• Volume 12, 2022
  • Volume 11, 2021
  • Volume 10, 2020
  • 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
Image Credit: BioProtoc.4409

Past Issues in 2022

Volume: 12 Issue: 9

Biochemistry

Expression, Purification, and in vitro Enzyme Activity Assay of a Recombinant Aldehyde Dehydrogenase from Thermus thermophilus, using an Escherichia coli host Authors:  Kim Shortall, Edmond Magner and Tewfik Soulimane, date: 05/05/2022, view: 549, Q&A: 0

Based on previous in-depth characterisation, aldehyde dehydrogenases (ALDH) are a diverse superfamily of enzymes, in terms of both structure and function, present in all kingdoms of life. They catalyse the oxidation of an aldehyde to carboxylic acid using the cofactor nicotinamide adenine dinucleotide (phosphate) (NAD(P)+), and are often not

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Immunoisolation of Endosomal Recycling Vesicles from Saccharomyces cerevisiae Authors:  Sho W. Suzuki and Scott D. Emr, date: 05/05/2022, view: 435, Q&A: 0

Endosomal recycling is essential for the appropriate function of the endosome. During this process, endosomal coat complexes (i.e., retromer, and Mvp1) are recruited to the endosome, and deform its membrane to form recycling vesicles. To further analyze this, we developed a protocol for the immunoisolation of recycling vesicles from budding yeast.

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Biophysics

Production and Crystallization of Nanobodies in Complex with the Receptor Binding Domain of the SARS-CoV-2 Spike Protein Authors:  Audrey Le Bas, Halina Mikolajek, Jiandong Huo, Chelsea Norman, Joshua Dormon, James H. Naismith and Raymond J. Owens, date: 05/05/2022, view: 712, Q&A: 0

The receptor binding domain (RBD) of the spike protein of SARS-CoV-2 binds angiotensin converting enzyme-2 (ACE-2) on the surface of epithelial cells, leading to fusion, and entry of the virus into the cell. This interaction can be blocked by the binding of llama-derived nanobodies (VHHs) to the RBD, leading to virus neutralisation. Structural

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Cell Biology

Quantitative Analysis of Actin Cable Length in Yeast Authors:  Shane G. McInally, Jane Kondev and Bruce L. Goode, date: 05/05/2022, view: 749, Q&A: 1

Polarized actin cables in S. cerevisiae are linear bundles of crosslinked actin filaments that are assembled by two formins, Bnr1 (localized to the bud neck), and Bni1 (localized to the bud tip). Actin is polymerized at these two sites, which results in cables extending along the cell cortex toward the back of the mother cell. These cables serve

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Computational Biology and Bioinformatics

A System to Easily Manage Metadata in Biomedical Research Labs Based on Open-source Software Author:  Manuel A. Castro-Alamancos, date: 05/05/2022, view: 447, Q&A: 0

In most biomedical labs, researchers gather metadata (i.e., all details about the experimental data) in paper notebooks, spreadsheets, or, sometimes, electronic notebooks. When data analyses occur, the related details usually go into other notebooks or spreadsheets, and more metadata are available. The whole thing rapidly becomes very complex and

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Microbiology

Bacterial Growth Curve Measurements with a Multimode Microplate Reader Authors:  Ariel T. Rogers, Kaitlin R. Bullard, Akash C. Dod and Yong Wang, date: 05/05/2022, view: 645, Q&A: 0

Bacterial studies based on growth curves are common in microbiology and related fields. Compared to the standard photometer and cuvette based protocols, bacterial growth curve measurements with microplate readers provide better temporal resolution, higher efficiency, and are less laborious, while analysis and interpretation of the microplate-based

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Ex vivo Human Skin Infection with Herpes Simplex Virus 1 Authors:  Nydia C. De La Cruz, Maureen Möckel, Lisa Wirtz and Dagmar Knebel-Mörsdorf, date: 05/05/2022, view: 328, Q&A: 0

Although herpes simplex virus 1 (HSV-1) is a well-studied virus, how the virus invades its human host via skin and mucosa to reach its receptors and initiate infection remains an open question. For studies of HSV-1 infection in skin, mice have been used as animal models. Murine skin infection can be induced after injection or scratching of the

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Neuroscience

Translating Ribosome Affinity Purification (TRAP) of Cell Type-specific mRNA from Mouse Brain Lysates Authors:  Catherine L. Salussolia, Kellen D. Winden and Mustafa Sahin, date: 05/05/2022, view: 434, Q&A: 0

Mammalian tissues are highly heterogenous and complex, posing a challenge in understanding the molecular mechanisms regulating protein expression within various tissues. Recent studies have shown that translation at the level of the ribosome is highly regulated, and can vary independently of gene expression observed at a transcriptome level, as

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Plant Science

Quantification of Soil-surface Roots in Seedlings and Mature Rice Plants Authors:  Eiko Hanzawa, Yuka Kitomi, Yusaku Uga and Tadashi Sato, date: 05/05/2022, view: 858, Q&A: 0

Soil-surface roots (SORs) in rice are primary roots that elongate over or near the soil surface. SORs help avoid excessive reduction of stress that occurs in paddy, such as in saline conditions. SORs may also be beneficial for rice growth in phosphorus-deficient paddy fields. Thus, SOR is a useful trait for crop adaptation to certain environmental

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Systems Biology

A Molecular Cloning and Sanger Sequencing-based Protocol for Detecting Site-specific DNA Methylation Authors:  Wei Guo, Anthony Cannon and Damon Lisch, date: 05/05/2022, view: 476, Q&A: 0

DNA methylation is a conserved chemical modification, by which methyl groups are added to the cytosine of DNA molecules. Methylation can influence gene expression without changing the sequence of a particular gene. This epigenetic effect is an intriguing phenomenon that has puzzled biologists for years. By probing the temporal and spatial patterns

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