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    Protocols in Current Issue
    Structural Analysis of Bordetella pertussis Biofilms by Confocal Laser Scanning Microscopy
    Authors:  Natalia Cattelan, Osvaldo Miguel Yantorno and Rajendar Deora, date: 08/05/2018, view: 98, Q&A: 0
    Biofilms are sessile communities of microbial cells embedded in a self-produced or host-derived exopolymeric matrix. Biofilms can both be beneficial or detrimental depending on the surface. Compared to their planktonic counterparts, biofilm cells ...
    Determination of Storage (Starch/Glycogen) and Total Saccharides Content in Algae and Cyanobacteria by a Phenol-Sulfuric Acid Method
    Authors:  Tomáš Zavřel, Petra Očenášová, Maria A. Sinetova and Jan Červený, date: 08/05/2018, view: 80, Q&A: 0
    This is a protocol for quantitative determination of storage and total carbohydrates in algae and cyanobacteria. The protocol is simple, fast and sensitive and it requires only few standard chemicals. Great advantage of this protocol is that both ...
    Direct Visualization of the Multicopy Chromosomes in Cyanobacterium Synechococcus elongatus PCC 7942
    Authors:  Ryudo Ohbayashi, Hirofumi Yoshikawa and Satoru Watanabe, date: 08/05/2018, view: 96, Q&A: 0
    Cyanobacteria are prokaryotic organisms that carry out oxygenic photosynthesis. The fresh water cyanobacterium Synechococcus elongatus PCC 7942 is a model organism for the study of photosynthesis and gene regulation, and for ...
    Structural Analysis of Bordetella pertussis Biofilms by Confocal Laser Scanning Microscopy
    Authors:  Natalia Cattelan, Osvaldo Miguel Yantorno and Rajendar Deora, date: 08/05/2018, view: 98, Q&A: 0
    [Abstract] Biofilms are sessile communities of microbial cells embedded in a self-produced or host-derived exopolymeric matrix. Biofilms can both be beneficial or detrimental depending on the surface. Compared to their planktonic counterparts, biofilm cells display enhanced resistance to killing by environmental threats, chemicals, antimicrobials and host ...
    Determination of Storage (Starch/Glycogen) and Total Saccharides Content in Algae and Cyanobacteria by a Phenol-Sulfuric Acid Method
    Authors:  Tomáš Zavřel, Petra Očenášová, Maria A. Sinetova and Jan Červený, date: 08/05/2018, view: 80, Q&A: 0
    [Abstract] This is a protocol for quantitative determination of storage and total carbohydrates in algae and cyanobacteria. The protocol is simple, fast and sensitive and it requires only few standard chemicals. Great advantage of this protocol is that both storage and total saccharides can be determined in the cellular pellets that were already used for ...
    Direct Visualization of the Multicopy Chromosomes in Cyanobacterium Synechococcus elongatus PCC 7942
    Authors:  Ryudo Ohbayashi, Hirofumi Yoshikawa and Satoru Watanabe, date: 08/05/2018, view: 96, Q&A: 0
    [Abstract] Cyanobacteria are prokaryotic organisms that carry out oxygenic photosynthesis. The fresh water cyanobacterium Synechococcus elongatus PCC 7942 is a model organism for the study of photosynthesis and gene regulation, and for biotechnological applications. Besides several freshwater cyanobacteria, S. elongatus 7942 also contains ...
    Bacterial Microcolonies in Gel Beads for High-throughput Screening
    Author:  Yolanda Schaerli, date: 07/05/2018, view: 1030, Q&A: 0
    [Abstract] High-throughput screening of a DNA library expressed in a bacterial population for identifying potentially rare members displaying a property of interest is a crucial step for success in many experiments such as directed evolution of proteins and synthetic circuits and deep mutational scanning to identify gain- or loss-of-function mutants.
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    Induction of Natural Competence in Genetically-modified Lactococcus lactis
    Authors:  Joyce Mulder, Michiel Wels, Oscar P. Kuipers, Michiel Kleerebezem and Peter A. Bron, date: 07/05/2018, view: 325, Q&A: 0
    [Abstract] Natural competence can be activated in Lactoccocus lactis subsp lactis and cremoris upon overexpression of ComX, a master regulator of bacterial competence. Herein, we demonstrate a method to activate bacterial competence by regulating the expression of the comX gene by using a nisin-inducible promoter in an L. ...
    Quantification of the Composition Dynamics of a Maize Root-associated Simplified Bacterial Community and Evaluation of Its Biological Control Effect
    Authors:  Ben Niu and Roberto Kolter, date: 06/20/2018, view: 726, Q&A: 0
    [Abstract] Besides analyzing the composition and dynamics of microbial communities, plant microbiome research aims to understanding the mechanism of plant microbiota assembly and their biological functions. Here, we describe procedures to investigate the role of bacterial interspecies interactions in root microbiome assembly and the beneficial effects of the ...
    Extraction and 16S rRNA Sequence Analysis of Microbiomes Associated with Rice Roots
    Authors:  Joseph Edwards, Christian Santos-Medellín and Venkatesan Sundaresan, date: 06/20/2018, view: 725, Q&A: 0
    [Abstract] Plant roots associate with a wide diversity of bacteria and archaea across the root-soil spectrum. The rhizosphere microbiota, the communities of microbes in the soil adjacent to the root, can contain up to 10 billion bacterial cells per gram of soil (Raynaud and Nunan, 2014) and can play important roles for the fitness of the host plant. Subsets ...
    Implementation of Blue Light Switchable Bacterial Adhesion for Design of Biofilms
    Authors:  Fei Chen and Seraphine V. Wegner, date: 06/20/2018, view: 581, Q&A: 0
    [Abstract] Control of bacterial adhesions to a substrate with high precision in space and time is important to form a well-defined biofilm. Here, we present a method to engineer bacteria such that they adhere specifically to substrates under blue light through the photoswitchable proteins nMag and pMag. This provides exquisite spatiotemporal remote control ...
    ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803
    Authors:  Joaquín Giner-Lamia, Miguel A. Hernández-Prieto and Matthias E. Futschik, date: 06/20/2018, view: 564, Q&A: 0
    [Abstract] Nitrogen is an essential nutrient for all living organisms. In cyanobacteria, a group of oxygenic photosynthetic bacteria, nitrogen homeostasis is maintained by an intricate regulatory network around the transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, the sets of genes under its control (i.e. ...
    Preparation of Cell-free Synthesized Proteins Selectively Double Labeled for Single-molecule FRET Studies
    Authors:  Mayuri Sadoine, Michele Cerminara, Jörg Fitter and Alexandros Katranidis, date: 06/20/2018, view: 718, Q&A: 0
    [Abstract] Single-molecule FRET (smFRET) is a powerful tool to investigate molecular structures and conformational changes of biological molecules. The technique requires protein samples that are site-specifically equipped with a pair of donor and acceptor fluorophores. Here, we present a detailed protocol for preparing double-labeled proteins for smFRET ...