Where to get project ideas for beginners

[Henry Burnett]

Hi all

I am new to DIYbio and would love to get started as soon as possible. I don't know a lot about it though, so I was wondering if any of you knew where to get good, simple ideas for a first project to do? And where could I get information as to exactly how to do it (a sort of step-by-step guide as to what the actual process is when doing a project)?

[Tobias Viehböck]

Hey,
what is your field of study/work?

Something that I wanted to try for years: QuantaBio is producing phase-lock gel, it seems pretty convenient for DNA/RNA extraction. Phase lock gel is pretty expensive (~1$ per ml). There are some links that try to mimic that, but so far I haven't found a report of actually trying to compare the commercially available and a DIY version.

[MC]

I'm in a similar situation. If you have a community lab nearby, that would be a great start. The-odin.com has some beginner kits with all the supplies and steps laid out for bacterial cultures and transformations that's been a wonderful starting point. 

[Reginald Smith]

Hi, my suggestion would be undertaking a few small projects that involve several steps that are critical to DIY Bio. I can speak from my experience as I own a small vinegar manufacturing company and often analyze my acetic acid bacteria to compare fermentation efficiencies, peak acidity, etc.

Start with a fermented food from the grocery store like (raw and unpasteurized) apple cider vinegar, probiotic yogurt with life culture, kefir, or sauerkraut. First step is learning to culture bacteria properly. You can buy media but it is more instructive to learn how to make it so order so petri dishes off Amazon (100 x 15 mm would be good). Openwetware has a  lot of growth media ingredient lists. For example, if you use raw vinegar you can use the media for Acetobacter Xylinum. I actually have a remix of this recipe adding ethanol and acetic acid (from store bought vinegar) and can post it if you would like. All the ingredients can be found online easily and if  you can't find yeast extract, Marmite works fine. If you are doing yogurt etc. a lactic acid bacteria media is preferable.

From here you would learn how to properly autoclave/sterilize the petri dishes, mix the media with agar in hot water and pour it into the petri dishes to solidify. Culture your bacteria, learn about serial dilution to try to get pure colonies on a new culture, and then the real fun starts.

At this point you can just send the petri dish to a lab to do 16S rRNA sequencing (I recommend Genewiz in NJ for this, about $20 a sample). When you get the sequence back, you can align it in NCBI Blast or download MEGA7 and download a bunch of bacterial 16S rRNA sequences to align and match. From here you can learn about basic bioinformatics like DNA distance metrics, alignment, and making phylogenetic trees to explore the approximate relationship of what you cultured.

If you want to do it the harder, but more educational way, you can learn how to extract chromosome DNA (don't confuse this with plasma DNA) from bacteria using centrifugation and boiling water to get raw DNA. Then you can make a homemade PCR (or buy mini PCR for $650) along with DNA bases, buffer, Taq DNA polymerase, and PCR water along with 16S rRNA primer you can buy from Odin to get a bunch of DNA you can send for Sanger sequencing at a lab for cheap.

Just remember 16S rRNA is a very conserved sequence (and has multiple regions) and evolves so slowly that it is better at distinguishing more distantly related bacteria (see the DIY Bio thread on Odin contamination) than distinguishing between species under the same genus.

Sorry this seems long winded and maybe not quite relevant but I am just trying to give you a simple project that teaches you basic culturing, bioinformatics and phylogeny, DNA extraction, PCR, and sequencing basics. From there you can go wherever you want. Have fun!

Reggie Smith

Supreme Vinegar LLC

[Dakota Hamill]

Great response Reggie.  You should do a post about how you make vinegar and at what scale, of course without giving away any proprietary recipe information!

Always neat to see how a real microbe can turn something into a product we use daily in our lives.

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[ukitel]

Where would you get peptone? or how would you substitute it?

[Cathal Garvey]

Peptone is an old word for "bunch of peptides derived from a digested protein source". Sometimes it implicitly means beef broth peptone, etcetera. You can digest proteins easily at home by adding meat tenderiser or bromelain/papain- containing digestive-aid tablets. You'll need to boil to kill the enzyme afterwards or it'll digest things too much, or digest things you don't want digested.

Bromelain and Papain are both neutral professes that, if memory serves, independently evolved the same basic catalytic activity as trypsin. So, while they're not identical to trypsin, and I think they're a bit more thermally stable, you can probably contrive a way to substitute them for trypsin wherever it's needed and unavailable.

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[Reginald Smith]

If you are in the US, Elemental Scientific LLC (http://www.elementalscientific.net/store/scripts/prodView.asp?idproduct=2383) sells it and they sell direct to individuals. They might ship abroad too but the shipping cost may not be worth it.

[Reginald Smith]

Yeah, I could do a post about that since I essentially use an industrial bioreactor process. I do only thousands of gallons per year, not the millions like the huge consolidated plants in most countries.

On Tuesday, January 2, 2018 at 9:48:00 AM UTC-5, Dakota Hamill wrote:

Great response Reggie.  You should do a post about how you make vinegar and at what scale, of course without giving away any proprietary recipe information!

Always neat to see how a real microbe can turn something into a product we use daily in our lives.

On Mon, Jan 1, 2018 at 12:05 AM, Reginald Smith <reg...@gmail.com> wrote:

Hi, my suggestion would be undertaking a few small projects that involve several steps that are critical to DIY Bio. I can speak from my experience as I own a small vinegar manufacturing company and often analyze my acetic acid bacteria to compare fermentation efficiencies, peak acidity, etc.

Start with a fermented food from the grocery store like (raw and unpasteurized) apple cider vinegar, probiotic yogurt with life culture, kefir, or sauerkraut. First step is learning to culture bacteria properly. You can buy media but it is more instructive to learn how to make it so order so petri dishes off Amazon (100 x 15 mm would be good). Openwetware has a  lot of growth media ingredient lists. For example, if you use raw vinegar you can use the media for Acetobacter Xylinum. I actually have a remix of this recipe adding ethanol and acetic acid (from store bought vinegar) and can post it if you would like. All the ingredients can be found online easily and if  you can't find yeast extract, Marmite works fine. If you are doing yogurt etc. a lactic acid bacteria media is preferable.

From here you would learn how to properly autoclave/sterilize the petri dishes, mix the media with agar in hot water and pour it into the petri dishes to solidify. Culture your bacteria, learn about serial dilution to try to get pure colonies on a new culture, and then the real fun starts.

At this point you can just send the petri dish to a lab to do 16S rRNA sequencing (I recommend Genewiz in NJ for this, about $20 a sample). When you get the sequence back, you can align it in NCBI Blast or download MEGA7 and download a bunch of bacterial 16S rRNA sequences to align and match. From here you can learn about basic bioinformatics like DNA distance metrics, alignment, and making phylogenetic trees to explore the approximate relationship of what you cultured.

If you want to do it the harder, but more educational way, you can learn how to extract chromosome DNA (don't confuse this with plasma DNA) from bacteria using centrifugation and boiling water to get raw DNA. Then you can make a homemade PCR (or buy mini PCR for $650) along with DNA bases, buffer, Taq DNA polymerase, and PCR water along with 16S rRNA primer you can buy from Odin to get a bunch of DNA you can send for Sanger sequencing at a lab for cheap.

Just remember 16S rRNA is a very conserved sequence (and has multiple regions) and evolves so slowly that it is better at distinguishing more distantly related bacteria (see the DIY Bio thread on Odin contamination) than distinguishing between species under the same genus.

Sorry this seems long winded and maybe not quite relevant but I am just trying to give you a simple project that teaches you basic culturing, bioinformatics and phylogeny, DNA extraction, PCR, and sequencing basics. From there you can go wherever you want. Have fun!

Reggie Smith

Supreme Vinegar LLC

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[Jonathan Cline]

On Monday, October 9, 2017 at 6:48:35 AM UTC-7, Henry Burnett wrote:

 

 where to get good, simple ideas for a first project to do?

Business section of different news sources is where to get ideas from.   For example,

https://www.xconomy.com/boston/2017/12/14/ginkgo-bioworks-pulls-in-275m-as-synthetic-biology-funding-soars/

Then choose a topic to do homework on, based on what skills you have to bring into it. 

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[J Pahara]

Hi Henry - if you're up for learning genetic engineering - try a starter kit : https://amino.bio/products/dna-playground-starter-set

If you're looking to learn how to grow cells, engineer them, and extract the stuff you engineered them to make, this is a good starting point - once you master this, then you can move onto a more independent project :)