Biohacking Start Equipment

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Tobias

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Sep 16, 2016, 2:18:26 PM9/16/16
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Hello

I recently found the topic Biohacking and think its really amazing.
Now i want to start on my one. The Question is what kind of Equipment I need.
I already startet reading and looing videos about gentik. 

Can someone suggest some general instruments and machines i need?

Mfg Tobias

Abizar Lakdawalla

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Sep 16, 2016, 4:49:12 PM9/16/16
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Hi Tobias, any sense what kind of projects you will be considering. Around plants, bacteria, environment, etc.? This would dictate the type of equipment you would need.


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Tobias

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Sep 17, 2016, 3:34:12 PM9/17/16
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I am not sure about that yet. What is less expensvie?
I have another question. Is it allowed in Germany to do Biohacking? 
I readed that in the EU only Labours with permission are allowed to perform such actions.

Abizar Lakdawalla

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Sep 17, 2016, 6:21:55 PM9/17/16
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Written high-level notes that might help you decide on directions. Basically most bio experiments require the following five steps. Have spelled out the first stage. If you are interested, I can expand on the methods and materials required for all five stages.
  • Grow - microbial cells, plant cells, animal cells. 
    • Sources of materials: 
      • Microbial cells: Brewers yeast, Curd yogurt for lactobacilli, feces for E.coli, Probiotic capsules (various)
      • Plant cells: Any small weeds (oxalis/wood sorrel is a great examples), algae from ponds
      • Animal cells: Protozoa from stagnant water (amoeba, paramecium, tetrahymena). Worms, insects. Fresh muscle cells from food meats (poultry, beef) for fibroblasts. 
      • Whole organisms
    • Equipment:
      • Incubators for growing cells (DIY options)
      • Blenders/homogenizers to break tissues into cells (Kitchen supplies)
      • Colorimeters to measure cell densities (DIY options)
      • Microscope (DIY or used options)
    • Consumables:
      • Growth medium to keep cells/tissues happy (bacterial cells in protein and yeast extract powders from health stores, same for yeast and most protozoa; hydroponics materials for plants)
      • Containers for medium and other materials
      • Measuring stuff. Measuring spoons, cups, pipettes. Weighing scale
  • Purify
    • DNA
      • Method 1: Grind, digest with proteases (contact lens cleaners, meat tenderizer tablets) and dissolve with detergents. Add some kind of salt, add alcohol. DNA precipitates out. Spool or centrifuge the DNA. Dissolve in buffer containing EDTA (Versene). EDTA blocks enzymes that digest DNA.
      • Method 2: Grind, digest and dissolve as in method 1. Add Silica or Alumina powders (check sand blasting suppliers). These powders bind to DNA preferentially at high salt. Remove powders with bound DNA by centrifugation. Wash once with high salt buffer. Release DNA with low salt buffer. Under some conditions DNA binds more tightly to alumina.
      • Method 3: Grind, digest and dissolve as in method 1. Add beads that have pores in them to hold back small molecules (Sephadex G50, etc.). The junk gets held back (amino acids, peptides, salts, small metabolites) and the large molecules like DNA and RNA are excluded. Remove the beads by centrifugation or filtration and the liquid (supernantant) will contain the crude nucleic acids.
    • RNA
      • Similar methods to purify as above but RNA is very labile, breaking down easily because of contaminating enzymes that digest RNA that are pretty much everywhere. Equipment used in RNA isolation needs to be pre-processed to be RNAse free. There are tricks to convert RNA directly into DNA and then doing some of the analysis on the cDNA made from the RNA. The steps are not difficult.
    • Proteins
    • Macromolecular complexes
    • Metabolites
  • Manipulate
  • Analyze

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Tobias

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Sep 18, 2016, 10:19:00 AM9/18/16
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Hi

thanks for the detailed answer.
Because we aren't allowed to modify living organism in Germany i cant do any manipulation.
But i am interested in Analyzing and growing organism. As an example i saw a kit where you can grow bacteria and test with natural solutions.

Grettings Tobias

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Tobias

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Sep 18, 2016, 10:19:39 AM9/18/16
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OK thank you for your detailed answer.
The both ideas you writed. In germany we aren't allowed to manipulate DNA on living organisms. Expect we have an signed Class 1 labor.
But analyzing and extracting DNA are still ok. In this both cases i don't manipulate any living organisms, do I ?

Greetings Tobias

Am Freitag, 16. September 2016 20:18:26 UTC+2 schrieb Tobias:

Ja ja ja

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Oct 3, 2016, 1:56:54 PM10/3/16
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ukitel

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Oct 4, 2016, 5:25:56 AM10/4/16
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Hi Tobias,

Where are you in Germany?
The law is indeed a bit tricky, but there are possibilities.
If you are in the nearbies of Berlin, Münich or Heidelberg you can try to join one of the DIYbio communities there.

Best,

ukitel

vasili111

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Oct 11, 2016, 8:57:43 AM10/11/16
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Jérôme Lutz

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Oct 18, 2016, 8:59:36 AM10/18/16
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Hi Tobias, 

we ve asked us the same question two months ago. We are building a biohackspace in Munich and started with setting up a basic chemistry lab. Next step is to buy or build the machines required for doing biology. However, its quite costs to get started.. i think you can expect something around 10.000 € to get started doing biology. But i think that's the beauty of open labs, there you already have everything you need and if not, you only add that one missing piece. 

So depending on where you are (heidelberg > ukitel, berlin > rüdiger / miriam, munich > me or graz > Andreas stürmer, and who else) feel free to join your local biocommunity!

Best, 

Jérôme

On Friday, 16 September 2016 20:18:26 UTC+2, Tobias wrote:

Kermit Henson

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Oct 21, 2016, 3:38:32 AM10/21/16
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10.000e to start a biohacker lab? really?

can you segment this 10k €? 

Patrik D'haeseleer

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Oct 22, 2016, 3:38:55 AM10/22/16
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You definitely don't need 10.000 € to "get started doing biology". If you don't mind working with improvised gear, you can get away with much less than that.

You can use a pressure cooker for autoclave, a beer cooler with a heating pad and thermostat for an incubator. A little dorm fridge/freezer combo.

You might want to buy a used PCR machine off eBay, but even those are not that expensive. Maybe get some cheap pipetters as well.


Felipe Tanaami

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Oct 22, 2016, 4:26:08 AM10/22/16
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If you need an cheap orbital shaker: http://biocracia.forumtupiniquin.com/t2-tutorial-agitador-orbital-para-microtubos-eppendorf
It can't get cheaper than this hhahhaha

John Griessen

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Oct 22, 2016, 1:54:43 PM10/22/16
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On 10/22/2016 03:26 AM, Felipe Tanaami wrote:
> If you need an cheap orbital shaker: http://biocracia.forumtupiniquin.com/t2-tutorial-agitador-orbital-para-microtubos-eppendorf
> It can't get cheaper than this hhahhaha

that unbalanced fan shaker does some really random, high quality shaking!

Felipe Tanaami

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Oct 23, 2016, 7:10:43 AM10/23/16
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Yes! It has two modes of vibration,The first, with a larger amplitude, doesn't work with 1.5 mL eppendorfs, but is good for Falcons; But if you hold the shaker with your hand for some seconds and release, it will start shaking in a smaller amplitude, perfect to brake the surface tension in eppendorfs! You can really see lots of micro drops flying in the tube!

Jérôme Lutz

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Oct 24, 2016, 11:53:37 AM10/24/16
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actually its true, you dont need that much.. especially you dont need an opentron but damn, i love that thing :) But you still need some money, even more than i expected in the beginning. i've cleared our shopping list of a few unneccessary things and in total would cost maybe 3.000 €: 

- 1 Microwave
- 1 5-60 C° Incubator
- 1 UV Light 
- 1 Ultrasonic Bath
- 1 Magnetic Stirrer
- 1 Bunsen Burner
- 1 Miligram scale
- 1 Centrifuge
- Lots of Glass, Petri and plastic dishes
- Liquid Pumps and Tubes

Tobias

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Oct 30, 2016, 3:16:43 PM10/30/16
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Thanks for all the Answers.
I currently try to build my on PCR. The Question is now:
Which Primer and Polymeras do i need? Where can i buy the chemicals?

djwr...@gmail.com

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Oct 30, 2016, 3:33:51 PM10/30/16
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The-Odin.com has everything you need at really cheap prices.
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Maria Chavez

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Oct 30, 2016, 5:50:25 PM10/30/16
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As an additional rescource you might want to check out the English Light version of this booklet on DIY that the SynTechBio group worked on.  Its got alot of info on equipment needs by type of experiment:


On Sun, Oct 30, 2016 at 12:33 PM, <djwr...@gmail.com> wrote:
The-Odin.com has everything you need at really cheap prices.

On Oct 30, 2016, at 12:16 PM, 'Tobias' via DIYbio <diy...@googlegroups.com> wrote:

Thanks for all the Answers.
I currently try to build my on PCR. The Question is now:
Which Primer and Polymeras do i need? Where can i buy the chemicals?

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Abizar Lakdawalla

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Oct 30, 2016, 7:18:54 PM10/30/16
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Hi Tobias, for molecular biology you need the following:
  1. Adjustable pipettors (ranging from 1 ul to 1000 ul). Ebay a good source. Typically US$50-100 per piece. Chinese brands for about US$20.
  2. Thermocycler. Again ebay a good source. US$100-1000 for used systems. Good brands are Applied Biosystems, MJ Research, BioRad ... Likely that the Peltier elements will have to be replaced. Also possible to make your own. Simplest is to have a halogen lamp based heating with an arduino controlling lamp on and off based on feedback from a thermistor. 
  3. Microcentrifuge. Easy to make your own or buy a used one. 
  4. Gel box for agarose gel electrophoresis and power supply. Gel boxes very easy to make your own. Will need to buy platinum wire. power supplies - if you are familiar with electronics - not hard to build your own or buy a used one, US$50-100 on ebay.
  5. Transilluminator - again make or buy with UV LEDs or get a handheld UV lamp (fluorescent tubes or LEDs)
  6. PCR reagents. BioRad sells kits for educational use. http://www.carolina.com also has cheap supplies. $100/kit.
  7. Ice buckets. Any small styrofoam box painted with multiple coats of water based acrylic paint.
  8. Cold storage. Domestic freezer set at coldest temperature. Typically -20C. Dry-ice + isopropanol slurry for -80C.
  9. Colorimeter/fluorometer. Easy to do DIY with LEDs and photodiodes.
  10. Plastics - tubes, pipettes, holders, pipette tips, ...
Methods
  1. DNA/RNA extraction - something to grind tissues (blenders, homogenizers), DNA binding powders (alumina, silica powders for sand blasting washed with alkali and water), centrifuge and pipettors
  2. DNA/RNA quantitation - by gel electrophoresis/transilluminator, by UV light colorimeter (260 nm), by fluorescence (led fluorometer), pipettors
  3. DNA cloning - Incubator, water bath, dry bath, or thermocycler. Pipettor. Gel electrophoresis/transilluminator. Centrifuge. Pipettors.
  4. Growing microbes - incubator (warm box - DIY), shaker, test tubes or flasks or Starbucks Frappucino bottles. Red LED colorimeter to measure growth. Pressure cooker or microwave to sterilize. 


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Tobias

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Oct 31, 2016, 2:00:16 AM10/31/16
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Ok thank for the Information
My own pcr works now.
The question is. IN German genetic modificaiton isnt allowed. But in some Countries crispr doesnt count as GMO. Do anyone know the laws about that in Germany?

Tobias

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Nov 1, 2016, 12:23:04 PM11/1/16
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Hello

I was looking in the internet how i sequenz the dna. Can i  do it myself or is it the best to let it do a company?

Abizar Lakdawalla

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Nov 1, 2016, 12:39:45 PM11/1/16
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Simpler and cheaper to get it done by a company.

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Kermit Henson

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Nov 2, 2016, 4:08:33 AM11/2/16
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yes, use a company. sanger secuencing is very cheap (3USD=1200bp). if you need deeper analisys, a company is also the way to go (sample extraction, library prep, etc..)


El martes, 1 de noviembre de 2016, 17:39:45 (UTC+1), Abizar Lakdawalla escribió:
Simpler and cheaper to get it done by a company.
On Tue, Nov 1, 2016 at 9:23 AM, 'Tobias' via DIYbio <diy...@googlegroups.com> wrote:
Hello

I was looking in the internet how i sequenz the dna. Can i  do it myself or is it the best to let it do a company?

Am Freitag, 16. September 2016 20:18:26 UTC+2 schrieb Tobias:
Hello

I recently found the topic Biohacking and think its really amazing.
Now i want to start on my one. The Question is what kind of Equipment I need.
I already startet reading and looing videos about gentik. 

Can someone suggest some general instruments and machines i need?

Mfg Tobias

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