Re: [DIYbio] Your opinion on reviving extinct species

9:21 PM |

I would fully support it.  Megafauna today are key to ecosystem functioning today (google "ecosystem engineers") where they are still extant, and places where they are missing (almost everywhere outside of Africa and tropical Asia) you find plants without dispersers (google Ghosts of Evolution) and generally unnatural plant communities that have arisen in the absence of ecosystem engineers (i.e., there really isn't any wilderness left, it's all been reshaped by recent extinction).

Further, people are the ones who killed off the megafauna.  High resolution, quantitative records have clarified the timing and order of human arrival, megafaunal extinction, and the subsequent changes in vegetation and fire regimes, all during periods of stable climate- evidence that humans were both necessary and sufficient to induce megafaunal extinctions:


On Tue, Mar 26, 2013 at 5:42 PM, Thomas Landrain <thomas.landrain@gmail.com> wrote:
Hello guys,

I need your assistance. I have been invited to give a talk in a big conference in Cambridge (UK) as a representative of young professionals ;) on how Synthetic Biology and Conservation can be linked together to save or improve the biodiversity on our planet. I'd be very interested in your opinion on the following questions:

- if you were to revive one single species, which one should it be?
- would you welcome such initiative or condemn it?
- what application or abuse can you imagine of such a technology?

I have compiled those questions and more in this web interface. Don't hesitate to use it and share it.

Thanks a lot!!

The conference is organized by the Wildlife Conservation Society. You can find a description of it on this link:

Thomas

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Re: [DIYbio] Good places for sequencing?

8:46 PM |

In Los Angeles both Retrogen and Laragen are alright.  Pickup locations at all the universities.  I've had better luck getting long, high quality reads from Retrogen, though.

-cory

On Mar 31, 2013 8:33 PM, "Avery louie" <inactive.e@gmail.com> wrote:
location is important for this.  I am in Boston, so Wyzer biotech will pick up my samples and have them done the next day or something, for $5.

--A


On Sun, Mar 31, 2013 at 11:18 PM, Koeng <koeng101@gmail.com> wrote:
Hey everyone. I was looking for advice on where I should get sequence verification, just for genes I clone into plasmids. Any places you guys recommend? So far I am looking at genescript because I got some DNA synthesized there and I was happy with their service. Any places you guys have tried?

-Koeng

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Posted by Science

[DIYbio] Re: Good places for sequencing?

8:41 PM |

wow that's awesome. I am near LA, and I don't know any biotech companies, so I don't think I am that lucky.... an other places???

On Sunday, March 31, 2013 8:18:19 PM UTC-7, Koeng wrote:

Hey everyone. I was looking for advice on where I should get sequence verification, just for genes I clone into plasmids. Any places you guys recommend? So far I am looking at genescript because I got some DNA synthesized there and I was happy with their service. Any places you guys have tried?

-Koeng

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Re: [DIYbio] Good places for sequencing?

8:33 PM |

location is important for this.  I am in Boston, so Wyzer biotech will pick up my samples and have them done the next day or something, for $5.

--A


On Sun, Mar 31, 2013 at 11:18 PM, Koeng <koeng101@gmail.com> wrote:
Hey everyone. I was looking for advice on where I should get sequence verification, just for genes I clone into plasmids. Any places you guys recommend? So far I am looking at genescript because I got some DNA synthesized there and I was happy with their service. Any places you guys have tried?

-Koeng

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Posted by Science

[DIYbio] Good places for sequencing?

8:18 PM |

Hey everyone. I was looking for advice on where I should get sequence verification, just for genes I clone into plasmids. Any places you guys recommend? So far I am looking at genescript because I got some DNA synthesized there and I was happy with their service. Any places you guys have tried?

-Koeng

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Posted by Science

Re: [DIYbio] Your opinion on reviving extinct species

4:09 PM |

I get the T.rex answer a lot :)

However we won't probably be ever able to get T.rex DNA in sufficiently high amount and quality.

Please use this survey page to compile your thoughts and answers (this is anonymous):
I'll be sharing all the raw data of the survey on this list after the conference has happened, which will be on the 11th of April.

Spoiler:
According to this survey we almost get half people welcoming such initiative and being ready to buy and pet a member of a de-extinct species (i.e. a Dodo) !



On Mar 27, 2013, at 4:13 PM, Ashley Heath wrote:

T. rex of course!

On Tuesday, March 26, 2013 7:42:37 PM UTC-5, Thomas Landrain wrote:
Hello guys,

I need your assistance. I have been invited to give a talk in a big conference in Cambridge (UK) as a representative of young professionals ;) on how Synthetic Biology and Conservation can be linked together to save or improve the biodiversity on our planet. I'd be very interested in your opinion on the following questions:

- if you were to revive one single species, which one should it be?
- would you welcome such initiative or condemn it?
- what application or abuse can you imagine of such a technology?

I have compiled those questions and more in this web interface. Don't hesitate to use it and share it.

Thanks a lot!!

The conference is organized by the Wildlife Conservation Society. You can find a description of it on this link:

Thomas

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Re: [DIYbio] Re: Where to get primers cheaply

2:04 PM |

Why is your promoter so big... I mean like normally promoters are like 35 bps..

http://partsregistry.org/wiki/index.php?title=Part:BBa_J23119

Are you getting a operator and a RBS too?  Also a recommendation from me is to preform mutagenesis if your strands are that big.

-Koeng
On Sunday, March 31, 2013 12:17:52 PM UTC-7, Mega wrote:

Hi,

No, I meant as a primer for PCR, where promoter is already attached...




On Sun, Mar 31, 2013 at 8:57 PM, SC <stac...@yahoo.com> wrote:
For the 200-mer, I'm assuming you mean a double-stranded fragment you can use for homologous recombination - is that what you had in mind?  I don't think a 200-mer can be used as a PCR primer.
 
You can have such fragments synthesized by Genscript.

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Re: [DIYbio] A Philosopher's Stone

12:48 PM |

Hey all!


Apologies if this is invasive-- I'm a 3rd year student studying biochemistry at The Ohio State University in Columbus, OH. I have a strong interest in bionanotech, specifically the multifunctionality of GNPs, which is sort of a side project of mine.

I've read through this group and was REALLY impressed with you all and am a huge proponent of the DIYbio movement in general.

Would anyone be open to me asking a few questions that I have? If you're interested, please email me! I'd rather not clog up your productive group with my likely pedestrian questions.

I can be reached at this email (carly.larosa@gmail.com). My questions are mostly about your personal interests in GNP synthesis/applications, what you think is promising for future applications, and what strengths or attributes of GNPs make them an interesting candidate for DIY projects.

Best wishes!

Carlyn LaRosa
OSU Biochemistry '15
FIRSTRobotics, Women in Math and Science, Alpha Chi Sigma (Gamma Nu Chapter)

On Tuesday, February 5, 2013 9:46:13 AM UTC-5, Bjonnh wrote:
On Mon, Feb 04, 2013 at 03:56:26PM -0700, leaking pen wrote:
>    There's a difference between a setup, "here's what what we did and what
>    happened" and a model of why it works.
A model is not devoted to an explication of why it works. But used to
try to find how you can try to explain it. By making a description
of a phenomenon, you try to mimic the characteristics of this
phenomenon. It's not meant to be true or false, but it needs to be able to be
falsifiable (proven that it's wrong or not accurate). And to be
falsifiable it means that you need to be able to reproduce it and
compare the whole set of results between the experiments…

--
Jonathan BISSON
PhD in Science, Technology and Health - Speciality : Chemistry-Biology interface

Actually in Oenology post-doc until end of February at :
Laboratoire d'Oenologie - Équipe Philippe Darriet
Institut des Sciences de la Vigne et du Vin (ISVV)
210 Chemin de Leysotte CS 50008
F-33882 Villenave d'Ornon Cedex

Cell: +33 (0) 6 81 39 02 92
E-mail (please use this one from now) : rese...@bjonnh.net

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Re: [DIYbio] Re: Where to get primers cheaply

12:17 PM |

Hi,

No, I meant as a primer for PCR, where promoter is already attached...




On Sun, Mar 31, 2013 at 8:57 PM, SC <stacy734@yahoo.com> wrote:
For the 200-mer, I'm assuming you mean a double-stranded fragment you can use for homologous recombination - is that what you had in mind?  I don't think a 200-mer can be used as a PCR primer.
 
You can have such fragments synthesized by Genscript.

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[DIYbio] East Bay DIY Bio - youtube video of our 4th-ish meeting at Sudo room in Downtown Oakland

12:00 PM |

Hi All,


Here's a video of our 4ish/5ish East Bay DIY bio meeting. Continuing on our two meeting tradition, please find attached the video of our second meeting (feel free to forward past my long drawn out set up process :) ):


Feel free to join us next time (google east bay diy bio)

Ryan

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[DIYbio] Re: Where to get primers cheaply

11:57 AM |

For the 200-mer, I'm assuming you mean a double-stranded fragment you can use for homologous recombination - is that what you had in mind?  I don't think a 200-mer can be used as a PCR primer.
 
You can have such fragments synthesized by Genscript.

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[DIYbio] Re: DIY DNA synthesis?

11:52 AM |

Hello,
Patrick is correct.  Primers are inexpensive to buy, but the companies that make them have purhcased expensive equipment.  Also, the research reagents to make the primers are expensive and perishable.  It really only makes financial sense to make your own if you need a large quantity.  If you are only doing a few experiments, you're much better off buying them premade. 

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[DIYbio] Re: How many of biohackers work in the industry?

10:56 PM |


On Thursday, March 14, 2013 8:09:10 PM UTC-7, Edward Perello wrote:

Do we have data (or estimates) on the ratio of enthusiast biohackers to industry and also academia biohackers? 

From what I've seen I'd estimate:

 10%-25% of biohackers are in the bio-pharma-chem industry. 
 10%-25% of peeps were previously employed in the industry, though currently unemployed and looking for work.
 10% freakazoid whackos often in need of better hygiene and fashion sense
 The remainder are normal people with a side interest in bio or students in bio/chem programs.  There also seems to be a consistent sprinkling of mechanical/industrial eng peeps.

Of those in the bio-industry or previously in the bio-industry, few discussions contain positive descriptions of it.  Common topics of disgust include poor project management practices, patent lockup, reagent waste, materials costs, lack of innovation, inability to obtain desired funding.


## Jonathan Cline
## jcline@ieee.org
## Mobile: +1-805-617-0223
########################

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Posted by Science

[DIYbio] "Chaste" Open Source C++ Library for Computational Physiology and Biology

10:37 PM |

The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste

Developer wiki https://chaste.cs.ox.ac.uk/trac/wiki/GettingStarted
Chaste is only supported on Linux/Unix platforms. The recommended route for Windows and Mac users is to install Chaste on a virtual machine running Ubuntu Linux.

Example showing how to create, run and cell-based simulations in Chaste 

https://chaste.cs.ox.ac.uk/trac/wiki/UserTutorials/CellBasedDemo


Chaste: An Open Source C++ Library for Computational Physiology and Biology


Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, et al. (2013) Chaste: An Open Source C++ Library for Computational Physiology and Biology. PLoS Comput Biol 9(3): e1002970. doi:10.1371/journal.pcbi.1002970 http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002970
 



Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt.

....


Chaste provides libraries for code which is common to many computational biology problems. Here we briefly describe the components of the code and their capabilities. We will present and discuss example simulations, and the new scientific insight Chaste has enabled, in the Results section.

  • global — contains code for basic mathematics (including a random number generator), time stepping, checkpointing (saving and loading simulations) using the Boost serialization library [20], parallel vector classes, and code to handle warnings and errors.
  • io (input/output) — code for reading, writing and conversion of various file formats, including modules to handle the HDF5 scientific file format [21], which enables distributed data to be collated and stored in a single file.
  • mesh — code for linear or quadratic tetrahedral meshes and vertex meshes; nodes, elements, boundary properties; mesh generation; mesh distribution using METIS/parMETIS [22]; readers and writers for Triangle/TetGen [23], [24], Meshalyzer, Cmgui (http://www.cmiss.org/cmgui) and VTK (Paraview) [25] formats.
  • linalg (linear algebra) — code which uses Boost uBLAS [20] and PETSc [26] for vector and matrix operations.
  • ode — code for defining ODEs; solvers, basic finite difference schemes, the Sundials CVODE solver [27]; termination on root-finding capabilities.
  • pde — code for defining elliptic and parabolic second-order PDEs; parallel finite element solvers of generic coupled systems of PDEs (using mesh and linalg).
  • continuum mechanics — code for solving compressible and incompressible general non-linear elasticity problems.




## Jonathan Cline
## jcline@ieee.org
## Mobile: +1-805-617-0223
########################

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Posted by Science

Re: [DIYbio] Re: A scale

5:26 PM |

I can measure the calibration weights on the amazon scale and the nice mettler balance in the lab.

--A

On Mar 30, 2013 8:24 PM, "Avery louie" <inactive.e@gmail.com> wrote:

I got the same scale.  Seems alright.

On Mar 30, 2013 7:56 PM, "Dakota Hamill" <dkotes@gmail.com> wrote:
I got the one off amazon and it's pretty accurate and tares nicely for
the price, it was $21 or $23 I can't remember, was ordering something
else off amazon so shipping was free.  Also, if you have a .edu email,
you can get free amazon prime (amazon student) which is free shipping
on a lot of items.  Free for 6 months.  Pretty good

On 3/30/13, Simon Quellen Field <sfield@scitoys.com> wrote:
> Looks the same to me.
>
>
> -----
> Get a free science project every week! "http://scitoys.com/newsletter.html"
>
>
>
> On Sat, Mar 30, 2013 at 3:18 PM, Mega <masterstorm123@gmail.com> wrote:
>
>> It may be this
>> http://www.aliexpress.com/item/0-001g-20g-Digital-Jewelry-Gram-Gem-Precision-Scale-Weigh-Mini-Electronic-Pocket/780083393.html
>>
>> exactly the same?
>>
>>  --
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Re: [DIYbio] Re: A scale

5:24 PM |

I got the same scale.  Seems alright.

On Mar 30, 2013 7:56 PM, "Dakota Hamill" <dkotes@gmail.com> wrote:
I got the one off amazon and it's pretty accurate and tares nicely for
the price, it was $21 or $23 I can't remember, was ordering something
else off amazon so shipping was free.  Also, if you have a .edu email,
you can get free amazon prime (amazon student) which is free shipping
on a lot of items.  Free for 6 months.  Pretty good

On 3/30/13, Simon Quellen Field <sfield@scitoys.com> wrote:
> Looks the same to me.
>
>
> -----
> Get a free science project every week! "http://scitoys.com/newsletter.html"
>
>
>
> On Sat, Mar 30, 2013 at 3:18 PM, Mega <masterstorm123@gmail.com> wrote:
>
>> It may be this
>> http://www.aliexpress.com/item/0-001g-20g-Digital-Jewelry-Gram-Gem-Precision-Scale-Weigh-Mini-Electronic-Pocket/780083393.html
>>
>> exactly the same?
>>
>>  --
>> -- You received this message because you are subscribed to the Google
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[DIYbio] Anyone interested in trading for 2-Mercaptoethanol? I am in need of other lysis buffer ingredients.

5:23 PM |

Kinda a weird post but I bought 25mL of 2-Mercaptoethanol from Sigma (M3148-25ML Suitable for Cell culture, Electrophoresis...) but no longer need it for my protocols. I am however in need of some of the below reagents.
  • NP-40 or Triton X-100
  • sodium deoxycholate
  • Anything else? Just add a message!

Let me know if your interested! I would prefer that this was to be used in a lab (with a fume-hood...) as it is not the best chemical to deal with.


-Conner
cbertholdbio at gmail dot com

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Re: [DIYbio] Re: A scale

4:56 PM |

I got the one off amazon and it's pretty accurate and tares nicely for
the price, it was $21 or $23 I can't remember, was ordering something
else off amazon so shipping was free. Also, if you have a .edu email,
you can get free amazon prime (amazon student) which is free shipping
on a lot of items. Free for 6 months. Pretty good

On 3/30/13, Simon Quellen Field <sfield@scitoys.com> wrote:
> Looks the same to me.
>
>
> -----
> Get a free science project every week! "http://scitoys.com/newsletter.html"
>
>
>
> On Sat, Mar 30, 2013 at 3:18 PM, Mega <masterstorm123@gmail.com> wrote:
>
>> It may be this
>> http://www.aliexpress.com/item/0-001g-20g-Digital-Jewelry-Gram-Gem-Precision-Scale-Weigh-Mini-Electronic-Pocket/780083393.html
>>
>> exactly the same?
>>
>> --
>> -- You received this message because you are subscribed to the Google
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Re: [DIYbio] Re: A scale

3:51 PM |

Looks the same to me.


-----
Get a free science project every week! "http://scitoys.com/newsletter.html"



On Sat, Mar 30, 2013 at 3:18 PM, Mega <masterstorm123@gmail.com> wrote:
It may be this http://www.aliexpress.com/item/0-001g-20g-Digital-Jewelry-Gram-Gem-Precision-Scale-Weigh-Mini-Electronic-Pocket/780083393.html

exactly the same? 

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[DIYbio] Re: A scale

3:18 PM |

It may be this http://www.aliexpress.com/item/0-001g-20g-Digital-Jewelry-Gram-Gem-Precision-Scale-Weigh-Mini-Electronic-Pocket/780083393.html


exactly the same? 

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Re: [DIYbio] Medium-term storage of bacteria

3:14 PM |

In the fridge, the bacteria aren't metabolically inactive. They're just less metabolically active. Diffusion also proceeds at a slower rate at lower temperatures too. A few months for a plate with visible colonies is probably stretching it, but my naive suggestion (i.e. I've never tried this, but it looks like it'd work) would be you could always streak them out onto a fresh plate and store the fresh plate at 4ºC for a few months, without sealing the plates with parafilm, and then stick them into 37ºC the night before you need to grow overnight cultures.

Now, the only thing is that you'd have to look out for contaminant fungi growing on those plates, that's all...  

Cheers,
Eric
-----------------------------------------------------------------------
Please consider the environment before printing this e-mail. Do you really need to print it?



On Sat, Mar 30, 2013 at 4:54 PM, Mega <masterstorm123@gmail.com> wrote:
Hi everyone,


I have got bacteria that carry a plasmid that encodes resistance ageainst tetracyclin.

They are on Tetracyclin-Agar plates. Can I just store them in the fridge for a few months?


I mean, I once stored Ampicillin resistant E.Coli on Amp plates for (don't remember the exact number 3-5 months). Then re-plated it on fresh LB Amp agar, and they grew without problems.

However tetracyclin has to be actively transported out of cells. Now that they were metabolically inactive, the tetracyclin has entered the cell by osmosis.
When they "wake up" again, they probably won't be able to pump it out again, right?

Other theory: It works bacteriostatic, that means, only when cells divide they get killed. So the bacteria resume metabolic activity, and pump out the antibiotic. Then they divide without any problems...


Anyone experience with this?

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[DIYbio] Re: A scale

3:06 PM |

The same thing on Amazone which costs 21$ there has a catch: 


Shipping is free above 25$ :/ 

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[DIYbio] Re: A scale

2:50 PM |

I wrote down the link weeks ago, but it doesn't work any more... 


Has anyone found other suppliers? 

http://www.aliexpress.com/item/New-0-001g-30g-Digital-Weighing-Gem-Jewelry-Diamond-Scale-Digital-Pocket-Jewelry-register-Free-shipping/555217458.html  is there evidence this one is possibly ok? 

Or that one? 
http://www.aliexpress.com/item/free-shipping-0-01Gram-200g-Digital-Electronic-Jewelry-Weigh-Precision-pocket-Scale-black/730852696.html






On Saturday, January 26, 2013 9:14:13 PM UTC+1, Koeng wrote:
So far I have been using a 10 dollar scale off of amazon, and I want something better because it is hard to make exact measurements for antibotics when the amount i need it 0.01 grams and it counts to 0.00. Anyone got recommendations for a new scale? Or should  I keep surfing ebay?
Since I don't want to "spam" I also wanted to ask if anyone knows of any good spectrometers.

-Koeng

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[DIYbio] Medium-term storage of bacteria

1:54 PM |

Hi everyone,


I have got bacteria that carry a plasmid that encodes resistance ageainst tetracyclin.

They are on Tetracyclin-Agar plates. Can I just store them in the fridge for a few months?


I mean, I once stored Ampicillin resistant E.Coli on Amp plates for (don't remember the exact number 3-5 months). Then re-plated it on fresh LB Amp agar, and they grew without problems.

However tetracyclin has to be actively transported out of cells. Now that they were metabolically inactive, the tetracyclin has entered the cell by osmosis.
When they "wake up" again, they probably won't be able to pump it out again, right?

Other theory: It works bacteriostatic, that means, only when cells divide they get killed. So the bacteria resume metabolic activity, and pump out the antibiotic. Then they divide without any problems...


Anyone experience with this?

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Re: [DIYbio] Amazing Breakthrough from Home Lab

6:04 PM |

On Fri, Mar 29, 2013 at 6:40 PM, Bryan Bishop <kanzure@gmail.com> wrote:
> On Fri, Mar 29, 2013 at 4:42 PM, SC <stacy734@yahoo.com> wrote:
>> Finally, a home lab in the news in a positive light.
>
> "In her research she developed a process of artificial selection where
> she killed off algae with low levels of acetyl-CoA carboxylase
> (ACCase), an enzyme crucial to lipid synthesis. Left behind in the
> beakers under her bed were an efficient bunch of high yield algae,
> which she discovered produced a significant increase in lipid
> production."
>
> I wonder what the selection technique was. Maybe just separating
> populations, taking a measurement, and then deciding which to dump.
>

Would be nice to hear more. Some more details:
http://www.intel.com/content/www/us/en/education/competitions/science-talent-search/winners.html
http://www.societyforscience.org/sts/2013finalists/svolz

BINGO

Optimizing Algae Biofuels: Artificial Selection to Improve Lipid Synthesis

http://www.csef.colostate.edu/2012_Abstracts/Volz_Sara.pdf

energy.colostate.edu/docs/7_Volz.ppt

Hmm, she's doing some quiet advanced stuff. qPCR, immunoblotting,
Trizol RNA extraction. So looks like she partnered the Colorado State
U. I didn't read it all yet.

BTW, Google, you broke gMail. *pulls out Thunderbird*

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Re: [DIYbio] Amazing Breakthrough from Home Lab

3:40 PM |

On Fri, Mar 29, 2013 at 4:42 PM, SC <stacy734@yahoo.com> wrote:
> Finally, a home lab in the news in a positive light.

"In her research she developed a process of artificial selection where
she killed off algae with low levels of acetyl-CoA carboxylase
(ACCase), an enzyme crucial to lipid synthesis. Left behind in the
beakers under her bed were an efficient bunch of high yield algae,
which she discovered produced a significant increase in lipid
production."

I wonder what the selection technique was. Maybe just separating
populations, taking a measurement, and then deciding which to dump.

- Bryan
http://heybryan.org/
1 512 203 0507

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[DIYbio] Amazing Breakthrough from Home Lab

2:42 PM |

Finally, a home lab in the news in a positive light.
 
 
 

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New Opening!! Looking for Oracle Techno-Funtional for 6+ Months Contract @ Keene, NH

7:43 AM |

Please send your resumes at niranjank@xperttech.com

Hi

My name is Niranjan and You can see the details and requirement of the position in the following description. If interested, please send me word formatted resumes to niranjank@xperttech.com.

Role: Oracle Techno functional Lead (Inventory)

Duration: 6+ Months Contract

Location: Keene, NH

 

Description:

·         They need to be very strong in Inventory module

·         Need to have PIM experience

·         Need to know FIFO (First in First Out)

 

 

Thank you,

 

Niranjan Kumar Chikkala

Technical Recruiter

400 W Cummings Park,

Suite#2850

Woburn, MA-01801

Email: niranjank@xperttech.com

Phone: 781-926-0781 EXT: 3017

Fax: 781-207-0709

www.XpertTech.com

 

Delivering the POWER of Technology



 


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