Reviewer
Damián Lobato-Márquez
  • Research associate, London School of Hygiene and Tropical Medicine
Research fields
  • Cell Biology, Microbiology, Molecular Biology
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: 5615, 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 measurements are less straightforward. Recently, we developed a new analysis method for evaluating bacterial growth with microplate readers based on time derivatives. Here, we describe a detailed protocol for this development and provide the homemade program for the new analysis method.

Marker Genes (16S and ITS) Protocol for Plant Microbiome Analyses
Author:  Geoff Zahn, date: 04/20/2022, view: 1168, Q&A: 0

Many research questions in plant science depend on surveys of the plant microbiome. When the questions depend on answering "who is there" rather than "what are they doing," the most cost-effective method for interrogating microbiomes is often via targeted meta-amplicon surveys. There are numerous platforms for processing and analyzing meta-amplicon data sets, but here we will look at a flexible, reproducible, and fully customizable pipeline in the R environment. This approach has the benefit of being able to process and analyze your data in the same setting, without moving back and forth between standalone platforms, and further benefits from being completely flexible in terms of analyses and visualizations you can produce, without being limited to pre-selected tools available in point-and-click analysis engines, such as QIIME, Galaxy, or MG-RAST.

In vitro Enzymatic Assays of Histone Decrotonylation on Recombinant Histones
Authors:  Rachel Fellows and Patrick Varga-Weisz, date: 07/20/2018, view: 6108, Q&A: 0
Class I histone deacetylases (HDACs) are efficient histone decrotonylases, broadening the enzymatic spectrum of these important (epi-)genome regulators and drug targets. Here, we describe an in vitro approach to assaying class I HDACs with different acyl-histone substrates, including crotonylated histones and expand this to examine the effect of inhibitors and estimate kinetic constants.
In vitro Histone H3 Cleavage Assay for Yeast and Chicken Liver H3 Protease
Authors:  Sakshi Chauhan, Gajendra Kumar Azad and Raghuvir Singh Tomar, date: 01/05/2017, view: 8684, Q&A: 0
Histone proteins are subjected to a wide array of reversible and irreversible post-translational modifications (PTMs) (Bannister and Kouzarides, 2011; Azad and Tomar, 2014). The PTMs on histones are known to regulate chromatin structure and function. Histones are irreversibly modified by proteolytic clipping of their tail domains. The proteolytic clipping of histone tails is continuously attracting interest of researchers in the field of chromatin biology. We can recapitulate H3-clipping by performing in vitro H3 cleavage assay. Here, we are presenting the detailed protocol to perform in vitro H3 cleavage assay.
Estimation of the Chromosomal Copy Number in Synechococcus elongatus PCC 7942
Authors:  Satoru Watanabe and Hirofumi Yoshikawa, date: 07/05/2016, view: 7697, Q&A: 0
Cyanobacteria are prokaryotic organisms that perform oxygenic photosynthesis. Freshwater cyanobacteria, such as Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, are model organisms for the study of photosynthesis, gene regulation, and biotechnological applications because they are easy to manipulate genetically. However, while studying these cyanobacteria, care has to be taken with respect to genetic heterogeneity in the establishment of gene disruptants, because these cyanobacteria contain multiple chromosomal copies per cell. Here, we describe a method for the estimation of chromosomal copy number in Synechococcus 7942. Using this method, we have recently observed that the chromosomal copy number of Synechococcus 7942 significantly changes during its growth phases. This technique is available for studying polyploidy not only in cyanobacteria, but also in other polyploid organisms.
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