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Yeast handbook

Manufactured by Takara Bio
Sourced in United States, Japan

The Yeast Handbook is a comprehensive reference guide published by Takara Bio. It provides detailed information on the characteristics and applications of various yeast strains.

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10 protocols using yeast handbook

1

Identifying TaPHT1;9-4B Promoter Regulators

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Total RNAs (2 μg) isolated from the roots of wheat seedlings grown in Pi‐deficient medium for 8 d were used to construct a cDNA library for yeast‐one‐hybrid (Y1H) assay to identify potential trans‐factors binding to the promoter region of TaPHT1;9‐4B, which was amplified from the cv Zhoumai 18. Screening this library led to the finding of the transcription factor TaMYB4‐7D capable of binding to the TaPHT1;9‐4B promoter. Details of the screening and related validation experiments are described in Methods S1. The transcriptional activation potency of TaMYB4‐7D was tested in the yeast strain AH109 as described in the Yeast Handbook (Clontech, Palo Alto, CA, USA). Functional analysis of TaMYB4‐7D by BSMV‐VIGS is outlined in Methods S1.
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2

Yeast Culture and Transformation

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Yeast strains were grown overnight at 30°C, with shaking at 250 RPM in standard yeast extract–peptone–dextrose (YPD) or synthetic selective media supplemented with dextrose and lacking appropriate amino acids for plasmid maintenance. Yeast was transformed by the Li-Acetate method according to the Clontech yeast handbook.
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3

Yeast-Based Transcription Factor Screening

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Yeast (Saccharomyces cerevisiae) strain Y1HGOLD (MAT α) was used as the
donor strain to express the TF library containing fusion proteins of GAL4-AD-TF. The components of
yeast complete medium and different synthetic drop-out (SD) media were obtained from Clontech and
prepared according to the manufacturer's instructions.
Promoter fragments of CUC2, LAS, MiR164c, and
STM were amplified from genomic DNA using specific primers (Supplementary Table
S12). The fragments were verified by sequencing and cloned into pAbAi (Clontech, Mountain View, CA,
USA). All the bait plasmids were linearized by BstBI and were integrated into yeast
strain Y1HGOLD using PEG-mediated transformation according to the user manual (Yeast Hand
Book
; Clontech, PT3024-1). Transformants were selected on media lacking uracil, verified by
PCR using a promoter-specific primer and a yeast chromosome primer (Supplementary Table S12), and
tested for auto-activation according to the manufacturer's instructions.
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4

Yeast Two-Hybrid Interaction Assay

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The coding regions of genes were amplified and cloned into the Y2H prey vector pGADT7 or bait vector pGBDT7 (Clontech). The pGADT7 and pGBDT7 constructs were then co-transformed into Gold yeast (Saccharomyces cerevisiae) following the Yeast Handbook (Clontech). The resultant yeast strains were grown on SD–Leu/–Trp plates for 3 d at 30 ºC. For each pair of interaction tests, five individual clones were mixed in 60 µl of 0.9% NaCl and diluted 10-, 100-, and 1000-fold. The dilution series were then spotted on the selective media -LTH (SD–Leu/–Trp/–His) or -LTHA (SD–Leu/–Trp/–His/–Ade) containing X-α-gal (40 µg ml–1).
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5

Two-Hybrid Assay for COP1-RGL2 Interaction

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Y2H assays were performed using the Matchmaker GAL4 two-hybrid system (Clontech, Mountain View, CA, USA). The FL and/or partial (RING; aa 1–104, coiled-coil [CC]; aa 121–213, WD-40 repeat; aa 371–675) cDNAs of COP1 were obtained by RT-PCR from WT (Col) plants (Yu et al., 2008 (link)) and cloned into the pGBK vector (as baits), and the FL RGL2 cDNA was cloned into the pGAD vector (as prey). Yeast (strain AH109) cotransformation was performed according to the Yeast Handbook (Clontech). An anti-HA (Roche, Basel, Switzerland) and an anti-myc (kindly provided by Xing Wang Deng) antibodies were used to check the expression of AD and BD fusion proteins.
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6

Yeast Two-Hybrid Protein Interaction Assay

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For the confirmation assays, the OSDLa and DcRAD51D coding sequences were inserted into the vectors pGADT7 and pGBKT7, respectively. The two plasmids were cotransformed into Y2HGold yeast cells to confirm their interactions. The transformants were grown in SD-Trp-Leu-His-Ade/X-α-Gal/AbA media at 30 °C for 3–5 days. Detailed procedures from the Yeast Handbook (Clontech, Japan) were followed. These assays were repeated at least three times.
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7

Yeast Two-Hybrid Assays for Protein Interactions

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Yeast two-hybrid assays were performed using the Matchmaker GAL4 two-hybrid system (Clontech). The full and partial cDNAs of each gene were cloned into the pGADT7 and pGBKT7 vectors as prey and bait, respectively. The full and partial (RING, aa 1–104; CC, aa 121–213; WD40, aa 371–675) cDNAs of COP1 were cloned into the pGBK vector (as baits)23 (link). FKF1 was cloned into the pGAD vector (as prey) with full and partial cDNAs (LOV, aa 1–174; LOV+F-box, aa 1–283; F-box+KELCH, aa 174–618; KELCH, aa 283–618)11 (link). The clones were co-transformed into the yeast strain AH109. The pBridge vector (Clontech) was used for yeast three-hybrid assays. COP1 or SPA1 cDNAs were cloned into the multi-cloning site I of the pBridge vector, in which the binding domain BD-COP1 or BD-SPA1 fusion protein was expressed. Then, FKF1 was cloned into multi-cloning site II of the pBridge vector, in which FKF1 expression was controlled by the Met-repressible pMET25 promoter. These vectors were co-transformed into the yeast strain AH109. Yeast transformation was performed according to the Yeast Handbook (Clontech). The colonies were used for yeast cell growth assay, and a liquid assay using chlorophenol red-β-D-galactoside (CPRG) was used to measure β-galactosidase activity.
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8

SPAK Regulatory Domain Yeast Two-Hybrid

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The regulatory domain of mouse SPAK (residues 353 to 556) fused to the GAL4 activating domain in pACT2 was originally isolated from a Clontech mouse brain library (Piechotta, et al., 2002 (link)). The clone was re-transformed into PJ69-4A cells (James, et al., 1996 (link))) according to standard yeast handling procedures (Yeast Handbook, Clontech) and plated on –LEU plates. Sense and anti-sense oligonucleotides were purchased from Sigma Genosys. Upon annealing, the oligonucleotides create overhanging 5’ EcoRI and 3’ BamHI sites that are directly used for ligation. The annealed adaptors encode 14 amino acid peptides that includes EF (EcoRI site), QLVG (linker), RFQVT or mutant (PF2 target peptides), and SSK followed by a stop codon. The QLVGRFQVTSSK sequence is original to the SPAK binding site in WNK4 ((Piechotta, et al., 2003 (link); Villa, et al., 2007 (link)). The adaptors are ligated downstream of the Gal4 binding domain in the pGBDUc2 vector. Yeast cells containing the regulatory domain of SPAK in pACT2 were then transformed with individual peptide clones in pGBDUc2 and plated on double dropout -LEU, -URA plates. Yeast clones were then re-streaked on double-dropout plates as controls and triple dropout –LEU, -URA, -His, 2 mM 3-amino-1,2,4-triazole plates.
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9

Yeast Two-Hybrid Assay of ZmSMC3 and ZmCENH3

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The coding sequence of ZmSMC3 was divided into three fragments: ZmSMC3-N (1 to 1,950 bp), ZmSMC3-M (901 to 2,700 bp), and ZmSMC3-C (1,951 to 3,615 bp). These three truncated coding sequences were inserted into the pGADT7 vector, and the full-length coding sequence of ZmCENH3 was inserted into the pGBKT7 vector. A yeast two-hybrid assay was conducted with the Matchmaker Gold Yeast Two-Hybrid system (catalog no. 630489; Clontech) using yeast strain Y2HGOLD. Detailed procedures are described in the Yeast Handbook (Clontech).
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10

Plasmid Construction for Giardia Gene Expression

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The plasmids used in this study were constructed by amplifying the glenth coding sequence from giardial genomic DNA and cloned in multicopy URA3 or HIS3 vectors. Expression was driven by the MET25 promoter. DNA manipulations were performed using standard techniques, employing T4 DNA polymerase-mediated ligations in Escherichia coli. Amino acid substitutions were made using the QuikChange XL site-directed mutagenesis kit (Stratagene, La Jolla, CA) according to the manufacturer’s instructions. All restriction enzymes were purchased from New England Biolabs (Ipswich, MA). Yeast was transformed by the Li-Acetate method following the Clontech yeast handbook.
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