Category: Uncategorized

Dense Phase Separating Gel / Homemade TRIzol combo

Published: November 13th, 2018   Last Modified: April 21st, 2019

Homemade phase lock gel, which we can generically call phase separating gel (PSG), can be a useful addition to your DNA extraction repertoire. The best part is that for many applications you can use 100% DOW High Vacuum grease, which makes it very economical. Unfortunately, for RNA extractions with TRIzol, the stock PSG is not dense enough to migrate between aqueous and organic phases, and simply settles on top of your aqueous phase. BOO!!! 

Now, I’ve been trying to solve this problem for a while, but this is the first time I think it’s been successful. Basically, by combining vacuum grease with 15% w/w silicone dioxide (i.e. 20g grease + 3g SiO2), you end up with PSG dense enough to work properly with TRIzol. Lets take a look at how to do it with a minimum of mess!

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A quick teardown of the Beckman Biomek P1000 Pipette Module

Published: November 2nd, 2018   Last Modified: November 14th, 2018

Some time ago I was pretty obsessed with building a pipetting robot, and to a degree it was a success. However, building it burnt me out pretty good. I will revisit the project and likely rebuild the whole thing to make it simpler and closer to the original plan. I tore down my opentrons clone, and this is all that remains:

Ahh, memories. But let’s not get all nostalgic and wax poetic. One aspect of the original opentrons robot (which has now been corrected, see their OT2) was that the pipetting section used a hand operated pipette strapped to some stepper motors. I was looking for inspiration from the pros to make my own pipetting module, so I got my grubby little paws on a Biomek P1000 module to tear down. Take a look, it’s a rare treat to see how a part of a 100,000$+ machine is made!

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MashUp-RT, purify your own reverse transcriptase (Beta testing phase)

Published: September 6th, 2018   Last Modified: April 21st, 2020

Purification of pfu-sso7d ended up being a stunningly popular article, only being beaten out by DIY decontamination mix (people really enjoy decon mixes, apparently). What it revealed was that there is a global demand by scientists who wish to purify their own enzymes to be used as tools in their labs. I’m glad that I’m not the only one who has adopted the DIY ethos.

Another detail that surfaced is that besides an enzyme useful for PCR, a reverse transcriptase (RT) was in equally high demand. This isn’t surprising when you consider that RTs are some of the most expensive enzymes for RNA biologists and if you’re between funding cycles, lost your funding or not in a central country it can be a barrier to entry/continuation in the field. So, you asked, and I have delivered: MashUp (MU)-RT, a custom, FeLV based RT available to academic users!

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Glowing Plants 2: Fluorescent Boogaloo

Published: July 7th, 2018   Last Modified: October 16th, 2018

Ever since my original post regarding making a DIY bandpass filter, I’ve been pretty obsessed with macro-view imaging of fluorescent proteins (FPs) in plants. The quality of pictures have come a long way, take a look, it’s a leaf infected with a potyvirus that carries eGFP within its genome:


Now, maybe it’s just me, but that looks beautiful. How did I get here?   Unfortunately I had to give up on using stage film, it’s cheap, you can use funny filters named “Pale Bastard Amber”, but when you’re looking at fluorescent proteins on this macro scale they don’t cut it. For a bit more money, you can get publication quality pictures with a few filters, some 3D printed parts and a cellphone camera. Let’s get into the nitty gritty logistics when it comes to looking at FPs in plants.

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Help support PipetteJockey! (Decision to monetize)

It makes me happy that people around the globe find this niche-of-niche website useful to them and their labs and I will keep this ship running as long as I can. However, the projects I do are done out of pocket on a grad student budget, so there’s a limit on the cool stuff I can do.

So, I’m deciding to monetize the website in an as non-obtrusive way as possible to get some cash flow going to fund more cool projects. Read on if you’d like to know how this will be done, in the sake of transparency between me and you as the reader.

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(PJ e7) The Dispensation Station, low cost buffer dispensing solution

Published: April 1st, 2018   Last Modified: April 2nd, 2018

Getting tired of measuring out your buffers with a graduated cylinder like an animal? Boy, do I have a project for you! Here’s a low cost buffer dispenser that you can whip up in a few days and will run you less than 100$.

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Quick and dirty bandpass filter for GFP viewing in plants

Published: January 11th, 2018   Last Modified: July 24th, 2018

Recently I had need to take macro scale pictures of plant leaves that had been infected with a virus that carries the eGFP coding sequence. Fluorescence microscopes would be the way to go, but you can only raise the lenses so far, and you’d need to remove any magnification to get a macro view. Generally, screwing around with a scope like that will make your local microscope tech pretty irate. What about a GFP illuminator that you can fit a whole plant into? These exist, but like any piece of super niche lab gear, it ain’t cheap.

How about a DIY option? Well, I’m definitely not the first to explore this area. Ian Chin-Sang and Weiwei Zhong, a couple of fellow canuks, did a write up about using LEDs and stage lighting filters to look at fluorescent proteins. Beauty, and for less than 100$ bucks! Sounds great right??? Well, once again, working with plants threw in some nice challenges!

This post will explore the implementation of their idea with a eGFP/plant/macro view use case.

(Update: Higher quality version)

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Making a Opentrons compatible liquid handling robot

Published: January 3rd, 2018   Last Modified: October 12th, 2018

It’s finally done, my very own liquid handling robot! The video goes over my trails and tribulations building this thing. Overall I’m glad I did it, the level of complexity forced me to challenge myself at every stage. This is definitely a step above assembling a ready to go 3D printer kit from ebay.

The next video will be doing some actual science with this thing…I think that was the reason to build it, right???

Thanks again to the Opentrons team for releasing their designs for us to play with 🙂

Additional improvements and pictures will go in the blog post as I make them.

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CNCd Electrophoresis Gear : The Reckoning

Published: March 19th, 2017   Last Modified: June 16th, 2017

In this video I talk about how you can apply technologies like CNC routers to do your bidding, in this case to make very professional looking electrophoresis gear. I’ve included the Fusion 360 files to make your own, click the “Continue Reading” button after the embedded video.

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