The Engineer-it Kit

 

I received "The Engineer-it Kit" from Amino Labs. It is a bacterial transformation kit.

I read about this kit in the book I talked about in an earlier post - "Zero to Genetic Engineering Hero: The Beginner's Guide To Programming Bacteria At Home, School and In the Makerspace."

By Justin Pahara and Julie Legault.

If you are a beginner in bio-engineering this is a good place to start. The kit is well priced, I felt shipping was a bit high but that is probably out of their control. It comes with almost everything you need, except the hardware. You do need a incubator (they do supply you with a video link to build a very simple one ), a hot and a cold water bath. I used an ice bath for my cold bath. They do have an all in one hardware that will do all of this, that you can purchase. Though it is expensive.

 

 

 

 

They made this kit to be as simple and easy to use as possible, even a beginner can do it. They supply you with everything you need:

Bacteria, plasmid, antibiotic, agar, petri-dishes, inoculation loop, streak template and even the sterile water.

They give you a manual.

Here is a video showing you all steps in the protocol.

You can even use a simulator to do the protocol.

If you are interested in bio-engineering this is a good way to start. As well they have other kits that you can purchase separately. This way it is not a huge outlay of money all at once.

Shaker

Shaker

Image 1

 

 

Visiting another second hand store I found this shaker. I have been thinking of making my own for quite sometime and I will still try to make my own at a later date. As can be seen (Image 1) it needed a lot of cleaning outside and in. It worked as is but seemed to struggle to get started. After taking it apart I saw it was full of grime and dirt. Once I cleaned that up it works really  well.

 

 

Image 2

 

Image 3

The platform holds 15 ml conical tubes. The platform comes off very easily so I am going to build different platforms to hold different types of tubes, flasks, beakers and jars. But in the mean time I 3D printed these holders (Image2) for 50 ml conical tubes, 250 ml flasks and 500 ml mason jars. I also printed a yellow tab (Image 3) that fits in the platforms holes to hold these holders in place(Image 4). This is until I can build new platforms to hold each item. I also want to build petri dish holders for it to.

 

Image 4

 

Again a second hand find turns out real well. You do have to visit many different second hand stores to find something you might need or can use. Many times I do not find anything that I can use, but I see things that gives me ideas of what I might be able to build or use.

Media Pump

Using a Syringe Filter to Sterilize Media:

Syringe and Filter

I picked up some syringe filters from Amazon figuring I could use a syringe to pass my media or water through the filter. As seen in photo the filter screws on to the top of syringe. This filter membrane has a pore size of .22 micrometers. This should easily sterilize the fluids.

Parts

 

Thinking there must be an easier way to run the media or water through the filter I picked up a 12V DC DIY Peristaltic Liquid Pump from Amazon. As seen in this image as well as the pump I picked up air hose tubing and airline tubing connectors from a pet store. The connectors allows different sized tubing to fit together.

Fitting to hold filter

I had a medical drop administration set I found at a flee market. This has the same type of connection as the syringe tip has, allowing the filter to screw on. As seen in the above image.

Unit put together

In the final image you can see the whole unit put together. I am using a 12 volt wall adapter hooked up to the motor speed controller (previous project) to control the pump motor. The filter holder was made with a 1/4 inch dowel and clothes pin glued together.

I pump the fluids through the system slowly as to hopefully not cause a big mess if it ever backs up. I intend to mount the pump into a weighted box so I don't set it up when I need to use it.

Laser Projector Microscope

Equipment needed:

Laser pointer(green 532 nm) or red, Syringe(10ml), screen or wall, apparatus to hold laser and syringe in place, sample(from my aquarium).

Green Laser Pointer

 

In the diagram above you can see how the microscope is set up. The laser beam runs through the specimen droplet that is formed below the syringe. This produces an image on a screen on the other side of the droplet.

 

 

Image on Screen

Moving the laser closer and further away will bring the object in focus. Even if not completely clear or bright you can see the organisms swimming around. You can make out some detail to try and identify the organism.

 

Beam on Droplet

After reading some more on the laser microscope I found that the drop of water acts as a small spherical lens which magnifies the image. I tried the red laser pointer but the image was not as bright. I will look further into this in the future.

Spectrometer Version 3 Continued

Figure 1

I have been continuing the build for version 3 which holds the sample inside the container. In figure 1 you see the 3D printed sample holder, here I have a test tube but it does hold cuvettes as well. Next to the holder on the right you can see an LED. This one is a bright white LED. I intend to use a RGB LED so I can choice different colours or wavelengths. It will also be removable so I can use IR and UV LEDs.

Figure 2

Figure 3

In figure 2, I use a 3D printed slit holder and then mount 2 single edge razor blades which are adjustable. With the other 3D printed parts I hold the slit mechanism in place within the spectrometer. This allows for removal of the slit so it can be adjusted. In Figure 3 you can see the unit put together.

Figure 4

And in figure 4 you see allthe components put together with the sample and slit holder, LED source, diffraction grading and web cam all in one box.

This is all put together in a wooden box I found at a dollar store. I still intend to make this smaller so I can easily carry with me. I do have access to a 3D printer so it was easier for me to print the parts I needed. But all the parts could be very easily cut from foamboard.

Digital Microscope Version 2

This microscope views the specimen from below. Here I use parts from an old CD-Rom drive, a web cam, block of wood to hold it together, laser pointer lens, some foam board and glue.

Fig. 1

Taking apart the CD-ROM (fig 1) I keep the carriage that moves laser LED along the CD. This allows the specimen stage to move up and down to focus it. The gears on the side are used for the focusing, the bottom gear is used for regular focus and the top gear is used for fine focusing. I manually move the gears. I may look into using the gear motor to electrically move the stage.

Fig. 2

I mount the carriage on a thick piece of wood (fig 2) to allow stage movement and support.

Fig. 3

The specimen mount (fig 2, right of image), is made from foam board. and (fig 3) then mounted on the carriage with Gorilla glue.

Fig. 4

Fig. 5

Fig 4 and 5 show the whole thing put together. You can see the stage is up and then is lowered to focus the image.

To raise the magnification of the camera I used the lens in a cheap laser pointer and mounting it  on the lens of the camera. This does give higher magnification, about 100-150x but is not as powerful as a compound microscope which can get to 800-1000x. I found that when using live mounts, living organisms many times it is best to view them from underneath.

All the parts I had were just laying around which made this a very inexpensive build. I am sure that it is easy to find a junked or used CD-Rom or DVD. The camera is just a cheap webcam again something you might be able to find from a friend or thrift shop. Mine was a dollar store purchase for $3. I find that this microscope does work better than my first version, especially with the focusing.

DIY Digital Microscope

Camera Placement

First Adaption

  
 
DIY Digital Microscope

Staying with microscopes, I have to build my own digital one. I want one with viewing from underneath.

Using a Dollar store $3 webcam, a piece of plywood, 3 4 inch bolts, 5 washers, 6 nuts, 4 wingnuts and 2 small pieces of 1/4 inch plastic. The only item I purchased was the webcam. Everything else I had laying around. This was just a quick work around I put together to see if it is worth while making.

I wanted to microscopically look at live samples from underneath. It actually works better than I thought it would. It looks to give about 4x the magnification, you are definitely not going to see bacteria. Though, I might be able to see other micro-organisms, I will further test this. As of yet this is not a final build, I will be making many improvements to this setup, especially with the magnification. I would like to at least get to 100x magnification. I just wanted to see if this would be worth while pursuing. And yes it is. And for a very low cost.

In this setup I have the camera is fixed and the sample is moving up and down.

Inspiration for this build came from here, they use a smartphone and laser pointer optics:
https://www.instructables.com/id/10-Smartphone-to-digital-microscope-conversion/

Here is another link using cardboard for the build:
https://www.youtube.com/watch?v=cHcX0vx4FZM

There also is the FlyPi that uses the Raspberry Pi system and camera:
https://open-labware.net/projects/flypi/

I will be looking further into the this version and the FlyPi.

3D Printing

Electrophoresis Chamber

Dremelfuge

Vessel Holders

3D Printing

3D printing is becoming more accessible to the average person. Maker spaces usually have one or two that would allow you to use. 3D printing is another good way to make lab equipment, here are a few items I have printed:

                   

In the top picture you will see a electrophoresis chamber made from a soap dish and 3D printed gel chamber and comb. I could have printed the whole chamber but I used a soap dish that I already had to save on plastic.

In the next picture I printed the dremelfuge which I have talked about in an earlier post. I printed both with chuck and with-out. So far I only used it with a drill. I still do not feel safe using it with a Dremel without enclosing it in some sort of housing to protect myself.

The last picture shows vessel holders for beakers, flasks and jars that I will attach to a shaker machine. I will talk about this in a later post.

You can find these items at :

http://www.thingiverse.com/

There are many other sites you can get 3D objects from.

Water Bath

Water Bath Prototype

Driver Board

With the help of a member from my maker space, we are trying to create a working water bath that uses a arduino to control the temperature. If we are able to make it work properly we will open source it. We are looking to develop either a arduino shield or it's own driver board to run the water bath.

We trying to have it set to 42 degrees C. This is the temperature used for bacterial transformation(the heat shock method). It is working very steady with about 0.25 degree C on either side of 42 C. We are going to try at different temperatures next.

The top picture shows the setup, it is a power supply(top middle of picture), an arduino on a driver board(black box next to the power supply) built by a member of my maker space, a heating pad, LM35 temperature sensor and a plastic container(sitting on the heating pad). The lid must be on to bring up the heat and keep it at a steady temperature.

The next picture shows an arduino temperature driver board.

Revisiting the Incubator Repair

Incubator

I have been working on improving my incubator. I picked up this incubator (see an earlier post) and had to repair it to get it to work. It is basically an old metal box. As you can see I have adding corrugated plastic to the sides and top. This will help keep the temperature stable for my cultures to grow in. It also makes it much easier to clean, disinfect and sterilize . The metal had a acid type smell of old metal. Once cleaned up and the plastic inserted this helped take away the small. I am not sure how long the plastic will last but it is inexpensive and can be found at hardware stores. Therefore I can replace it when needed.

New Centrifuge From the Old

New Incubator

I found this inexpensive centrifuge and brought it home to find it not working. I took it apart and cleaned it up. It only needed rewiring to get it up and running. Now with this I am able to retire my blenderfuge. In the blenderfuge the center piece kept warping and had to be replaced. I believe this was caused by the very high speeds of the blender. The blenderfuge was much faster than this centrifuge but this one will work for my needs.

Sample Rotator

Parts

Front View

Side View

With very simple items I had laying around I was able to build this sample rotator. It rotates very slowly. This will allow samples to be mixed. I hope to place it in my incubator to attempt to use as a shaker for the media broth for cultures (continual mixing).

Parts: the motor came from an old hand-held vacuum, I bolted a disk from the bottom of a cd holder on to it. The frame is from an old computer power supply box (the top half). I use 1 inch PVC conduit clamps to hold the motor in place. I use broom handle wall clips to hold my culture tubes. They had to be adjusted to fit both 15 ml and 50 ml tubes. They are mounted on the plastic disk with nuts and bolts. It runs using a power supply that ranges from 1.5v - 12 v.

Incubator

Older Incubator

I picked this old incubator up very inexpensively. It was not working. I took it apart and the wiring was removed. I rewired it and tested it out. The heating panel works and so does the thermostat.

It is an old metal box. I intend to add some insulation, either Styrofoam or corrugated cardboard or plastic to keep the temperature more stable. At first I thought maybe I would mount it on the outside of the incubator but as I think more about it I believe it might work better on the inside as this might be easier to clean than metal walls.

I will revisit this when it is finished.

I now have 2 incubators the earlier one I built which goes up to about 30 degrees C and this one which goes up to at least 40 degrees.

I found this link to the pdf file for The Amateur Scientist by C. L. Stong. This is a classic with experiments in archaeology, biology, physics, electronics, etc. These are projects from Scientific American's The Amateur Scientist column.

http://ia801502.us.archive.org/33/items/TheAmateurScientist/Stong-TheAmateurScientist.pdf

Sterile Chamber

Baby Incubator Cover

I found this item, a baby incubator cover that was very inexpensive. I am using it to build a sterile chamber to do culturing in. It has plenty of room inside it and plenty of arm maneuverability to be comfortable to do projects in it.

I will mount it on a vinyl covered piece of plywood or press board. Add a fan that blows the air out and in through a Hepa filter. I will sterilize it with a Lysol/alcohol solution. This will keep the work area in a fairly stable environment, I won't be breathing over the work area or as I move sending dust and particles into the chamber. This should work better than the aquarium that was put together earlier.

I will keep post further as I finish it up.

Update Link

The Golden Book of Chemistry Experiments:

http://chemistry.about.com/library/goldenchem.pdf

DremelFuge - centrifuge

Warning - be careful when using or building a centrifuge, they are very dangerous. If at all possible try and buy a professional one.

Here is a centrifuge created by Cathal Garvey called DremelFuge. It can be found here:

http://www.thingiverse.com/thing:1483

It uses standard 1.5ml/2ml Eppendorf/Microcentrifuge tubes. Works with both a drill or Dremel.

DremelFuge

I was trying to get it printed out but I was having trouble with it. So I decided I would try to make my own from parts laying around. It consists of a 3.5 inch PVC plumbing cap and a bolt, nut and washer. As seen below I have it running on a drill press. I did try it on a dremel, it worked, but I would not use it that way unless a closed off compartent is built for it (later project).

Homemade dremelfuge

Working in drill press

DIYBIO and Genetics

Over the past weekend I did some web surfing and I found this site called "Learn Genetics":

1) http://learn.genetics.utah.edu/

It teaches the basics of genetics. It shows you how to virtually build a DNA molecule, talks about DNA to protein and all the basics needed to understand genetics. There virtual labs such as 1) DNA extractions, 2) PCR, 3) Gel Electrophoresis and 4) DNA Microarray.

2) There is a link to HOW TO EXTRACT DNA FROM ANYTHING LIVING:

http://learn.genetics.utah.edu/content/labs/extraction/howto/

3) A link on how to build a gel electrophoresis chamber, including power supply (one of the best I have found):

http://learn.genetics.utah.edu/content/labs/gel/build_gel_box.pdf

A lot of what is on there can be transferred to using plastic dishes instead of building the chamber completely form scratch. But still the lessons for working with plastics are good an can be beneficial if you go that route.

4) Another link that shows you how to run that chamber using kitchen supplies such as agar, table salt, food colouring and filter papers (I would use coffee filters):

http://learn.genetics.utah.edu/content/labs/gel/electrophoresis/

5) Teachers Lesson Plans:

http://teach.genetics.utah.edu/content/

I have not had much time to go through this content yet but I plan to.

Over all a very interesting site with a lot of do-it-yourself projects.

More Books

I have picked up a couple of interesting books, a couple of older 1960's books and one a little newer late 1990's:

1) Junior Science Projects - 1967 by the Editors of Science Experimenter:

This book has many experiments you can do and many pieces of equipment that you can build. Such as a milli-microampere detector, ion-exchange fuel cell, diffraction grating-type spectrscope, thermistor thermometer, make your own plastic lab equipment (see picture above) and more. Some of the electronic projects require specific tubes, but I am sure with internet searches you can find other ways to make them. A real interesting read.

2) Exploring Science in your Home Laboratory - 1963 by Richard Harbeck:

This book discusses how to build a home science laboratory for chemistry, biology, physics and geology. It walks you through choosing where to locate the lab, which one you would like to build first. Then helps you set it up, from building a work bench with shelves and then a way to remove the air if you don't have a window in your area. From here it helps you build different lab equipment for your lab, such as a simple electric heater, alcohol lamp, drying and sterilizing oven, test tube racks, stands, beam balance and more. This book must have been a real gem back in it's day.

3) A Low Cost Approach to PCR - 1998 by Eva Harris:

This is a good book for the DIYBIO groups. The low cost approach outlined in this book can be useful for the DIYBIO group. It provides a description of the theoretical basis of the technique and practical details of the method. There is a section on materials and chemicals needed in your lab. A section on building your own equipment ie. electohoresis chamber, micro centrifuge, etc. A section on preparing your reagents. I believe a very useful book for the DIYBIO person.

Over Head Solution Mixer

Over Head Solution Mixer

I have been away for awhile. Other things came up and I was unable get back to doing any science and or experimenting. Here is something I did put together this weekend.

Using an old single head mixer, a cocktail swivel stick (it has a propeller at the end of it), lab stand and clamp I am able to make a solution mixer (see second picture). This mixer or stirrer works over head of the solution. Solution container can be a beaker, jar, glass or anything else.

It is very simple to make. I had to heat the end of the swivel stick (the portion that goes into the mixer) and then take a pair of pliers to some what flatten the end to fit it into the notches of the mixer. This holds the stick in and allows for the mixer to spin it.

Other items can be used instead of the mixer, such as, electric screwdriver(very inexpensive to buy or can be found. Most people through them away when the batteries stop holding their charge.), electric motors(such as found in dollar store fans and electric toothbrushes), etc.

Future Projects

Future Projects

I have been very busy lately and with Christmas coming I haven't had as much time to play around as I would like. But here is a list of projects I am working on:

1) converting an old fridge, the bottom section I will use it for chemicals storage unit and convert the top freezer compartment into an incubator.

2) build a flask and plate shaker from an old turntable

3) a roller from an old printer (it rotates and mixes solutions in tubes)

4) a new transfer (sterile) chamber

5) video add-on for the microscope

6) a new work area

So stay tuned in the new year and have a Merry Christmas.

More Lab Chemicals

Here is more to add to the list of chemicals that you can collect for your home lab and where you might be able to get them:

Acetone - (H, D)
Alcohol – Isopropyl (D)
Aluminum potassium sulfate - Alum (G)
Ammonium carbonate - smelling salts (D)
Butane - lighter fluid (department stores)
Calcium Hydroxide - Garden lime (garden stores)
Calcium Oxide - quicklime (H)
Ferric Chloride – circuit board etching (electronics store)
Hydrogen Peroxide – (D)
Lead - fishing weights (sports stores)
Methanol – methyl hydrate solvent (paint stores)
Naphthalene - moth balls (Department stores)
Sulfuric acid - car battery acid (car supply)
Toluene – solvent (paint stores)

I will continue to look for everyday chemicals that can be used in a citizen of science's lab.