Box: Freezing and shipping skin-derived precursors (SKPs)
Taken from: Isolation of skin-derived precursors (SKPs) and differentiation and enrichment of their Schwann cell progeny
Published in: Nature Protocols
Monday, 21 April 2008
Freezing and shipping skin-derived precursors (SKPs)
Box: Freezing and shipping skin-derived precursors (SKPs)
Taken from: Isolation of skin-derived precursors (SKPs) and differentiation and enrichment of their Schwann cell progeny
Published in: Nature Protocols
Friday, 18 April 2008
Regeneration test of three rice varieties
Image Title: Regeneration test of three rice varieties. (a) A japonica variety, "Nipponbare," that has a high-regeneration frequency. (b) A japonica variety, "Koshihikari," that has a low-regeneration frequency. (c) An indica variety, "Kasalath," that exhibits a high-regeneration frequency.
Taken from: A protocol for Agrobacterium-mediated transformation in rice
Sunday, 13 April 2008
Transformation of Agrobacterium
Box: Transformation of Agrobacterium
From: Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants
Published in: Nature Protocols
YEB medium Yeast extract (1.0 g l-1), beef extract (5.0 g l-1), peptone (5.0 g l-1), sucrose (5.0 g l-1), MgSO47H2O (0.5 g l-1), pH 7.0. Also include the proper antibiotic resistance selection drug for the FP fusion construct carried by these bacteria.
The Boxed protocol is for a reagent used in the Nature Protocol. It is based on the method described in Storage of competent cells for Agrobacterium transformation.
From: Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants
Published in: Nature Protocols
YEB medium Yeast extract (1.0 g l-1), beef extract (5.0 g l-1), peptone (5.0 g l-1), sucrose (5.0 g l-1), MgSO47H2O (0.5 g l-1), pH 7.0. Also include the proper antibiotic resistance selection drug for the FP fusion construct carried by these bacteria.
The Boxed protocol is for a reagent used in the Nature Protocol. It is based on the method described in Storage of competent cells for Agrobacterium transformation.
Thursday, 10 April 2008
Quantifying pollen viability in Arabidopsis
Box: Quantifying pollen viability
From: Fluorescent Arabidopsis tetrads: a visual assay for quickly developing large crossover and crossover interference data sets
Published in: Nature Protocols
The PGM solution used in the Boxed protocol is prepared as follows:
To 950 ml H2O, add 170 g sucrose (17% wt/vol), 2 ml 1 M CaCl2 (2 mM), 3.25 ml 0.5 M boric acid (1.625 mM) and 100 mul Triton-X (0.1% vol/vol).
Deriving Linkage Distance and Gene Order From Three-Point Crosses contains some background information about the ABC genotype reference...
From: Fluorescent Arabidopsis tetrads: a visual assay for quickly developing large crossover and crossover interference data sets
Published in: Nature Protocols
The PGM solution used in the Boxed protocol is prepared as follows:
To 950 ml H2O, add 170 g sucrose (17% wt/vol), 2 ml 1 M CaCl2 (2 mM), 3.25 ml 0.5 M boric acid (1.625 mM) and 100 mul Triton-X (0.1% vol/vol).
Deriving Linkage Distance and Gene Order From Three-Point Crosses contains some background information about the ABC genotype reference...
Tuesday, 8 April 2008
BIO-RAD protein assay
Box: BIO-RAD protein assay
Taken From: Southwestern blotting in investigating transcriptional regulation
Published in: Nature Protocols
This is a short protocol for determining protein concentrations.
The main protocol is open access during 2008 being part of the sample issue.
Taken From: Southwestern blotting in investigating transcriptional regulation
Published in: Nature Protocols
This is a short protocol for determining protein concentrations.
The main protocol is open access during 2008 being part of the sample issue.
Monday, 7 April 2008
Preparation of the per-O-trimethylsilylated glucoside 1a and 1b
Box: Preparation of the per-O-trimethylsilylated glucoside 1a and 1b
Taken from: Regioselective one-pot protection of glucose
Published in: Nature Protocols
Glucosides 1a and 1b, shown in Figure 1 of the protocol, are the starting materials for a series of reactions to protect different combinations of hydroxyl groups in the glucose molecule.
Taken from: Regioselective one-pot protection of glucose
Published in: Nature Protocols
Glucosides 1a and 1b, shown in Figure 1 of the protocol, are the starting materials for a series of reactions to protect different combinations of hydroxyl groups in the glucose molecule.
Sunday, 6 April 2008
Tissue preparation, microscopy methods and imaging techniques
Box: Tissue preparation, microscopy methods and imaging techniques
Taken from: Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images
Published in: Nature Protocols
The correct links for the figures are:
Figure 4
Figure 5
Taken from: Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images
Published in: Nature Protocols
The correct links for the figures are:
Figure 4
Figure 5
Saturday, 5 April 2008
Removal of internal peptides by biotinylation and streptavidin purification
Box: Removal of internal peptides by biotinylation and streptavidin purification
Taken from: Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization
Published in: Nature Protocols
The boxed method was originally published in Nature Methods in an article entitled "Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides".
One of the problems with looking at all of the proteins in a cell is that there are a lot of them! A further complication is that most methods of identifying the proteins by mass spectroscopy involve chopping them up into smaller pieces before HPLC separation. This protocol is a way to simplify this mixture by selectively isolating the "pieces" corresponding to the N-termini.
Taken from: Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization
Published in: Nature Protocols
The boxed method was originally published in Nature Methods in an article entitled "Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides".
One of the problems with looking at all of the proteins in a cell is that there are a lot of them! A further complication is that most methods of identifying the proteins by mass spectroscopy involve chopping them up into smaller pieces before HPLC separation. This protocol is a way to simplify this mixture by selectively isolating the "pieces" corresponding to the N-termini.
Confirmation of the Mutation by RFLP Analysis
Box: Confirmation of the Mutation by RFLP Analysis
Taken from: Rapid identification of unknown heteroplasmic mutations across the entire human mitochondrial genome with mismatch-specific Surveyor Nuclease
Published in: Nature Protocols
RFLP Analysis stands for: Restriction fragment length polymorphism analysis.
Taken from: Rapid identification of unknown heteroplasmic mutations across the entire human mitochondrial genome with mismatch-specific Surveyor Nuclease
Published in: Nature Protocols
RFLP Analysis stands for: Restriction fragment length polymorphism analysis.
Preparation of bovine thymocytes
Box: Preparation of bovine thymocytes
Taken from: Flow cytometry and FISH to measure the average length of telomeres (flow FISH)
Published in: Nature Protocols
I really like the first step in the boxed method: "Arrange for fresh bovine thymus through a local meat packer. Request the collection of 2–3 small (e.g., cubic inch) pieces in a 1,000 ml container filled with digest solution. Arrange for pickup and process immediately."
FISH is another one of these very clever acronyms that make it so that if you search for them in PubMed or Scopus (or anywhere else for that matter) you are initially puzzled by the presence of large numbers of articles that are completely uninteresting to you. In this case FISH stands for fluorescent in situ hybridization.
[moderately amusing aside: the first search that I EVER did on Medline was for PET (as in positron emission tomography), but of course I got quite a lot more than that...]
Taken from: Flow cytometry and FISH to measure the average length of telomeres (flow FISH)
Published in: Nature Protocols
I really like the first step in the boxed method: "Arrange for fresh bovine thymus through a local meat packer. Request the collection of 2–3 small (e.g., cubic inch) pieces in a 1,000 ml container filled with digest solution. Arrange for pickup and process immediately."
FISH is another one of these very clever acronyms that make it so that if you search for them in PubMed or Scopus (or anywhere else for that matter) you are initially puzzled by the presence of large numbers of articles that are completely uninteresting to you. In this case FISH stands for fluorescent in situ hybridization.
[moderately amusing aside: the first search that I EVER did on Medline was for PET (as in positron emission tomography), but of course I got quite a lot more than that...]
Separation of dendritic cells
Box: Separation of dendritic cells
Taken from: Collection of lymph-borne dendritic cells in the rat
Published in: Nature Protocols
The method described in box would be performed after you had collected lymph from the rat (the procedure of the main protocol).
Taken from: Collection of lymph-borne dendritic cells in the rat
Published in: Nature Protocols
The method described in box would be performed after you had collected lymph from the rat (the procedure of the main protocol).
Examples of DNA isolation protocols
Box: Examples of DNA isolation protocols
Taken from: DNA methylation: Bisulphite modification and analysis
Published in: Nature Protocols
The abovementioned box contains four short protocols for isolating DNA from (1) tissue samples and cell lines, (2) Paraffin block samples, (3) Slide samples, and (4) small numbers of cultured cells (103-105) after isolation of RNA using TRIzol.
You might used your isolated DNA for any number of things, but in this protocol the idea is to find sites of DNA methylation.
Quote from the abstract: "The process of bisulphite treatment exploits the different sensitivities of cytosine and 5-methylcytosine (5-MeC) to deamination by bisulphite under acidic conditions—in which cytosine undergoes conversion to uracil, whereas 5-MeC remains unreactive."
Taken from: DNA methylation: Bisulphite modification and analysis
Published in: Nature Protocols
The abovementioned box contains four short protocols for isolating DNA from (1) tissue samples and cell lines, (2) Paraffin block samples, (3) Slide samples, and (4) small numbers of cultured cells (103-105) after isolation of RNA using TRIzol.
You might used your isolated DNA for any number of things, but in this protocol the idea is to find sites of DNA methylation.
Quote from the abstract: "The process of bisulphite treatment exploits the different sensitivities of cytosine and 5-methylcytosine (5-MeC) to deamination by bisulphite under acidic conditions—in which cytosine undergoes conversion to uracil, whereas 5-MeC remains unreactive."
Preparation of celery juice extract
Box: Preparation of celery juice extract
Taken from: A protocol for TILLING and Ecotilling in plants and animals
Published in: Nature Protocols
TILLING and Ecotilling sound very agricultural, but (possibly disappointingly) TILLING actually stands for "Targeting-Induced Local Lesions IN Genomes".
So why would you (ever) want to make a celery juice extract? It turns out that celery juice contains an enzyme, a single-strand-specific nuclease, and the extract is used as a reagent in the TILLING protocol.
Here is a picture showing its activity:
Gel image showing the effect of the amount of celery juice extract used to cleave mismatches
This figure was originally published in Nucleic Acids Research.
Taken from: A protocol for TILLING and Ecotilling in plants and animals
Published in: Nature Protocols
TILLING and Ecotilling sound very agricultural, but (possibly disappointingly) TILLING actually stands for "Targeting-Induced Local Lesions IN Genomes".
So why would you (ever) want to make a celery juice extract? It turns out that celery juice contains an enzyme, a single-strand-specific nuclease, and the extract is used as a reagent in the TILLING protocol.
Here is a picture showing its activity:
Gel image showing the effect of the amount of celery juice extract used to cleave mismatches
This figure was originally published in Nucleic Acids Research.
Introducing Me and My Lunch Box
Who am I?
Bronwen Dekker, Associate Editor at Nature Protocols and a blogger on the Nature Network.
Why am I creating (yet) another blog?
Well. I wanted a place to try out posting small snippets of content from our site that is available without a site license. Some of it will probably get added to the "Nature Protocols News" type posts in the Nature Network blog, but the people that read that blog might get a bit annoyed if I am posting protocols content every day!
Bronwen Dekker, Associate Editor at Nature Protocols and a blogger on the Nature Network.
Why am I creating (yet) another blog?
Well. I wanted a place to try out posting small snippets of content from our site that is available without a site license. Some of it will probably get added to the "Nature Protocols News" type posts in the Nature Network blog, but the people that read that blog might get a bit annoyed if I am posting protocols content every day!
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