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    Protocols in Current Issue
    Transplantation of Fecal Microbiota Shaped by Diet
    Authors:  Keiran H. McLeod, Linda Mason and Eliana Mariño, date: 01/05/2018, view: 90, Q&A: 0
    Alterations in diet and gut microbial ecology underlie the pathogenesis of type 1 diabetes (T1D). In the non-obese diabetic (NOD) mouse, we found high concentrations of bacterial metabolites acetate and butyrate in blood and faeces correlated with ...
    Targeted Genome Editing of Virulent Phages Using CRISPR-Cas9
    Authors:  Marie-Laurence Lemay, Ariane C. Renaud, Geneviève M. Rousseau and Sylvain Moineau, date: 01/05/2018, view: 219, Q&A: 0
    This protocol describes a straightforward method to generate specific mutations in the genome of strictly lytic phages. Briefly, a targeting CRISPR-Cas9 system and a repair template suited for homologous recombination are provided inside a bacterial ...
    Analysis of Direct Interaction between Viral DNA-binding Proteins by Protein Pull-down Co-immunoprecipitation Assay
    Authors:  Ana Lechuga, Mónica Berjón-Otero, Margarita Salas and Modesto Redrejo-Rodríguez, date: 01/05/2018, view: 221, Q&A: 0
    This protocol analyzes the direct interaction between two DNA-binding proteins by pull-down co-immunoprecipitation. One of the proteins is overexpressed in E. coli as HA-tagged recombinant protein and cell-free extracts are ...
    Fatty Acid Content and Composition of Triacylglycerols of Chlorella kessleri
    Authors:  Motohide Aoki and Norihiro Sato, date: 01/05/2018, view: 110, Q&A: 0
    Triacylglycerols (TAGs) are esters formed from one glycerol and three fatty acids. TAGs are induced to accumulate in algal cells under environmental stress conditions including nutrient-limitation, hyperosmosis, and low temperature, for the storage ...
    Bacterial Aggregation Assay in the Presence of Cyclic Lipopeptides
    Authors:  Pengyuan Xiu, Rui Liu, Dechao Zhang and Chaomin Sun, date: 01/05/2018, view: 83, Q&A: 0
    Lipopeptides is an important class of biosurfactants having antimicrobial and anti-adhesive activity against pathogenic bacteria. These include surfactin, fengycin, iturin, bacillomycin, mycosubtilin, lichenysin, and pumilacidin (Arima et al. ...
    Easy and Efficient Permeabilization of Cyanobacteria for in vivo Enzyme Assays Using B-PER
    Authors:  Simon Matthé Erstad and Yumiko Sakuragi, date: 01/05/2018, view: 172, Q&A: 0
    Cyanobacteria are photosynthetic bacteria that thrive in diverse ecosystems and play major roles in the global carbon cycle. The abilities of cyanobacteria to fix atmospheric CO2 and to allocate the fixed carbons to chemicals and biofuels ...
    Transplantation of Fecal Microbiota Shaped by Diet
    Authors:  Keiran H. McLeod, Linda Mason and Eliana Mariño, date: 01/05/2018, view: 90, Q&A: 0
    [Abstract] Alterations in diet and gut microbial ecology underlie the pathogenesis of type 1 diabetes (T1D). In the non-obese diabetic (NOD) mouse, we found high concentrations of bacterial metabolites acetate and butyrate in blood and faeces correlated with protection from disease. We reconstituted germ free (GF) NOD mice with fecal bacteria from protected ...
    Targeted Genome Editing of Virulent Phages Using CRISPR-Cas9
    Authors:  Marie-Laurence Lemay, Ariane C. Renaud, Geneviève M. Rousseau and Sylvain Moineau, date: 01/05/2018, view: 219, Q&A: 0
    [Abstract] This protocol describes a straightforward method to generate specific mutations in the genome of strictly lytic phages. Briefly, a targeting CRISPR-Cas9 system and a repair template suited for homologous recombination are provided inside a bacterial host, here the Gram-positive model Lactococcus lactis MG1363. The CRISPR-Cas9 system is ...
    Analysis of Direct Interaction between Viral DNA-binding Proteins by Protein Pull-down Co-immunoprecipitation Assay
    Authors:  Ana Lechuga, Mónica Berjón-Otero, Margarita Salas and Modesto Redrejo-Rodríguez, date: 01/05/2018, view: 221, Q&A: 0
    [Abstract] This protocol analyzes the direct interaction between two DNA-binding proteins by pull-down co-immunoprecipitation. One of the proteins is overexpressed in E. coli as HA-tagged recombinant protein and cell-free extracts are immunoprecipitated in HA-affinity resin. Cell extracts are treated with nuclease to degrade DNA and RNA, which rules ...
    Fatty Acid Content and Composition of Triacylglycerols of Chlorella kessleri
    Authors:  Motohide Aoki and Norihiro Sato, date: 01/05/2018, view: 110, Q&A: 0
    [Abstract] Triacylglycerols (TAGs) are esters formed from one glycerol and three fatty acids. TAGs are induced to accumulate in algal cells under environmental stress conditions including nutrient-limitation, hyperosmosis, and low temperature, for the storage of metabolic energy and carbon, and also for the consumption of excess energy (e.g., Hirai ...
    Bacterial Aggregation Assay in the Presence of Cyclic Lipopeptides
    Authors:  Pengyuan Xiu, Rui Liu, Dechao Zhang and Chaomin Sun, date: 01/05/2018, view: 83, Q&A: 0
    [Abstract] Lipopeptides is an important class of biosurfactants having antimicrobial and anti-adhesive activity against pathogenic bacteria. These include surfactin, fengycin, iturin, bacillomycin, mycosubtilin, lichenysin, and pumilacidin (Arima et al., 1968; Naruse et al., 1990; Yakimov et al., 1995; Steller and Vater, 2000; ...
    Easy and Efficient Permeabilization of Cyanobacteria for in vivo Enzyme Assays Using B-PER
    Authors:  Simon Matthé Erstad and Yumiko Sakuragi, date: 01/05/2018, view: 172, Q&A: 0
    [Abstract] Cyanobacteria are photosynthetic bacteria that thrive in diverse ecosystems and play major roles in the global carbon cycle. The abilities of cyanobacteria to fix atmospheric CO2 and to allocate the fixed carbons to chemicals and biofuels have attracted growing attentions as sustainable microbial cell factories. A better understanding ...
    Oral Microbiome Characterization in Murine Models
    [Abstract] The oral microbiome has been implicated as a trigger for immune responsiveness in the oral cavity, particularly in the setting of the inflammatory disease periodontitis. The protocol presented here is aimed at characterizing the oral microbiome in murine models at steady state and during perturbations of immunity or physiology. Herein, we describe ...
    Infection of Soybean Plants with the Insect Bacterial Symbiont Burkholderia gladioli and Evaluation of Plant Fitness
    Authors:  Paul Gaube, Martin Kaltenpoth and Laura V. Flórez, date: 12/20/2017, view: 400, Q&A: 0
    [Abstract] To investigate the establishment and consequences of host-microbe interactions, it is important to develop controlled infection assays suitable for each system, as well as appropriate methods to evaluate successful infection and its associated effects. Here, we describe a procedure for bacterial inoculation of soybean plants, followed by the ...
    Rice Black-streaked Dwarf Virus Preparation and Infection on Rice
    Authors:  Zongtao Sun, Hehong Zhang, Kaili Xie, Xiaoxiang Tan, Hengmu Zhang and Jianping Chen, date: 12/20/2017, view: 317, Q&A: 0
    [Abstract] Rice black-streaked dwarf virus (RBSDV), a member of genus Fijivirus in the family Reoviridae, infects rice, maize, barley and wheat, and can seriously affect crop yields. RBSDV is transmitted by the small brown planthopper (Laodelphax striatellus, SBPH) in a persistent manner. RBSDV has 10 linear dsRNA genomic segments, ...
    Lentiviral Knockdown of Transcription Factor STAT1 in Peromyscus leucopus to Assess Its Role in the Restriction of Tick-borne Flaviviruses
    Authors:  Adaeze O. Izuogu and R. Travis Taylor, date: 12/05/2017, view: 376, Q&A: 0
    [Abstract] Cellular infection with tick-borne flaviviruses (TBFVs) results in activation of the interferon (IFN) signaling pathway and subsequent upregulation of numerous genes termed IFN stimulated genes (ISGs) (Schoggins et al., 2011). Many ISGs function to prevent virus pathogenesis by acting in a broad or specific manner through protein-protein ...