Microbiology

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    Protocols in Current Issue
    Experimental Setup for a Diffusion Bioreactor to Isolate Unculturable Soil Bacteria
    Authors:  Dhiraj Kumar Chaudhary and Jaisoo Kim, date: 10/05/2019, view: 138, Q&A: 0
    [Abstract] Unculturable bacteria are those bacteria which proliferate in their native habitat but unable to grow or thrive in the normal laboratory media and conditions. The molecular techniques have revealed the significance of these uncultured bacteria in terms of their functional diversity and potential to produce secondary metabolites. To achieve these ...
    Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
    [Abstract] Single-cell RNA-seq (scRNA-seq) has become an established method for uncovering the intrinsic complexity within populations. Even within seemingly homogenous populations of isogenic yeast cells, there is a high degree of heterogeneity that originates from a compact and pervasively transcribed genome. Research with microorganisms such as yeast ...
    Detachment Procedure of Bacteria from Atmospheric Particles for Flow-cytometry Counting
    Authors:  Carolina M. Araya, Alberto Cazorla and Isabel Reche, date: 06/20/2019, view: 741, Q&A: 0
    [Abstract] The protocol separates bacteria from atmospheric particles, obtaining with greater precision their abundance in the atmospheric deposition. This procedure is similar to the one used to separate bacteria in streambed sediments. The detachment procedure consists of a chemical treatment with sodium pyrophosphate and Tween 20 and a physical treatment ...
    Long-term in vitro Culture of Cryptosporidium parvum
    Authors:  Nigel Yarlett and Mary Morada, date: 08/05/2018, view: 2415, Q&A: 0
    [Abstract] Continuous in vitro growth of Cryptosporidium parvum has proved difficult and conventional in vitro culture techniques result in short-term (2-5 days) growth of the parasite resulting in thin-walled oocysts that fail to propagate using in vitro cultures, and do not produce an active infection using ...
    Alphavirus Purification Using Low-speed Spin Centrifugation
    Authors:  Vamseedhar Rayaprolu, Jolene Ramsey, Joseph Che-Yen Wang and Suchetana Mukhopadhyay, date: 03/20/2018, view: 3690, Q&A: 2
    [Abstract] Chemical and sedimentation procedures are used to purify virus particles. While these approaches are successful for wild-type viruses, they are often not feasible for purifying mutant viruses with assembly defects. We combined two published methods (Atasheva et al., 2013; Moller-Tank et al., 2013), to generate a protocol that ...
    Isolation of Commensal Escherichia coli Strains from Feces of Healthy Laboratory Mice or Rats
    Authors:  Tingting Ju and Benjamin P. Willing, date: 03/20/2018, view: 3612, Q&A: 0
    [Abstract] The colonization abundance of commensal E. coli in the gastrointestinal tract of healthy laboratory mice and rats ranges from 104 to 106 CFU/g feces. Although very well characterized, the family that E. coli belongs to has a very homogeneous 16S rRNA gene sequence, making the identification from 16S rRNA ...
    Isolation and Purification of Viruses Infecting Cyanobacteria Using a Liquid Bioassay Approach
    Authors:  Caroline Chénard and Amy M Chan, date: 01/20/2018, view: 3710, Q&A: 0
    [Abstract] The following protocol describes the isolation and purification of viruses infecting cyanobacteria using a liquid bioassay approach. Viruses infecting cyanobacteria are also known as cyanophages. This protocol was written specifically for the isolation of cyanophages infecting freshwater cyanobacteria particularly, cyanobacteria that cannot be ...
    A Bioreactor Method to Generate High-titer, Genetically Stable, Clinical-isolate Human Cytomegalovirus
    [Abstract] Human cytomegalovirus (HCMV) infection is a major cause of morbidity and mortality in transplant patients and a leading cause of congenital birth defects (Saint Louis, 2016). Vaccination and therapeutic studies often require scalable cell culture production of wild type virus, represented by clinical isolates. Obtaining sufficient stocks of ...
    Induction, Isolation and Counting of Akinetes in Aphanizomenon ovalisporum
    Authors:  Assaf Sukenik, Ruth N. Kaplan-Levi, Yehudit Viner-Mozzini, Achsa Lupu and Dotan Sela, date: 05/20/2016, view: 4777, Q&A: 0
    [Abstract] Akinetes are spore-like resting (dormant) cells formed by strains of filamentous cyanobacteria for surviving long periods of unfavorable conditions. During deprivation for potassium, vegetative photosynthetic cells along the filaments of the cyanobacterium Aphanizomenon ovalisporum (A. ovalisporum) (strain ILC-164) differentiate ...
    Establishing a Biofilm Co-culture of Pseudomonas and Aspergillus for Metabolite Extraction
    Authors:  He Zheng, Nancy P. Keller and Yun Wang, date: 12/05/2015, view: 7147, Q&A: 0
    [Abstract] Filamentous fungi and bacteria form mixed-species biofilms in nature and diverse clinical contexts (Frey-Klett et al., 2011; Peleg et al., 2010). The interactions between fungi and bacteria, often mediated by secreted metabolites, have important ramifications for the biology of the interacting partners (Frey-Klett et al. ...



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