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  Section: Biotechnology Methods » Molecular Biology
 
 
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Karyotype Analysis

 
     
 
Content
Molecular Biology
  The Central Dogma
  Protein Synthesis in Cell Free Systems
  Chromosomes
  Polytene Chromosomes of Dipterans
  Salivary Gland Preparation (Squash Technique)
  Extraction of Chromatin
  Chromatin Electrophoresis
  Extraction and Electrophoresis of Histones
  Karyotype Analysis
  In Situ Hybridization
  Culturing Peripheral Blood Lymphocytes
  Microslide Preparation of Metaphases for In-Situ Hybridization
  Staining Chromosomes (G-Banding)
  Nucleic Acids
  Extraction of DNA from Bovine Spleen
  Purification of DNA
  Characterization of DNA
  DNA-Dische Diphenylamine Determination
  Melting Point Determination
  CsCl-Density Separation of DNA
  Phenol Extraction of rRNA (Rat liver)
  Spectrophotometric Analysis of rRNA
  Determination of Amount of RNA by the Orcinol Method
  Sucrose Density Fractionation
  Nucleotide Composition of RNA
  Isolation of Genomic DNA—DNA Extraction Procedure
  Isolation of Genomic DNA from Bacterial Cells
  Preparation of Genomic DNA from Bacteria
  Extraction of Genomic DNA from Plant Source
  Extraction of DNA from Goat Liver
  Isolation of Cotton Genomic DNA from Leaf Tissue
  Arabidopsis Thaliana DNA Isolation
  Plant DNA Extraction
  Phenol/Chloroform Extraction of DNA
  Ethanol Precipitation of DNA
  Isolation of Mitochondrial DNA
  Isolation of Chloroplast DNA
  DNA Extraction of Rhizobium (CsCl Method)
  Isolation of Plasmids
  RNA Isolation
  Preparation of Vanadyl-Ribonucleoside Complexes that Inhibit Ribonuclease Activity
  RNA Extraction Method for Cotton
  Isolation of RNA from Bacteroids
  Isolation of RNA from Free-Living Rhizobia
  Estimation of DNA purity and Quantification
  Fungal DNA Isolation
  Methylene Blue DNA Staining
  Transformation
  Blotting Techniques—Southern, Northern, Western Blotting
  Preparing the Probe
  Southern Blotting (First Method)
  Southern Blotting (Second Method)
  Western Blotting
  Western Blot Analysis of Epitoped-tagged Proteins using the Chemifluorescent Detection Method for Alkaline Phosphatase-conjugated Antibodies
  Southern Blot
  Southern Analysis of Mouse Toe/Tail DNA
  Northern Blotting
  Restriction Digestion Methods—Restriction Enzyme Digests
  Restriction Digestion of Plasmid, Cosmid, and Phage DNAs
  Manual Method of Restriction Digestion of Human DNA
  Preparation of High-Molecular-Weight Human DNA Restriction Fragments in Agarose Plugs
  Restriction Enzyme Digestion of DNA
  Electroelution of DNA Fragments from Agarose into Dialysis Tubing
  Isolation of Restriction Fragments from Agarose Gels by Collection onto DEAE Cellulose
  Ligation of Insert DNA to Vector DNA
  PCR Methods (Polymerase Chain Reaction)
  Polymerase Chain Reaction
  DNA Amplification by the PCR Method

Materials
  • Fresh venous blood
  • Heparinized syringes
  • Eagle’s spinner modified media with PHA
  • Culture flasks
  • Tissue culture grade incubator at 37°C
  • 10 mg/µL Colcemid
  • Clinical centrifuge and tubes
  • 0.075 M KCl
  • Absolute methanol and glacial acetic acid (3:1 mixture, prepared fresh)
  • Dry ice
  • Slides, cover slips and permount
  • Alkaline solution for G-banding
  • Saline-citrate for G-banding
  • Ethanol (70% and 95% (v/v))
  • Giemsa stain

Procedure

Draw 5 mL of venous blood into a sterile syringe containing 0.5 mL of sodium heparin (1000 units/mL). The blood may be collected in a heparinized vacutainer, and transferred to a syringe.
  1. Bend a clean, covered 18-gauge needle to a 45° angle and place it on the syringe. Invert the syringe (needle pointing up, plunger down), and stand it on end for 1½ to 2 hours at room temperature. During this time the erythrocytes settle by gravity, leaving approximately 4 mL of leukocyte-rich plasma on the top, and a white buffy coat of leukocytes in the middle.
  2. Carefully tip the syringe (do not invert) and slowly expel the leukocyte-rich plasma and the fluffy coat into a sterile tissue culture flask containing 8 mL of Eagle’s spinner modified media supplemented with 0.1 mL of phytohemaglutin (PHA).
  3. Incubate the culture for 66–72 hours at 37°C. Gently agitate the culture once or twice daily during the incubation period.
  4. Add 0.1 mL of colcemid (10 micrograms/mL) to the culture flasks and incubate for an additional 2 hours.
  5. Transfer the colcemid-treated cells to a 15-mL centrifuge tube and centrifuge at 225 xg for 10 minutes.
  6. Aspirate and discard all but 0.5 mL of the supernatant. Gently tap the bottom of the centrifuge tube to resuspend the cells in the remaining 0.5 mL of culture media.
  7. Add 10 mL of 0.075 M KCl, dropwise at first, and then with gentle agitation to the centrifuge tube. Gently mix with each drop. Start timing the next step immediately with the first drop of KCl.
  8. Let the cells stand exactly 6 minutes in the hypotonic KCl. The hypotonic solution should not be in contact with the cells in excess of 15 minutes from the time it is added.
  9. Centrifuge the cells at 225 xg for 6 minutes. Aspirate the KCl and discard all but 0.5 mL of the supernatant. Gently resuspend the cells in this small volume of fluid.
  10. Add 10 mL freshly prepared fixative, dropwise at first and then with gentle agitation. Gentle and continuous agitation is important at this step to prevent clumping of the cells. If the cells were not properly resuspended in step 10, the cells will clump beyond any further use.
  11. Allow the cells to stand in fixative at room temperature for 30 minutes.
  12. Centrifuge at 200 xg for 5 minutes and remove all but 0.5 mL of supernatant. Resuspend the cells in fresh fixative.
  13. Wash the cells twice more in 10-mL volumes of fixative. Add the fixative slowly, recentrifuge, and aspirate the fixative as previously directed. The fixed, pelleted cells may be stored for several weeks at 4°C.
  14. Resuspend the pellet of cells in just enough fixative to cause a slightly turbid appearance.
  15. Prop a piece of dry ice against the side of a styrofoam container and lace a clean slide onto the dry ice to chill the slide. Use a siliconized Pasteur pipette to draw up a few drops of the suspended cells and drop the cells onto the surface of the chilled slide. The spreading of the chromosomes may be enhanced by dropping the cell suspension from a height of at least 12 inches. As soon as the cells strike the slide, blow hard on the slide to rapidly spread the cells.
  16. Remove the slides from the dry ice and allow them to air dry. Perform the desired banding and/or staining procedures. Preparation of chromosomes for karyotype analysis can be performed in a number of ways, and each will yield differing pieces of information. The chromosomes may be stained with aceto-orcein, feulgen, or a basophilic dye such as toluidine blue or methylene blue if only the general morphology is desired. If more detail is desired, the chromosomes can be treated with various enzymes in combination with stains to yield banding patterns on each chromosome. These techniques have become commonplace and will yield far more diagnostic information than giemsa stain alone (the most commonly used process). A band is an area of a chromosome that is clearly distinct from its neighboring area, but may be lighter or darker than its neighboring region. The standard methods of banding are the Q, G, R, and C banding techniques. These are defined as follows:
    • Q-banding
      1. Quinacrine stain
      2. Fluorescence microscopy
    • G-banding
      1. Giemsa stain
      2. Additional conditions
        1. Heat hydrolysis
        2. Trypsin treatment
        3. Giemsa at pH 9.0
    • R-banding
      1. Giemsa or acridine orange
      2. Negative bands of Q and G reversed
      3. Heat hydrolysis in buffered salt
    • C-banding
      1. Giemsa stain
      2. Pretreatment with BaOH or NaOH followed by heat and salt.
        The following directions are for a G-banding:
    • Treat fixed and flamed slides in alkaline solution, room temperature for
      30 seconds.
    • Rinse in saline-citrate solution, 3 changes for 5–10 minutes each.
    • Incubate in saline-citrate solution, 65°C for 60–72 hours.
    • Treat with 3 changes of 70% ethanol and 3 changes of 95% ethanol (3 minutes) each.
    • Air dry.
    • Stain in buffered Giemsa for 5 minutes.
    • Rinse briefly in distilled water.
    • Air dry and mount.
  17. Photograph appropriate spreads and produce 8 × 10 high contrast photographs of your chromosome spreads.
  18. Cut each chromosome from the photograph and arrange the chromosomes according to size and the position of the centromere.
  19. Tape or glue each chromosome to the form supplied for this purpose.
 
     
 
 
     




     
 
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