Month: January 2019

DNA extraction – improved phenol:chloroform method

DNA extraction (PCI) of PCR or other enzyme reactions

Phenol:Chloroform:Isoamyl alcohol (25:24:1) (PCI) DNA extraction can be used to clean up DNA from pretty much any sample. After trying lots of methods like kits with columns, I prefer the PCI method over any other method for applications like PCR purification. This PCI method gives better yield than column based methods and the DNA is suitable for any application like sequencing, ligating, or Gibson Assembly. The video below describes an improved PCI extraction that gives the best yield and purity, is very fast, and costs next to nothing.

Advantages of this Phenol:Chloroform DNA Extraction

  • Results in DNA of high yield and purity.
  • Fast
  • Cheap (costs just a few cents including tubes)
  • Eco-friendly. Produces much less plastic waste than column based methods. Produces 10 times less phenol:chloroform waste than traditional PCI methods.
  • Extremely scalable. Works for any range between femtograms and milligrams of DNA.

Down load a printable phenol:chloroform DNA extraction protocol here.

Using a micropipette

Correctly using a micropipette

Molecular biology requires the manipulation of micro-liter quantities of liquid. Thus the micropipette is one of the most frequently used pieces of equipment in the lab. This video will help get newbie’s skills with micropipettes up to speed quickly.

The video is for using Eppendorf brand micropipettes. Gilson pipets can be used in a near identical manner and this video can help you to set the pickup volume with Gilson micropipettes.

Symbiotic Nitrogen Fixation

Soybean symbiosis with Rhizobia

Legumes (beans) are capable of symbiotic nitrogen fixation. The bacteria turn atmospheric nitrogen into ammonia that the plant can use. Soybean Rhizobia inoculum can really make soybeans grow much bigger and healthier without adding fertilizer. The time-lapse video below shows how beneficial Rhizobia can be to soybean growth. All pots had identical soil. The only difference is the seeds that went into the pots on the right had Cel-Tech soybean inoculum on them. The Rhizobia form a symbiotic relationship with the soybean plants leading to nodule formation on the roots. These root nodules provide the plants with an abundant source of nitrogen.

Soybean growth details

  1. Soil (Promix BX) was autoclaved to kill residual bacteria.
  2. Seeds were planted into wet soil. Plants with Rhizobia were made by touching the seeds to Cel-Tech Inoculant prior to planting.
  3. Plants were grown in 16 hours of light per day at 23 degrees Celsius. Plants were watered as needed.
  4. Note: Extreme care is needed to prevent non-inoculated plants from “catching” the Rhizobia from the inoculated plants (ie. do not cross contaminate by splashing water or soil between the treatments). Soybeans are very susceptible to Rhizobia colonization.

Here are several other plant time-lapse videos.