Microbiology

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    Protocols in Current Issue
    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 ...
    Development of an Efficient Transformation System for Halotolerant Yeast Debaryomyces hansenii CBS767
    Authors:  Anu P. Minhas and Dipanwita Biswas, date: 09/05/2019, view: 154, Q&A: 0
    [Abstract] Debaryomyces hansenii is one of the most osmotolerant and halotolerant yeasts. Further, its association with traditional cheese and meat products imparting special flavors to these products project this yeast with enormous biotechnological potential in the agrofood sector. However, lack of an efficient transformation system in D. hansenii ...
    Measurement of the Length of the Integrated Donor DNA during Bacillus subtilis Natural Chromosomal Transformation
    Authors:  Ester Serrano and Begoña Carrasco, date: 08/20/2019, view: 259, Q&A: 0
    [Abstract] For natural transformation to occur, bacterial cells must first develop a programmed physiological state called competence. Competence in Bacillus subtilis, which occurs only in a fraction of cells, is a transient stress response that allows cells to take up DNA from the environment. During natural chromosomal transformation, the ...
    Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coli genomes
    Authors:  Takahiro Masuda, Nobuaki Kono, Masaru Tomita and Kazuharu Arakawa, date: 08/05/2019, view: 344, Q&A: 0
    [Abstract] Most bacterial genomes have biased nucleotide composition, and the asymmetry is considered to be caused by a single-stranded DNA (ssDNA) deamination arising from the bacterial replication machinery. In order to evaluate the relationship experimentally, the position and frequency of ssDNA formed during replication must be verified clearly. Although ...
    Imaging Gene Expression Dynamics in Pseudomonas fluorescens In5 during Interactions with the Fungus Fusarium graminearum PH-1
    Authors:  Rosanna C. Hennessy, Peter Stougaard and Stefan Olsson, date: 06/20/2019, view: 690, Q&A: 0
    [Abstract] Genomics, transcriptomics and metabolomics are powerful technologies for studying microbial interactions. The main drawback of these methods is the requirement for destructive sampling. We have established an alternative but complementary technique based on a microplate system combined with promoter fusions for visualizing gene expression in space ...
    Multiple Modification of Chromosomal Loci Using URA5.3 Selection Marker in the Unicellular Red Alga Cyanidioschyzon merolae
    Authors:  Tokiaki Takemura, Sousuke Imamura, Yuki Kobayashi and Kan Tanaka, date: 04/05/2019, view: 931, Q&A: 0
    [Abstract] The unicellular red alga Cyanidioschyzon merolae has been used as a eukaryotic photosynthetic model for various basic and applied studies. Although the nuclear genome of C. merolae can be modified by homologous recombination with exogenously introduced DNA, it has been difficult to modify multiple chromosome loci within the same ...
    Quantification of Hepatitis B Virus Covalently Closed Circular DNA in Infected Cell Culture Models by Quantitative PCR
    Authors:  Bingqian Qu and Stephan Urban, date: 04/05/2019, view: 1195, Q&A: 0
    [Abstract] Persistence of the human hepatitis B virus (HBV) requires the maintenance of covalently closed circular (ccc)DNA, the episomal genome reservoir in nuclei of infected hepatocytes. cccDNA elimination is a major aim in future curative therapies currently under development. In cell culture based in vitro studies, both hybridization- and ...
    Measuring Homologous Recombination Rates between Chromosomal Locations in Salmonella
    Authors:  Gerrit Brandis, Sha Cao and Diarmaid Hughes, date: 02/05/2019, view: 1238, Q&A: 0
    [Abstract] Homologous recombination between two similar DNA molecules, plays an important role in the repair of double-stranded DNA breaks. Recombination can occur between two sister chromosomes, or between two locations of similar sequence identity within the same chromosome. The assay described here is designed to measure the rate of homologous ...
    Assessing Yeast Cell Survival Following Hydrogen Peroxide Exposure
    Authors:  Khoa Tran and Erin M. Green, date: 01/20/2019, view: 2285, Q&A: 0
    [Abstract] In the presence of oxidative stress, cellular defense systems that can detoxify reactive oxygen species are activated through multiple signaling cascades and transcriptional reprogramming. The budding yeast Saccharomyces cerevisiae has served as an excellent model for genetically-identifying factors important for the response to oxidative ...
    Quantitative Transformation Efficiency Assay for Bacillus subtilis
    Authors:  Christian L. Loyo and Briana M. Burton, date: 12/05/2018, view: 1731, Q&A: 0
    [Abstract] Bacillus subtilis (B. subtilis) is a model Gram-positive organism used to study a variety of physiological states and stress responses, one of which is the development of competence. Competence refers to the physiological state of a cell which allows it to be transformed naturally. Through induction of competence, the efficiency ...



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