authors: Taylor Kennedy, Sandhya Neupane, Bryn Merritt, Orlando Argüello-Miranda

Molecular Biology

Analyzing the Translatome of Lymphatic and Venous Endothelial Cells In Vivo via Translating Ribosome Affinity Purification (TRAP)

Authors: Olamide Olayinka, Leia Zarinebaf, Hyun Min Jung

Bridging PCR-Based Genome-Walking Protocol

Authors: Mou Li, Yinwei Gu, Qingchun Tang, Haixing Li

Implementation of Fusion Primer-Driven Racket PCR Protocol for Genome Walking

Authors: Yinwei Gu, Jinfeng Pei, Mou Li, Qingchun Tang, Haixing Li

Neuroscience

A One-Step Mouse Model of Parkinson’s Disease Combining rAAV-α-Synuclein and Preformed Fibrils of α-Synuclein

Authors: Santhosh Kumar Subramanya, Devendra Singh, Poonam Thakur

Whole-Mount Immunostaining for the Visual Separation of A- and C-Fibers in the Study of the Sciatic Nerve

Authors: Valeriia Ustymenko, Tetyana Pivneva, Volodymyr Medvediev, Pavel Belan, Nana Voitenko

Revisiting Primary Microglia Isolation Protocol: An Improved Method for Microglia Extraction

Authors: Jianwei Li, Zijian Zheng, Menglin Zhang, Cheng Xue, Xinran Zhang, Guohui Lu

Intraepidermal Nerve Fiber Quantification of the Mouse Hind Paw Footpads: A Detailed and Simplified Protocol

Authors: Anastasia Yerushkin, Shani Berkowitz, Valery Golderman, Zehavit Goldberg, Yael Eshed-Eisenbach, Efrat Shavit-Stein, Amir Dori

Plant Science

Synchronizing Germination Rates Across Plant Species for Fabricated Ecosystems EcoFAB 2.0

Authors: Romane S. F. Charbeaux, Vicky J. Waymouth, Jacob Calabria, Troy Miller, Peter Andeer, Michelle Watt

Preparation and Negative Staining for Visualization of Cyanoglobule Lipid Droplets Using Transmission Electron Microscopy

Authors: Febri A. Susanto, Alicia Withrow, Peter K. Lundquist

Highly Efficient Agrobacterium-Mediated Transformation of Tomato cv Micro-Tom From Cotyledon Explants

Authors: Débora Pagliuso, Magdalena Rossi, Luciano Freschi

Stem Cell

A Protocol to Induce Brown and Beige Adipocyte Differentiation From Murine and Human Adipose-Derived SVF

Authors: Rohit Raj Yadav, Nandita Mishra, Narendra Verma

A Simplified 3D-Plasma Culture Method for Generating Minimally Manipulated Autologous Equine Muscle-Derived Progenitor Cells

Authors: Hélène Graide, Julien Duysens, Thierry Frank, Ange Mouithys-Mickalad, Ariane Niesten, Charlotte Sandersen, Justine Ceusters, Didier Serteyn

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