Microbiology

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    Protocols in Current Issue
    Hypochlorite Stress Assay for Phenotypic Analysis of the Halophilic Archaeon Haloferax volcanii Using an Improved Incubation Method and Growth Monitoring
    Authors:  Paula Mondragon, Sungmin Hwang, Amy Schmid and Julie A. Maupin-Furlow, date: 11/20/2022, view: 317, Q&A: 0

    The study of haloarchaea provides an opportunity to expand understanding of the mechanisms used by extremophiles to thrive in and respond to harsh environments, including hypersaline and oxidative stress conditions. A common strategy used to

    ...
    Efficient Generation of Genome-wide Libraries for Protein–ligand Screens Using Gibson Assembly
    Authors:  Tamara Sternlieb, Mira Loock, Mengjin Gao and Igor Cestari, date: 11/20/2022, view: 488, Q&A: 0

    Genome-wide screens using yeast or phage displays are powerful tools for identifying protein–ligand interactions, including drug or vaccine targets, ligand receptors, or protein–protein interactions. However, assembling libraries

    ...
    Fluorescent Binding Protein Sensors for Detection and Quantification of Biochemicals, Metabolites, and Natural Products
    Authors:  Salete M. Newton and Phillip E. Klebba, date: 11/20/2022, view: 805, Q&A: 0

    Membrane transporters and soluble binding proteins recognize particular nutrients, metabolites, vitamins, or ligands. By modifying genetically engineered single cysteine residues near the active sites of such proteins with extrinsic maleimide

    ...
    Babesia duncani in Culture and in Mouse (ICIM) Model for the Advancement of Babesia Biology, Pathogenesis and Therapy
    Authors:  Vandana Kumari, Anasuya C. Pal, Pallavi Singh and Choukri Ben Mamoun, date: 11/20/2022, view: 314, Q&A: 0

    Babesiosis is a tick-borne disease caused by pathogens belonging to the genus Babesia. In humans, the disease presents as a malaria-like illness and can be fatal in immunocompromised and elderly people. In the past few years, human babesiosis has

    ...
    Hypochlorite Stress Assay for Phenotypic Analysis of the Halophilic Archaeon Haloferax volcanii Using an Improved Incubation Method and Growth Monitoring
    Authors:  Paula Mondragon, Sungmin Hwang, Amy Schmid and Julie A. Maupin-Furlow, date: 11/20/2022, view: 317, Q&A: 0
    [Abstract]

    The study of haloarchaea provides an opportunity to expand understanding of the mechanisms used by extremophiles to thrive in and respond to harsh environments, including hypersaline and oxidative stress conditions. A common strategy used to investigate molecular mechanisms of stress response involves the deletion and/or site-directed mutagenesis

    ...
    Efficient Generation of Genome-wide Libraries for Protein–ligand Screens Using Gibson Assembly
    Authors:  Tamara Sternlieb, Mira Loock, Mengjin Gao and Igor Cestari, date: 11/20/2022, view: 488, Q&A: 0
    [Abstract]

    Genome-wide screens using yeast or phage displays are powerful tools for identifying protein–ligand interactions, including drug or vaccine targets, ligand receptors, or protein–protein interactions. However, assembling libraries for genome-wide screens can be challenging and often requires unbiased cloning of 105–107 DNA

    ...
    Fluorescent Binding Protein Sensors for Detection and Quantification of Biochemicals, Metabolites, and Natural Products
    Authors:  Salete M. Newton and Phillip E. Klebba, date: 11/20/2022, view: 805, Q&A: 0
    [Abstract]

    Membrane transporters and soluble binding proteins recognize particular nutrients, metabolites, vitamins, or ligands. By modifying genetically engineered single cysteine residues near the active sites of such proteins with extrinsic maleimide fluorophores, the approaches that we report create sensitive fluorescent sensors that detect, quantify,

    ...
    Babesia duncani in Culture and in Mouse (ICIM) Model for the Advancement of Babesia Biology, Pathogenesis and Therapy
    Authors:  Vandana Kumari, Anasuya C. Pal, Pallavi Singh and Choukri Ben Mamoun, date: 11/20/2022, view: 314, Q&A: 0
    [Abstract]

    Babesiosis is a tick-borne disease caused by pathogens belonging to the genus Babesia. In humans, the disease presents as a malaria-like illness and can be fatal in immunocompromised and elderly people. In the past few years, human babesiosis has been a rising concern worldwide. The disease is transmitted through tick bite, blood transfusion, and

    ...
    In vitro Di-ubiquitin Formation Assay and E3 Cooperation Assay
    Authors:  Rebecca J. Burge, Katie H. Jameson, Anthony J. Wilkinson and Jeremy C. Mottram, date: 11/05/2022, view: 487, Q&A: 0
    [Abstract]

    Ubiquitination is a post-translational modification conserved across eukaryotic species. It contributes to a variety of regulatory pathways, including proteasomal degradation, DNA repair, and cellular differentiation. The ubiquitination of substrate proteins typically requires three ubiquitination enzymes: a ubiquitin-activating E1, a

    ...
    Negative Staining Transmission Electron Microscopy of HIV Viral Particles Permeabilized with PFO and Capsid Stabilized with IP6
    Authors:  Derrick Lau, Chantal L. Márquez, Michael W. Parker and Till Böcking, date: 10/20/2022, view: 623, Q&A: 0
    [Abstract]

    The human immunodeficiency virus 1 (HIV-1) consists of a viral membrane surrounding the conical capsid. The capsid is a protein container assembled from approximately 1,500 copies of the viral capsid protein (CA), functioning as a reaction and transport chamber for the viral genome after cell entry. Transmission electron microscopy (TEM) is a

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    Assay for Protealysin-like Protease Inhibitor Activity
    Authors:  Igor M. Berdyshev, Maria A. Karaseva and Ilya V. Demidyuk, date: 10/05/2022, view: 534, Q&A: 0
    [Abstract]

    Here, we present the first quantitative method for the activity analysis of protealysin-like protease (PLP) inhibitors. This approach is based on a previously developed method for protealysin activity determination by hydrolysis of internally quenched fluorescent peptide substrate

    ...
    Analysis of Lipid-linked Oligosaccharides Synthesized in vivo in Schizosaccharomyces pombe
    [Abstract]

    Dolichol diphosphate-linked oligosaccharides (LLO) are the sugar donors in N-glycosylation, a fundamental protein post-translational modification of the eukaryotic secretory pathway. Defects in LLO biosynthesis produce human Congenital Disorders of Glycosylation Type I. The synthesis of LLOs and the transfer reactions to their protein

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    Incorporation of a Chemically Diverse Set of Non-Standard Amino Acids into a Gram-Positive Organism
    Authors:  Devon A. Stork, Michaela A. Jones, Ethan C. Garner and Aditya M. Kunjapur, date: 09/05/2022, view: 621, Q&A: 0
    [Abstract]

    The incorporation of non-standard amino acids (nsAAs) within proteins and peptides through genetic code expansion introduces novel chemical functionalities such as photo-crosslinking and bioconjugation. Given the utility of Bacillus subtilis in fundamental and applied science, we extended existing nsAA incorporation technology from Escherichia

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    Split-Chloramphenicol Acetyl Transferase Assay to Study Protein-Protein Interactions and Ubiquitylation in Escherichia coli
    Authors:  Amir Florentin, Alina Kordonsky, Elon Yariv, Reut Avishid, Noa Efron, Edache Akogwu and Gali Prag, date: 09/05/2022, view: 753, Q&A: 0
    [Abstract]

    Protein-protein interactions and protein modifications play central roles in all living organisms. Of the more than 200 types of post-translational modifications, ubiquitylation is the most abundant, and it profoundly regulates the functionality of the eukaryotic proteome. Various in vitro and in vivo methodologies to study protein interactions

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