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Tag: PCR

Eat hagfish, work at LUMCON, clone Vaquita, question floating trash collectors, and more! Monday Morning Mega-Salvage: August 13, 2018

Posted on August 13, 2018August 12, 2018 By Andrew Thaler
Weekly Salvage

Foghorn (A Call to Action!)

  • It’s time for Africosh! The annual Africa Open Science and Hardware Summit Heads is in Dar es Salaam, Tanzania this year!
  • LUMCON is hiring! They’re looking for two exceptional coastal and marine science faculty hires in any discipline. And they have the best “come work for us” video!

Flotsam (what we’re obsessed with right now)

  • Hakai Magazine is my jam this month.
    • How an Epidemic Exposed the Ecological Importance of Sea Stars: The near eradication of British Columbia’s sea stars demonstrated the dynamic role they play in regulating kelp forests.
    • How to Dismantle a Blue Whale: In Chile, a team of volunteers confronts stench and gore to ensure a new life for a dead whale. [Warning: Link contains graphic pictures of whale evisceration]
  • I’ve been following this project for almost 2 years. Awesome to see how far they’ve come. NinjaPCR is a WiFi enabled, Opensource DNA Amplifier and Thermocycler for Polymerase Chain Reaction developed by 2 hackers in Tokyo.
  • Plastic wrap made from shellfish and plants is completely compostable.

Hagfish (just Hagfish)

  • Yes, people do eat hagfish. Yum! Snake-like creature writhes, squirms on grill.
  • Hagfish are the emissaries of love, not war. Stop it. Synthetic ‘Slime’ To Help US Navy Trap Enemy Ships.

Read More “Eat hagfish, work at LUMCON, clone Vaquita, question floating trash collectors, and more! Monday Morning Mega-Salvage: August 13, 2018” »

Monday Morning Salvage: February 20, 2017

Posted on February 20, 2017 By Andrew Thaler 1 Comment on Monday Morning Salvage: February 20, 2017
Weekly Salvage

For all our US-based Readers: Happy President’s Day! For everyone else, this is the reason none of you USian colleagues are answering e-mails. Unless they are, in which case, *grumble grumble grumble* *something about work-life balance*

Flotsam (what we’re obsessed with right now)

  • The ocean is full of garbage and even the deepest trenches aren’t safe. Here’s an interview I did with KSPN Saipan where I talked about the garbage the precedes us everywhere we go.
  • Also: Banned chemicals persist in deep ocean. This seems important.

Read More “Monday Morning Salvage: February 20, 2017” »

Establishing Best Practices to Minimize Waste in a Conservation Genetics Lab

Posted on November 14, 2012 By Andrew Thaler
Conservation, Science

I am, among other things, a conservation geneticist. What that means is that I use the tools of molecular ecology and population genetics to make observations about species and populations in at-risk ecosystems, assess the status of anthropogenically disturbed populations, and generate data that has direct applications to conservation and management issues. Essentially, the only difference between what I do and what a population geneticist or molecular ecologist does is the motivation—I select systems to work in that have a high conservation priority.

This motivation leads to a constant intellectual conflict at the bench. The tools of molecular ecology—PCR, gene sequencing, and, more frequently, high-throughput sequencing—are waste intensive. In order to avoid cross-contamination and practice precise, clean, technique, we use thousands of tiny plastic consumables every day. These come in the form of pipette tips, sterile packaging material, micro-centrifuge tubes, and numerous other plastic widgets. Often, because of the biohazard potential, these consumable cannot be recycled.

So we have a problem. As a conservation geneticist, we need these tools to produce the data necessary to make wise conservation and management decisions. As a sustainability minded individual, I find the massive daily accumulation of plastic waste inexcusable. Do we just accept this waste as the cost of conservation genetics? I believe that the answer is no. I think we can and should develop best practices to minimize the amount of plastic waste produced by a molecular lab while maintaining good, sterile technique. I would like to propose four guidelines, based off the principles of Reduce, Reuse, and Recycle, for minimizing waste in a conservation genetics lab.

Read More “Establishing Best Practices to Minimize Waste in a Conservation Genetics Lab” »

WhySharksMatter’s 2nd PCR

Posted on April 5, 2010April 5, 2010 By David Shiffman 1 Comment on WhySharksMatter’s 2nd PCR
Science

After the failure of my first PCR, we tried again. This one is more successful. Of my 7 samples, 5 amplified. We aren’t sure why the other two didn’t, so I’m going to try to re-extract DNA from them and try a few different primers with them this week.

Read More “WhySharksMatter’s 2nd PCR” »

An update on WhySharksMatter’s first PCR

Posted on March 31, 2010April 4, 2010 By David Shiffman 1 Comment on An update on WhySharksMatter’s first PCR
Science

I know that many of you have been losing sleep over the questionable quality of my first PCR and gel. Well, the mystery has been solved! My lab partner made the gel with DI water instead of with TAE/agarose solution. Not only is that an easily fixable problem for the future… it’s something that, for … Read More “An update on WhySharksMatter’s first PCR” »

Kary Mullis’ Eureka Moment

Posted on March 26, 2010April 4, 2010 By Andrew Thaler
Science

In honor of Dave’s first PCR result (or lack thereof), here’s Dr. Kary Mullis discussing the discovery of the polymerase chain reaction. ~Southern Fried Scientist

WhySharksMatter’s first PCR!

Posted on March 25, 2010April 21, 2010 By David Shiffman 10 Comments on WhySharksMatter’s first PCR!
Science

As promised, here are the results of my first ever PCR. Here is some background:

I am going to be running some population genetics on sandbar shark DNA with the intention of comparing subpopulations from South Carolina with those from Virginia.

I am in the very early stages- seeing which primers work for PCR. Four primers each were tested- called A, B, C and D- on three shark DNA samples and a negative control. Ignore the samples on the bottom, they are from another student’s project. The four samples in the upper right are my negative controls.

The PCR was run yesterday (my first PCR), and I ran the gel today (my first gel).

It seems to me that Primer A is successfully copying my DNA during PCR, while B, C, and D are not.

Read More “WhySharksMatter’s first PCR!” »

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