Loggerhead and Green Sea Turtle Podcast

Cyprus is split in half, with a Turkish sector in the north and a Greek sector in the south. The unofficial division makes scientific collaboration in this Mediterranean island nation all but impossible; it also complicates management of the island’s endangered sea turtles. While the conflict between the Turkish Cypriots and Greek Cypriots dates back centuries, twenty-first century problems such as climate change make it urgent for scientists in the north and south to find ways around the old differences, before the turtles slip across a different kind of dividing line—from living to extinct. Ari Daniel Shapiro reports.

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Learn more about Loggerhead and Green Sea Turtles on the Encyclopedia of Life

Podcasts are hosted by Ari Daniel Shapiro. Brought to you by the Encyclopedia of Life and Atlantic Public Media.

Mapping the Retinal Connectome

The connectome is the map of the connections between each of your neurons. According to Sebabstian Seung it is the connectome, more so than your DNA, that is responsible for the uniqueness of a person.  To develop this theory Seung and his lab have recently launched a webapp called EyeWire to allow anyone to take part in charting the connections in the human retina.

To take part you simply explore a 3D section layer by layer coloring in the spaces where the computer algorithm missed. It’s as easy as coloring in between the lines. And as you can see by my score of 0 up above I’m not too good at coloring between the lines.

If you are interested in learning more about the connectome Sebastien has given a wonderful talk on the subject and if you’re interested in delving deeper, a massive amount of data and the tools to process it have been made freely available courtesy of the the Human Connectome Project.

 

The Corpse Flower Podcast

Corpse Flowers
Amorphophallus

Let’s face it—when you think of charismatic megaflora, chances are you have in mind something majestic, like a towering Sequoia, or something ancient, like a Joshua tree. But a plant with a four-foot stalk that smells like a cross between rotting stinky cheese and animal feces? This week’s podcast takes us to a sacred island off the coast of Madagascar, where an intrepid botanist braved fever and worse to bring a specimen of this unlikely botanical superstar back alive. Ari Daniel Shapiro reports.

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One Species at a Time podcasts are hosted by Ari Daniel Shapiro. Brought to you by the Encyclopedia of Life and Atlantic Public Media

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About the Encyclopedia of Life

The Encyclopedia of Life is a collaborative effort among scientists and the general public to bring information together about all 1.9 million named and known species, in a common format, freely available on the internet. Learn more at www.eol.org.

 

Giant Ant Colony Excavated

Researchers filled a Giant Ant colony full of concrete to reveal the amazingly complex structure below. Of course, they probably could have used ground penetrating radar to accomplish the same thing without wiping out the ants.

Cheapass science – DIY Vortex Mixer Tube Holder

 

The protocol I use for collecting human DNA samples requires tubes to be vortexed for 10 minutes.  Standing around for a sixth of an hour is not my idea of fun so I decided to get a foam tube holder.  Unsurprisingly a piece of foam with holes in it costs 50 dollars.  As per my usual I wanted to be a cheapass and thus I built my own foam tube holder with some things I had lying around.  If you want to see the DIY tube holder in action, watch the youtube video below and scroll further down for instructions for building your own.

 

Guide

 

Compatibility

Before attempting this guide make sure your vortexer will work with this method.  Check the type of head piece present on your vortexer, consult the diagram below for an example of two different types (#12+13 and #14).  This guide works for vortexers with head pieces that match #14. New vortexers usually come with both of these pieces and used vortexers (like the one I bought) may only come with one type.

Materials

The tools and consumables I list are not absolute. Use your noggin and substitute if necessary.

  • Tools
    • Dremel (a drill can be used for some steps but not for carving foam)
      • Sanding bits are needed for foam carving (see image below)
      • Cutting tool
      • Drill bit
  • Ruler or measuring tape
  • Hand saw
  • Marker
  • Compass (optional)
  • Consumables
    • Foam block
    • plastic box (I used a large pipette tip box that was 4”x5”)
    • Rubber bands

These are the two dremel tips I used to carve the foam.

 

Instructions

Two types of modifications need to be done to the plastic box.  First, a hole needs to be made in the center that will allow the vortexer head to poke through.  This alteration will prevent the tube holder from wobbling off of the vortexer head.  For my vortexer the size of the required hole was 1-1/4”.  The second modification is the addition of 4 grooves to the top of the box so that the rubber bands do not slip.

Prior to drilling and cutting grooves.  Yellow circles indicate approximate target locations for the grooves.

After drilling and cutting grooves

 

Close-up of the grooves

How the box fits onto the vortexer head.

Now it is time to carve the block of foam.  My box was not perfectly square; the top of the box (the opening) is larger than the bottom of the box.  This odd shape can be ignored but do make sure to use the top of the box for determining the foam block size.  I made a block that was 4-1/4” x 5-1/4” x 2”.  It is very important that the width and length match or slightly exceed the size of the box so that the foam sits tightly inside the box.

My block

My original block was too tall.  Rather than cut grooves in the foam for the rubber bands and have a tall block (which is preferable for large tubes), I decided to cut the foam down so that it was flush with the box.

Carving and cutting the holes in the foam can be frustrating. Make as few cuts and holes as possible because with each tear the foam becomes more likely to get caught on the Dremel bit and then it will twist and tear the foam block.  Also note that the edges of the foam block are likely to get caught by the Dremel bits.

I used sanding bits to make the holes you see below.  I started with the cylindrical dremel bit I pictured in the materials section.  I went into the block about 0.5” with the cylindrical drill bit (this made the cleanest looking hole opening) and then I switched to the conical bit which I used to go straight down to the bottom of the tray.  Use tubes to test each hole you make to ensure they fit.  A snug fitting tube is better than a loose fitting tube.

When the Dremel grabs the foam and twists some areas of the block will be torn.

Another view of the finished block.

 

All that is left is to attach the box to the vortexer and for that we just need rubber bands.  The way the rubber bands rest on the vortexer head and on the box is important, consult the images below.

The first rubber band is hooked under the left side of the vortexer head and hooked over the right side of the box.

The second rubber band is a mirror of the first rubber band.

 

That is it, the attachment is finished.

Before

After

Glamour shot

If you build a vortexer attachment send me a picture and let me know how it turns out.

 

How to make glow-in-the-dark or Flourescent Yoghurt

Photoshop Mockup.

Glow in the dark yoghurt is something that has been floating around the DIYbio community for a while now, though to my knowledge no one has actually made a batch. Hopefully that will change now that Cathal Garvey of IndieBiotech has released a “Beginners” guide to hacking yoghurt. As you can see from the excerpt below beginner here is code for you are going to learn alot.

For our project then, we want DNA that resembles the following:

A diagram showing the format of the desired DNAColourised and labelled sections of the DNA, presented with the unnamed section of target DNA. This assumes the simplest scenario where no “cleanup” mechanisms are included to remove the resistance gene.

The promoter (Prom) should be a constantly “on” promoter, termed “constitutive”. The terminator (Term) is a region of DNA that prevents the gene from transcribing beyond its normal context, which could cause unintended interruptions of cellular functions; unhappy bacteria could result, and the gene could end up unstable. The antibiotic should be chosen to avoid medically significant antibiotics such as ampicillin; this is a civic responsibility matter, as otherwise your yoghurt could end up assisting dangerous pathogens in becoming resistant to medicines. Ideally your antibiotics would be self-excising once they become unnecessary, leaving a yoghurt containing only harmless fluorescent proteins and nothing else.

Ediacaran Fossils Podcast

Photo Credit: Phoebe A. Cohen

When the cod fishery collapsed in Newfoundland in the early 1990s, the hopes of the local fish harvesters collapsed with it. Hundreds of Newfoundlanders moved away and businesses that depended on the cod fishery closed. But retired schoolteacher Kit Ward of Portugal Cove South wasn’t content to watch her community vanish with the cod. She and some friends teamed up to find a solution that was right under their feet, in the reddish rocks of Mistaken Point.

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Learn more about Ediacaran Fossils at the Advent of Complex Life and on the Encyclopedia of Life.

This podcast was funded by the NASA Astrobiology Institute.

How to make quantum dots

Charlie Dvorchak(apologies if misspelt name) of John Hopkins University walks us through how to make Cadmium Selenide semiconductor nanocrystals, also known as a type of Quantum Dot.

Caution: Cadmium Selenide is dangerous to human health, so be sure to take proper precautions if you choose to work with it.

P.s. Just one cool possible use of quantum dots is a BioLaser.

How to add a double decker to your shaker

Joseph Elsbernd, of the Cheap Ass Science Blog brings us a rather simple but ingenious way to get double the area out of your shaker/rocker using nothing but a bit of pvc tubing and your choice of decking material.

Via Cheap Ass Science

Red-Shouldered Soapberry Bug Podcast!

In the lab at American University in Washington, DC, evolutionary biologist David Angelini and graduate student Stacey Baker are studying a snazzy red-and-black insect called the red-shouldered soapberry bug. These tiny insects with the big name are speedy and hard to catch—and speedy in other ways, too, as Ari Daniel Shapiro discovers.

Learn more about Red Shouldered Soapberry bugs (aka Jadera haematoloma) on the Encyclopedia of Life and at Soapberrybug.org.

Photo Credit: Crystal Perreira, Soapberrybug.org

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