How to make a DNA Bracelet

From any organism and any gene!

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I study plant-pathogen interactions, so I chose to make a sequence from a wild tobacco gene that is important for plant defense against pathogens.

What you’ll need:

  • Four colors of beads
  • Elastic string
  • The sequence of a gene

If you don’t have a sequence of a gene on hand, there are some great suggestions in this instruction manual or you can find one by following the instructions below…

To find the sequence for a gene you are interested in, NCBI is a great resource: https://www.ncbi.nlm.nih.gov/. You can search by gene name and by organism. Google can also be useful to find the NCBI identifier for a given gene.

Once you have the sequence of your gene of interest, you can use a program called PrimerBLAST to pick unique regions for your DNA bracelet. Since genes are on average 1000 basepairs (letters) long, we first need to pick a short sequence from the gene that we will use as a template for our bracelet. Since many genes are shared across organisms, if we want to pick a sequence that is unique to our organism and gene, we need to check that the same sequence doesn’t exist in a related organism or a related gene.

To use PrimerBLAST, paste your sequence or use the NCBI accession number for the gene. Make sure you select “Enable search for primer pairs specific to the intended PCR template”. I use the “nr” database (non-redundant sequences from all organisms) and delete the default “Homo sapiens” from organism name.

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Next, to get a sequence that is the right length for the bracelet, scroll down to the bottom and specify 24 basepairs as the optimum primer length. You can do larger or smaller depending on the size of your wrist. I think 21 basepairs is a good size for kids, but you could probably make it up to 27 bp for adults with larger wrists. You could always start with a longer sequence and then make it shorter depending on the size of your wrist.

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Next, hit “Get Primers” to find sequences unique to your gene. PrimerBLAST will probably give a warning and a list of genes which will probably correspond to the gene you are searching for. Select all targets as intended or acceptable and hit ok.

Here PrimerBLAST will give you some sequences. Pick one of the “forward” primers that you like best and copy the sequence down. I like to pick one that doesn’t have too many repeated letters for my bracelet due to aesthetic reasons.

Now you can make a bracelet representing your sequence! There are four letters of DNA representing the four chemicals that encode all of the genetic information. You can use different colored beads to represent the four letters of DNA.

A = adenine = green beads
T = thymine = red beads

C = cytosine = yellow beads
G = guanine = blue beads

You could use other colors of beads if you don’t have these four colors on hand, but these are the colors that correspond to the fluorescent dyes used for the four bases in DNA sequencing.

DNA is double stranded and the first strand is the template for the second strand, following these complementary base pairing rules: A pairs with T and C pairs with G.

For your DNA bracelet, I’d recommend that you make one strand first and then use it as a template to make the second strand, following the base pairing rules.

We recently made DNA bracelets as an outreach activity at UC Davis Picnic Day and it was very successful. Kids, parents, and undergrads alike loved making the bracelets and learned something about the structure of DNA and how the base pairing rules are used for DNA replication in the process.

If you decide to make a bracelet, I’d love to see it! Let me know on Twitter (@klsywd) or leave it in the comments here! If you post a pic on Twitter use the hashtag #DNAbracelets.

Feel free to reach out to me if you are having any problems finding a gene or following these instructions or if you have any questions!

The original DNA bracelet making activity was created by Wellcome Sanger Trust. A PDF of their instructions can be found here: ftp://ftp.sanger.ac.uk/pub/yourgenome/downloads/activities/sequence-bracelets/ftsequencebracelets.pdf

How can genomics help neglected crops fight disease?

 

I recently attended a Plant Pathology symposium on “Genomics Strategies for Developing Sustainable Disease Resistance for Neglected Crops in the Developing World“. The symposium was held at the University of California, Berkeley and was hosted by the Innovative Genomics Institute (IGI) and the Open Philanthropy Project.

As it is only a ~1 hour drive from Davis, myself and 10 others from the Michelmore lab woke up early to commute to Berkeley for the symposium. There was a great lineup of speakers that kept the audience engaged for the day-long event.

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As is my habit, instead of taking notes by pen and paper or on my Evernote, I used Twitter to simultaneously take notes and share the information with my followers and the greater Twitter-verse. I used the hashtag #PlantPathIGI to tag all of my tweets related to the conference so myself and others could easily find them.

Since many of my followers are fellow plant geneticists and plant pathologists, my tweets received a lot of attention from scientists and others across the world. This is one of my favorite things about Twitter, the ability to have real time conversations and sharing of information across geographical barriers!

For those of you who may have missed it on Twitter, I will give a summary of the conference highlights in this blog post. Read More

What’s lurking in your lettuce?

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Everyone knows that eating salads is good for your health. As it turns out, microbes like to eat lettuce too, with serious consequences for farmers and consumer health.

monterey

Salinas Valley is located a few miles inland of the Monterey Bay.

In California, lettuce brought in $2.2 billion dollars in 2015, which was half a billion more than tomatoes and almost double the amount brought in by oranges and avocados combined [1]. Most of this lettuce is grown in Salinas Valley, also known as the “Salad Bowl of the World”, which can provide over 80% of lettuce for the whole US [2].

The climate and soil in the Salinas Valley make it perfect for growing lettuce, unfortunately the cool, damp coastal areas also provide prime conditions for lettuce downy mildew, the most damaging disease of lettuce leaves. When the weather is right and downy mildew strikes, losses can be up to 100% for an individual lettuce field.

The downy mildew parasite resembles a fungus, but is actually part of a group of organisms known as the oomycetes (this group includes the famous late blight pathogen that caused the Irish potato famine). Downy mildew by itself does not actually kill the lettuce plant, but it does ruin leaves and weakens the plant immune system, allowing bacterial infection and other diseases to proliferate.

Video showing what downy mildew looks like in the field:

To help fight downy mildew, lettuce breeders take resistance genes from wild lettuce varieties and cross them into commercial varieties; this is known as genetic resistance. Most of the time, neither the breeders nor plant scientists know exactly what genes are being introduced, only that they give downy mildew resistance in selection tests. One problem with this approach is that there are multiple strains of downy mildew present in California and an individual resistance gene won’t provide resistance to all pathogen strains. Also, the pathogen is able to rapidly evolve to overcome the resistance genes faster than breeders can come up with new varieties.

When downy mildew overcomes genetic resistance, the next approach used by farmers is application of pesticides. Over 1/2 of fungicide use on lettuce is specifically targeted to control downy mildew [3]. Some of these pesticides are being phased out due to concerns about human health. One can go organic to avoid the pesticides, but will pay a premium: organic lettuce faces the greatest losses from downy mildew, as there are currently no organic pesticides that are effective at controlling the pathogen.

Scientists in California and elsewhere are studying both the lettuce and the downy mildew pathogen to better understand what biological weapons are used by each side during infection. When a new strain of downy mildew is discovered that can attack lettuce that was previously resistant, we can sequence its genes and find out which ones have changed. We hope to get a better idea of the existing downy mildew strain variation in California to better predict which varieties will be resistant in the future. More resistant lettuce will mean less pesticide use, meaning cheaper and healthier lettuce for use in your salads!

[1] http://www.nass.usda.gov/Quick_Stats/Ag_Overview/stateOverview.php?state=CALIFORNIA

[2] http://californiacountry.org/features/article.aspx?arID=563

[3] http://cesantabarbara.ucanr.edu/files/75296.pdf

Note: this blog post was originally written as part of the excellent SciFund Challenge outreach class