Microbiology

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    Protocols in Current Issue
    Tracking the Reversed Oxidative Tricarboxylic Acid Cycle in Bacteria
    [Abstract]

    Different pathways for autotrophic CO2 fixation can be recognized by the presence of genes for their specific key enzymes. On this basis, (meta)genomic, (meta)transcriptomic, or (meta)proteomic analysis enables the identification of the role of an organism or a distinct pathway in primary production. However, the recently discovered variant of the

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    Activity-based Crosslinking to Identify Substrates of Thioredoxin-domain Proteins in Malaria Parasites
    Authors:  David W. Cobb, Grace S. Woods and Vasant Muralidharan, date: 02/20/2022, view: 1177, Q&A: 0
    [Abstract] Malaria remains a major public health issue, infecting nearly 220 million people every year. The spread of drug-resistant strains of Plasmodium falciparum around the world threatens the progress made against this disease. Therefore, identifying druggable and essential pathways in P. falciparum parasites remains a major area of ...
    Isolation of Mitochondria from Ustilago maydis Protoplasts
    [Abstract]

    Ustilago maydis, a basidiomycete that infects Zea mays, is one of the top ten fungal models for studying DNA repair, signal transduction pathways, and dimorphic transitions, among other processes. From a metabolic point of view, U. maydis lacks fermentative capacity, pointing to mitochondria as a key player in central metabolism. Oxidative

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    Extraction and Electrophoretic Analysis of Bacterial Lipopolysaccharides and Outer Membrane Proteins
    Authors:  Yue-Jia Lee and Thomas J. Inzana, date: 12/20/2021, view: 1697, Q&A: 0
    [Abstract]

    Lipopolysaccharides (LPS) (or lipooligosaccharides [LOS], which lack the O-antigen side chains characteristic of LPS), and outer membrane proteins (OMP) are major cell-surface molecules in the outer membrane (OM) of gram-negative bacteria. The LPS is responsible for causing endotoxic shock in infected hosts and, in conjunction with some OMPs,

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    Quantification of Duloxetine in the Bacterial Culture and Medium to Study Drug-gut Microbiome Interactions
    Authors:  Prasad B. Phapale, Sonja Blasche, Kiran R. Patil and Theodore Alexandrov, date: 11/05/2021, view: 1318, Q&A: 0
    [Abstract]

    Expanding our understanding of drug-gut bacteria interactions requires high-throughput drug measurements in complex bacterial cultures. Quantification of drugs in the cultures, media, and cell pellets is prone to strong matrix effects. We have developed a liquid chromatography–high resolution mass spectrometry (LC–HRMS) method for

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    Production, Titration, Neutralisation, Storage and Lyophilisation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lentiviral Pseudotypes
    [Abstract]

    This protocol details a rapid and reliable method for the production and titration of high-titre viral pseudotype particles with the SARS-CoV-2 spike protein (and D614G or other variants of concern, VOC) on a lentiviral vector core, and use for neutralisation assays in target cells expressing angiotensin-converting enzyme 2 (ACE2) and

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    An Assay to Determine NAD(P)H: Quinone Oxidoreductase Activity in Cell Extracts from Candida glabrata
    Authors:  Anamika Battu, Rajaram Purushotham and Rupinder Kaur, date: 11/05/2021, view: 1113, Q&A: 0
    [Abstract]

    Flavodoxin-like proteins (Fld-LPs) are an important constituent of the oxidative stress defense system in several organisms and highly conserved from bacteria to humans. These proteins possess NAD(P)H:quinone oxidoreductase activity and convert quinones to hydroquinones through two-electron reduction, using NAD(P)H and quinone as electron donor

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    Simple Methods for the Preparation of Colloidal Chitin, Cell Free Supernatant and Estimation of Laminarinase
    Author:  Ananthamurthy Koteshwara, date: 10/05/2021, view: 1647, Q&A: 0
    [Abstract]

    Colloidal chitin (CC) is a common substrate used in research work involving chitin-active enzymes (chitinases). Cell free supernatant (CFS) is prepared from fermented broth. Preparation of CC and CFS usually involve large amounts of liquid, which must be separated from the solids. This necessitates the use of a large volume centrifugation

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    Protocol for RNA-seq Expression Analysis in Yeast
    Author:  Stefan Bohn, date: 09/20/2021, view: 1819, Q&A: 0
    [Abstract]

    Genome-wide sequencing of RNA (RNA-seq) has become an inexpensive tool to gain key insights into cellular and disease mechanisms. Sample preparation and sequencing are streamlined and allow the acquisition of hundreds of gene expression profiles in a few days; however, in particular, data processing, curation, and analysis involve numerous steps

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    Acid Hydrolysis for the Extraction of Archaeal Core Lipids and HPLC-MS Analysis
    Authors:  Maxime Tourte, Philippe Schaeffer, Vincent Grossi and Philippe M. Oger, date: 08/20/2021, view: 1092, Q&A: 0
    [Abstract]

    Lipid membranes are essential cellular elements as they provide cellular integrity and selective permeability under a broad range of environmental settings upon cell growth. In particular, Archaea are commonly recognized for their tolerance to extreme conditions, which is now widely accepted to stem from the unique structure of their lipids. While

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