Gene Essentiality: Methods and Protocols by Long Jason Lu

By Long Jason Lu

This quantity opens through masking major varieties of techniques typical to figure out crucial genes: single-gene knockouts and transposon mutagenesis, in either prokaryotes and Candida albicans. Given the numerous development within the computational predictions of microbial crucial genes, the second one 1/2 the e-book examines 4 major different types of methods: comparative genomics, supervised computer studying, constraint-based tools, and corrections of transposon mutagenesis information, in addition to databases and servers which are frequently utilized in learning gene essentiality. Written within the hugely profitable Methods in Molecular Biology sequence layout, chapters comprise an advent to their respective subject matters, lists of the mandatory fabrics and reagents, step by step, easily reproducible laboratory protocols, and pointers on troubleshooting and keeping off recognized pitfalls.

Authoritative and up to date, Gene Essentiality: equipment and Protocols will relief researchers who desire to additional our wisdom during this important box of study.

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Extra resources for Gene Essentiality: Methods and Protocols

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In addition, we developed tools for identification of synthetic lethal gene combinations by systematic construction of double-gene knockout mutants. We introduce these methods herein. Key words Gene deletion, Escherichia coli, FLP recombinase, FRT, Gene knockout, Homologous recombination, In-frame deletion, Lambda Red recombinase, Essential genes, KEIO collection, ASKA collection 1 Introduction Defining gene essentiality is not simple for it depends on a variety of physiological properties, such as growth media, temperature, and other environmental factors, as well as on genetic background.

Bryan G, Garza D, Hartl D (1990) Insertion and excision of the transposable element mariner in Drosophila. Genetics 125:103–114 12. Lampe DJ, Churchill MEA, Robertson HM (1996) A purified mariner transposase is sufficient to mediate transposition in vitro. EMBO J 15:5470–5479 13. Lampe DJ, Akerley BJ, Rubin EJ, Mekalanos JJ, Robertson HM (1999) Hyperactive transposase mutants of the Himar1 mariner transposon. Proc Natl Acad Sci U S A 96: 11428–11433 14. Barquist L, Boinett CJ, Cain AK (2013) Approaches to querying bacterial genomes with transposon-insertion sequencing.

Replace DNA with sterile ddH2O as a control (see Note 7). 5. Place the block on ice and spread 100 μl of each transformation on BHI agar plates (see Note 8) containing 500 μg/ml kanamycin. Incubate the plates at 37 °C for 2 days under microaerobic conditions. 3 Identification of Essential Genes 1. Check transformants on kanamycin plates. If no transformants are present, the target gene is identified as an essential gene candidate. 2. If transformants are present on the kanamycin plates, record the approximate number of total colonies on each plate (see Note 9).

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