November 2014 | Science

Re: [DIYbio] [diybio-eu] Indie.bio - Any interest in a "curated call" list?

6:36 PM |

I really like this idea and we've already seen interest in this from many of the applicants to indie bio, teams that need specific skill sets as the start accelerating. So how best could we set it up to give idea generators credit as Patrik mentioned? Like a hackernews for bio ideas?

On Saturday, November 29, 2014 10:17:09 PM UTC-8, Patrik D'haeseleer wrote:

On Saturday, November 29, 2014 12:08:54 PM UTC-8, Nathan McCorkle wrote:
Exactly, I have a few ideas/projects that I would love to farm out to
the right/interested team. A platform for this would probably allow an
idea-poster to choose what license/business-model (trade-secret,
patents, open-source). For these such projects, I've done lots and
lots of research but am too busy with other things currently, so I
would really just want to be an adviser. Open-source projects would
obviously be easier to get going and develop trust, I think... but I
do think non-open projects could gain from this sort of system.

Basically it would like posting your idea to indie.bio's list of
'project ideas' (with their approval) and then choosing a team from
the people who showed up saying it was interesting to them.

I might be interested in something like this as well. I have way more ideas than I can pursue by myself anyway. But it would be nice to at least get credit for the idea.

I don't care much for patents, and equity doesn't truly excite me. My "coin of the realm" is to be recognized and acknowledged for the ideas that I bring to the table. Of course, anyone writing a patent would totally be shooting themselves in the foot by acknowledging that the idea came from someone else. But that just goes to show how messed up the patent system is...

Patrik

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[DIYbio] Re: Another project suggestion: oral weathermaps

5:34 PM |

Hey, I know this thread is old, but I'm very interested in this project idea, especially when combined with other CAMBRA or preventative dentistry methods. Did anything come of this project? If so please let me know! cetesyes@gmail.com

On Sunday, February 15, 2009 2:02:56 PM UTC-5, Andrew Hessel wrote:

Last week, I was at the dentist. These trips haven't changed much since I was a child: X-rays, oral inspection, cleaning with metal pick and floss, fluoride rinse, admonition about brushing, flossing, etc, and a freebie toothbrush.

My dental clinic seems like a well-run car dealership. I'm getting regularly scheduled maintenance but little more. The focus is prevention, managing expectations and, ultimately, mediocre care.

Teeth are complex, living structures. And they aren't alone. The mouth is colonized by bacteria shortly after birth. They grow easily there, feeding on the plentiful sugars and other foods to found there. To a bacteria, each tooth is an entire planet, with a population of billions.

Bacteria form complex ecosystems on their teeth-planets. There are hundreds of species known considered "normal flora" in the mouth; these were identified by culturing, which means there may be 10X or 100X more, plus viruses and fungi. It is these microorganisms that ultimately determine whether one has cavities, health gums, bad breath, etc.

Saliva helps control microbial growth. Brushing and flossing helps knock back the population numbers to a more manageable level. Still, the bacteria have formidable defenses, including the ability to organize into biofilms that are very resistant to chemical or mechanical attack. They also swap genes all the time.

Most dentists recognize Streptococcus mutans, which converts sugar to acids that can attack enamel, as a prominent microbial cause of cavities. But what about gingivitis, periodontal disease, or even foul breath? Chances are good there are complex ecosystems that haven't been teased apart yet with modern gene-based identification technologies.

I propose a DIYbio oral weathermap, something along these lines:

1. Brushing of teeth with a moistened brush (no toothpaste) then spitting into a commercial spit kit.

2. The 16S ribosomal RNA genes amplified and sequenced. The species and relative proportions thereof could be determined, produce a "weathermap" of bacteria. (We might be able to find a sponsor for this work, given it has downstream commercial applications.)

3. Correlate results to known oral histories. We could get copies of our dental charts if necessary. Mouths with health gums and no cavities would represent the gold standard "balance" of bacteria, while bacterial patterns that correlate with high cavities or more serious diseases would flag the mouth for more vigilant attention, or possible treatment.

4. Time-course studies could be done. How do the numbers change over a typical day in a normal mouth? In a cavity prone mouth?

5. Explore treatment considerations, eg alternatives for balancing the oral flora back to a healthy mix in ways that ideally do not require lengthy approval processes. We might think about what could be done with bacterocins, natural compounds, or peptides known to selectively knock back various species, block attachment (see the related 2008 MIT iGEM project here), or interfere with biofilm formation.

 Anyone trained in dentistry out in DIY world? :)

Andrew

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[DIYbio] Re: Questions about Noctiluca scintillans-bio illuminant Dinoflagellate

3:48 PM |

hi, I raised it around 4month.

在 2014年11月13日星期四UTC上午7时26分03秒，Patrik D'haeseleer写道：

On Monday, November 10, 2014 1:46:32 AM UTC-8, 陳彥吟 wrote:
Hi,

Thanks for your reply.

I grow it was quite successful in the hackerspace.

Excellent - do you have them growing as an isolate? If so, how do you feed them, and how long have you been able to keep them?

If you're already growing them in thelab, then you're the expert here..

Patrik.

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[DIYbio] Re: Uptake of food transgenes by guy bacteria

3:25 PM |

It's funny - Dow and DuPont are also big developers of GMO crops, but you never hear poeple complaining about them. I guess they just keep a low profile. I bet they're amused about Monsanto's bad PR though.

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Re: [DIYbio] Re: Uptake of food transgenes by guy bacteria

2:20 PM |

On Sun, Nov 30, 2014 at 11:37 AM, Mega [Andreas Stuermer]
<masterstorm123@gmail.com> wrote:
> I kinda wish I would be on Monsanto's paylist, because people think I am
> anyway :P
> Wouldn't be too bad to have sufficient money for a few DNA synthesis'es.

And they are industry-leaders in general, even if they're not a very
friendly player.

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[DIYbio] Sending Adult Fireflies

1:47 PM |

I am a senior undergraduate planning a firefly research project that will start in January. I am in the process of collecting materials and have collected firefly larvae from my area, but would much rather work with adult fireflies but do not have any adults, and they will not be around until May/June. I have been unsuccessful in getting responses from universities and entomological societies in Brazil and Australia. I am wondering if anyone on here who lives in the southern hemisphere or a warm climate and has access to adult fireflies, would be willing to send some to me. Or if you know anyone that could help me out. I am located in Ohio in the US and I can pay for shipping and your time. PM me if you can help :)

Thanks!

Corey

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[DIYbio] Re: Isolating sequences from scratch

1:12 PM |

Hi Nico,

I would suggest practicing the techniques on a readily available plant, like a cheap houseplant. Once you can do library prep easily, then send for the target plant.

Plants have large genomes, so doing the entire genome with the usual combination of PacBio/Illumina assembly would be expensive, in excess of $100K. Instead, if you make a clone library you can identify the likely genomic fragment by doing a relatively inexpensive end-sequence for each clone and comparing it to the plant species with known genome sequence. It is more of an exclusionary process: you can eliminate the clones which are not likely to contribute to the trait. For example, genes involved in central metabolism will not influence flower morphology. The clones you are left with are the ones to focus on. That;s the fun part: you can compare clone sequence to the many mRNA sequences of plants known to be expressed in flowers only (as opposed to leaves, roots, etc.)

As always, the more you can do yourself, the cheaper it will be. Library construction and plasmid prep can be done in your home or a community lab or school. Sequencing will probably have to be sent out unless you know someone with a sequencer.

I am in th DC area - are you nearby? I would be happy to show you how to make a library. I do this very often.

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Re: [DIYbio] O'Reilly BioHacker Issue 4: Open Source Biotech Consumables

1:05 PM |

On Sun, Nov 30, 2014 at 3:03 PM, Pieter <pietervanboheemen@gmail.com> wrote:

CC made it easy to share pictures on the web. I still have no proper way to share strains from our collection under a simple attribution condition except for setting up contracts with every peer, which is practically speaking impossible.

What problems are you encountering or what problems would you expect to encounter with the contracting scheme?

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

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Re: [DIYbio] O'Reilly BioHacker Issue 4: Open Source Biotech Consumables

1:03 PM |

The subject has been on the agenda of a few of the latest biomedia meetings I've been, such as biocommons Helsinki and biofiction in Vienna. Anyone is more than welcome to join the conversation on biocommons@bioartsociety.fi or contribute to the github of http://www.bio-commons.org/

The challenge is huge. WTO, WIPO, Rio de Janeiro, etc etc conventions. Mutual benefit agreements, material transfer agreements, contracts rights. Copyright, patents and other rights. You have to be careful what you wish for when talking about new license or right models. Remember that copyright was invented to protect individual artists from the influence of large reproduction companies to begin with.

CC made it easy to share pictures on the web. I still have no proper way to share strains from our collection under a simple attribution condition except for setting up contracts with every peer, which is practically speaking impossible.

On Sunday, 30 November 2014 17:32:29 UTC+1, John Griessen wrote:

On 11/29/2014 12:33 PM, Cathal (Phone) wrote:
> However, there's little (compared to equipment) money or excitement
> in open source platforms. I know: I tried!
> There's a great core community
> (here!) who create and support openness, but outside that core are
> people who just want features and don't care if it's theirs to hack or not.

Not caring if it's open is the mainstream of scientists -- they operate on
as high an abstraction level as they can, because that's what their jobs
demand, so yes, "scientists need money, too".

Mainstream in this context is the 99% of them with jobs. The rest of the planet
is the bigger mainstream, for which science is a niche market. So, there
are high prices for equipment and supplies. I'm working on developing
some gear that is up to the minute enough, and convenient enough
to be a tool for maybe a third of those 99% job holding scientists and
still is open source/open-hardware. I'm OK with copycats taking away
the initial idea in about 3 years, since I come up with new all the time
and the 3 year sales flow will pay for development if you're careful.
Patent danger does not go away for 20 years, so I may have to drop some
design chunks and redevelop them to be non-patent-infringing -- or drop that product...

The life cycles of open-hardware products is not well known yet, but there are some
that last a while. They have to be more than a break out board to last.
I'm going to find out if a complex system that can have features added
still sells in version 2, 3, 4 after the initial hard-to-copy-cat phase.

The evil mad science eggbot is selling still, and demonstrates this
kind of product life cycle is possible. The wiki page for using it
has been accessed 208,455 times.

The core to all my open equipment design thinking is to keep the IP
chunks really close to old patent-expired tech and the innovation
is in using chips and combinations, which will trigger less
patent problems than new science. To really open-hardware some
reagents may require using the patent system to own it, then
contractually releasing it as the owner.

Like Bryan said. And like Josh said about designing around patent research.

Josh: Are you giving patent research lessons these days?

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[DIYbio] Re: Isolating sequences from scratch

12:49 PM |

Hey Stacy,

If I were to order the plant today it would take a few weeks to arrive.

In interim, how could I go about prepping? I'm a novice and am not extensively familiar with these terms and procedures. How would I go about making a large insert shotgun library and the following steps of plasmid preps and end-sequencing? not to mention, what exactly would the end sequencing help me accomplish?

Its easy to order the plants online, seeds as well. however I'm not sure when I will have a blooming flower (tissue), once I receive seeds/plant. Its cultivated.

Thanks,
Nico

On Tuesday, November 25, 2014 12:06:44 PM UTC-8, SC wrote:

Hi Nico,

The cheapest way to get going would be to make a large insert shotgun library. You'll need access to live plant tissue for that; if you don't have access to live plant tissue, you can make a small insert library. That would be followed by some plasmid preps (not expensive), and some end-sequencing (a little expensive).

I'd be happy to help you through the project.

To start with, do you have access to live tissue? Is this species wild-collected or cultivated?

Stacy

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[DIYbio] Re: Ethics of Guerrilla planting Transgenic plants

12:36 PM |

Thanks for the responses. This is predominantly a hypothetical question. some of the ideas for projects at the space had been circling around this topic but I'm sure there is no palpable desire to release transgenes with out permissions.

I have read some interesting articles about trangenic poplars with CYP2E1 expression. I've given some thought into putting a similar gene of the P450 family into a transgenic P. virgatum for hastier root establishment. Sebastian made a point that nuclear transform then gives the pollen the same traits, which could possibly be accepted by another plant that could receive the transgene. Would this necessarily be a bad thing if its an expression for the metabolism of VOCs, BTEX, and halogenated compounds?

On Friday, November 21, 2014 7:49:34 PM UTC-8, Nico B. wrote:

A few of the projects that are being done at the maker space I go to for synbio classes are directed towards bioremediation through transgenic guerrilla gardening. We've been discussing the need for heavy monitoring to prevent propagation for the potential of ecosystem/food web disruption, but I'd like to hear more reasons for why and why not guerrilla garden transgenic species of grasses/shrubs for biodegradation of pollutants, sequestration of heavy metals in urban soils, ground water filtration, etc.

Thanks

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Re: [DIYbio] Ethics of Guerrilla planting Transgenic plants

12:18 PM |

I'm mainly looking into urban soils. Where I live, I have found that many large-scale infrastructural projects are aware of the use of industrial debris and wastes in their foundations in a layer of sediment that is called 'artificial fill.' The EPAs definition of this debris is quite limited for the state of CA, where other state's definitions are quite detailed. I've found reports of asbestos and lead based paints being used in this fill layer, along with some experience in construction and knowing what is often left behind or neglected.

Now there are many organizations working in the clean up efforts, I had just thought of transgenic introduction after reading an article on CYP2E1 transgenic Poplars and their ability to degrade and sequester incredible amounts of such pollutants in brownfield or at superfund sites.

On Monday, November 24, 2014 10:22:57 AM UTC-8, Pieter wrote:

Life finds a way my friend. Just watch Jurassic Park and you'll understand that heavy monitoring alone will not keep your mutants strictly on your field.

Why do you believe it is necessary to clean up soil in the first place? Is there a need for it, or do you think it is better in some way?

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[DIYbio] Re: Uptake of food transgenes by guy bacteria

11:37 AM |

I kinda wish I would be on Monsanto's paylist, because people think I am anyway :P

Wouldn't be too bad to have sufficient money for a few DNA synthesis'es.

On the other hand, of course, choosing your projects yourself is what most of us wanna do. For the benefit of humanity, not for profit-maximizing....

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[DIYbio] Re: Need some help starting a project (Agrobacteria-mediated transformation of a dicot via floral dip)

9:21 AM |

Ah I forgot to mention, you can also try a transient transformation. Just streak the leaves with the agobacterium solution, and they will get the gene inserted. However, the leaves get brown after x weeks, and die off. So the whole plant is not a transgene, it's a mosaic. Still nice to try with GFP. For some plants you cann add vanillin to agrobacterium to enhance the aggressivity (it acts as a wound signal).

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Re: [DIYbio] Re: update on the liquid handler

9:00 AM |

On 11/29/2014 02:20 PM, Yuriy Fazylov wrote:
> John, for Otto's design you are offering a projection out of the relatively 2D frame to navigate about a series of cascading shelves. Is that correct?

Yes. I was seeing how tilt can be an advantage. It allows lots of terraces of area to be accessed
without such a wide/heavy moving part on the gantry. A small projection away from vertical
would be enough to reach under the terrace above -- same as terrace overlap.
Terrace vertical spacing can be about human hands getting in there.

Being vertical can be seen as a disadvantage, but once you get past issues like "It's tippy!",
you might find people like its small footprint. Sell it with clamps to
fasten on the edge of lab benches, or even on the edges of upper lab bench shelves that are solid.

Here's an idea:

Q: What if it goes up vertically from a top lab bench shelf so high it's out of reach mostly
except for the bottom two terraces?

A: Make it a liquid handler with a latch thingy so it can also be a tray handler to
deliver trays down where people can reach them. Have designated lower shelves for
humans to use -- not needing very much vertical spacing, and each shelf has a readout
showing what the tray name and contents are. No confusion, and results of some programmed
sequences of mixology are ready to go on a lower shelf. Add a clean air box around all this
and voila -- automation! Maybe later even add humidity, incubation, CO2 to the liquid handling space...

And all that might take up 15 inches of lab bench top shelf space.
The shelves that are a little below eye level.

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Re: [DIYbio] O'Reilly BioHacker Issue 4: Open Source Biotech Consumables

8:32 AM |

On 11/29/2014 12:33 PM, Cathal (Phone) wrote:
> However, there's little (compared to equipment) money or excitement
> in open source platforms. I know: I tried!
> There's a great core community
> (here!) who create and support openness, but outside that core are
> people who just want features and don't care if it's theirs to hack or not.

Not caring if it's open is the mainstream of scientists -- they operate on
as high an abstraction level as they can, because that's what their jobs
demand, so yes, "scientists need money, too".

Mainstream in this context is the 99% of them with jobs. The rest of the planet
is the bigger mainstream, for which science is a niche market. So, there
are high prices for equipment and supplies. I'm working on developing
some gear that is up to the minute enough, and convenient enough
to be a tool for maybe a third of those 99% job holding scientists and
still is open source/open-hardware. I'm OK with copycats taking away
the initial idea in about 3 years, since I come up with new all the time
and the 3 year sales flow will pay for development if you're careful.
Patent danger does not go away for 20 years, so I may have to drop some
design chunks and redevelop them to be non-patent-infringing -- or drop that product...

The life cycles of open-hardware products is not well known yet, but there are some
that last a while. They have to be more than a break out board to last.
I'm going to find out if a complex system that can have features added
still sells in version 2, 3, 4 after the initial hard-to-copy-cat phase.

The evil mad science eggbot is selling still, and demonstrates this
kind of product life cycle is possible. The wiki page for using it
has been accessed 208,455 times.

The core to all my open equipment design thinking is to keep the IP
chunks really close to old patent-expired tech and the innovation
is in using chips and combinations, which will trigger less
patent problems than new science. To really open-hardware some
reagents may require using the patent system to own it, then
contractually releasing it as the owner.

Like Bryan said. And like Josh said about designing around patent research.

Josh: Are you giving patent research lessons these days?

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[DIYbio] Re: Need some help starting a project (Agrobacteria-mediated transformation of a dicot via floral dip)

8:01 AM |

http://www.markergene.com/Categories/plants.php

e.g. this one

M1593	pCambia1302 Plant Expression Vector		20 μg	$114.45	114.45
Vector contains kanamycin resistance gene for bacterial selection, hygromycin B resistance gene for plant selection and the mgfp5 reporter gene

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[DIYbio] Re: Need some help starting a project (Agrobacteria-mediated transformation of a dicot via floral dip)

7:56 AM |

Hi! AFAIK there already are pCambia Vectors which already contain EGFP unter a plant promoter. So ready to use for your floral dip.

It may be best to try floral dip for you, because it yields quick results without needing tissue culture.

On Thursday, November 27, 2014 12:03:13 PM UTC+1, antomicblitz wrote:

I'm currently an undergrad studying molecular biology, and I recently joined a community lab after taking biochemistry lab at my school. In my class, we transformed a colony of E. coli using egfp and I thought it was really cool, and I've kind of been obsessed with trying it with other organisms as well, so I wanted to see if maybe I could do the same thing with a plant. After spending a few days at the library and searching through a couple of scientific journals, I found that I could do a similar procedure with agrobacteria, which can use a disarmed tumor-inducing plasmid to inject a segment of tDNA from another binary plasmid into a plant genome (I'm still not 100% sure how that works or where in the genome it gets incorporated, but I know it works at least). I would like to try and put egfp into a plant and have it expressed at detectable levels. I've had people tell me it's not too difficult to do. If any of you have done it before, or if you know what is involved, could you possibly give me some pointers on how/where I can order the appropriate plasmids, and which strain of agrobacteria I can use? I found a couple of protocols, so I have a general idea of what I'm gonna do (floral dip), but I'm still a bit iffy on how to select the right plasmids and bacteria, and where exactly on the binary plasmid I should ligate my gene of interest. Any help is much appreciated :).

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Re: [DIYbio] Need some help starting a project (Agrobacteria-mediated transformation of a dicot via floral dip)

12:50 AM |

Wow! Than you sebastian! That was some incredible information! I will try to do this next weekend. With any luck, I'll have some glowing plants 😊. I would love to get in touch with you and follow you as well, since I am just starting to learn this stuff and I think it's really fun :).

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Re: [DIYbio] [diybio-eu] Indie.bio - Any interest in a "curated call" list?

10:17 PM |

On Saturday, November 29, 2014 12:08:54 PM UTC-8, Nathan McCorkle wrote:

Exactly, I have a few ideas/projects that I would love to farm out to
the right/interested team. A platform for this would probably allow an
idea-poster to choose what license/business-model (trade-secret,
patents, open-source). For these such projects, I've done lots and
lots of research but am too busy with other things currently, so I
would really just want to be an adviser. Open-source projects would
obviously be easier to get going and develop trust, I think... but I
do think non-open projects could gain from this sort of system.

Basically it would like posting your idea to indie.bio's list of
'project ideas' (with their approval) and then choosing a team from
the people who showed up saying it was interesting to them.

I might be interested in something like this as well. I have way more ideas than I can pursue by myself anyway. But it would be nice to at least get credit for the idea.

I don't care much for patents, and equity doesn't truly excite me. My "coin of the realm" is to be recognized and acknowledged for the ideas that I bring to the table. Of course, anyone writing a patent would totally be shooting themselves in the foot by acknowledging that the idea came from someone else. But that just goes to show how messed up the patent system is...

Patrik

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Re: [DIYbio] O'Reilly BioHacker Issue 4: Open Source Biotech Consumables

7:27 PM |

I'm the guy behind Open qPCR, and while I don't believe all patents are evil, I do believe it's in society's best interests for certain fundamental technologies to be open and available to all. We on this mailing list can't change the patent system, but we can work to open up these key technologies and reagents.

There's a lot of confusion amongst researchers as to what is patented and it takes extra work to release an open project -- first researching and understanding the IP landscape to see what is truly protected, and then design around the remaining true obstacles. We're trying to do this again right now with our Chai Green reagent, an IP-free intercalating dye suitable for Real-Time PCR or basic gel staining.

As Cathal said the number of people that truly appreciate the openness is small compared with the number of people who just want cheap products. If we want open source science to succeed we need to find ways to grow the number of people who specifically support open projects, as well as grow the number of people open sourcing new technologies.

-Josh

On Sat, Nov 29, 2014 at 6:07 AM, Aizan Fahri <vilafrantez@gmail.com> wrote:

Hi there, Aizan's here from Rochester NY. Couple things I want to say here, and let me hear your thoughts.

1. I've been keeping eyes and ears on few Kickstarter projects like the extremely successful Open QPRC that got 100% funded less than 5 days. Couple more cool projects like Open Trons and MiniPCR, and I like these projects because they are trying to keep the cost to do science as low as possible, which is what exactly we need to move this field forward.

2. Based on the point number 1, and from the article Open Source Biotech Consumables, the only thing we are quite lagging behind is the patent this! culture through bureaucratic processes and mutual trust agreements. Schloendorn proposes in the article by saying that the reagents (proteins, RNA, DNA), some of the important ones, should be open source assets instead of being patented assets. It makes the field of bio and biotechnology more accessible and cheaper, and faster to move forward as in the advancement in the world of technology. For example the widespread adoption of Android mobile operating system is really a huge success, thanks to the fact that Android itself is open source.

3. So the question is, can we really open source the reagents? Or we still need to patent them because "scientists need money, too"?

Thanks!

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[DIYbio] Re: Indie.bio - Any interest in a "curated call" list?

3:05 PM |

Hm, I can see the value in Nathan's suggestion of a system that mediates idea licensing, ownership, terms of collaboration, etc.. very clever. That'd be pretty cool, and obviously tying it in to sources of funding or acceleration would be great. :)

Definitely food for thought!

On 29 November 2014 21:32:46 GMT+00:00, Chowe <coreyhowe99@gmail.com> wrote:

As a graduating bachelors-bioengineer, I agree with Nathan that I, for one, am ready to be put to work and my main focus right now is finding the right project/idea to pursue. I would love to participate in the Indiebio program, because it seems like it would be a great experience for a recent graduate, however I do not have many of my own ideas that are business worthy and I also lack the networking to join existing teams.

I would definitely utilize a list of "suggested ideas" and would eventually love to see a place dedicated to matching independent biotech projects/ideas with people, so you do not have to look very far or for very long to find your team or project. I realize this is possible through the DIYbio group and many other places, and has been successful many times, however a place specifically meant to match projects to people would make this process a lot more efficient, saving lots of time and effort, especially for a recent graduate.

On Friday, November 28, 2014 10:37:07 AM UTC-5, Cathal Garvey wrote:
Hey all,
So, in discussing Indie.bio recently, an idea occurred to me, which is
that many of us have the technical skill or access to cofounders to
accomplish great stuff, but may be going through a dry period for ideas
or products.

So, while applications are still expected to describe their own project
and product from scratch and all ideas are welcome, we could publish a
list of "suggested ideas"; stuff that we think would be really cool, and
for which we'd be interested to see well-considered applications.

Would this be useful to anyone? Is anyone out there interested in taking
part, and thinks they could do a great job at indie.bio, but lacks an
actual project to work on?

Best,
Cathal
PS: Note new domain name, indie.bio ! Yay for new TLDs!

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[DIYbio] Re: Indie.bio - Any interest in a "curated call" list?

1:32 PM |

As a graduating bachelors-bioengineer, I agree with Nathan that I, for one, am ready to be put to work and my main focus right now is finding the right project/idea to pursue. I would love to participate in the Indiebio program, because it seems like it would be a great experience for a recent graduate, however I do not have many of my own ideas that are business worthy and I also lack the networking to join existing teams.

I would definitely utilize a list of "suggested ideas" and would eventually love to see a place dedicated to matching independent biotech projects/ideas with people, so you do not have to look very far or for very long to find your team or project. I realize this is possible through the DIYbio group and many other places, and has been successful many times, however a place specifically meant to match projects to people would make this process a lot more efficient, saving lots of time and effort, especially for a recent graduate.

On Friday, November 28, 2014 10:37:07 AM UTC-5, Cathal Garvey wrote:

Hey all,
So, in discussing Indie.bio recently, an idea occurred to me, which is
that many of us have the technical skill or access to cofounders to
accomplish great stuff, but may be going through a dry period for ideas
or products.

So, while applications are still expected to describe their own project
and product from scratch and all ideas are welcome, we could publish a
list of "suggested ideas"; stuff that we think would be really cool, and
for which we'd be interested to see well-considered applications.

Would this be useful to anyone? Is anyone out there interested in taking
part, and thinks they could do a great job at indie.bio, but lacks an
actual project to work on?

Best,
Cathal
PS: Note new domain name, indie.bio ! Yay for new TLDs!

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Re: [DIYbio] Red-tide and dinoflagellate

1:25 PM |

On Sat, Nov 29, 2014 at 1:19 PM, Mark Szepieniec <mszepien@gmail.com> wrote:
> So to summarize, you're interested in positive applications for the ammonia
> H2S and phosphorus that dinoflagellates produce, and which are harmful for
> other life.

I got the idea that they were also interested non-harmful remediation
methods... i.e. dumping something into the sea to neutralize the
negative dino-effluent.

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Re: [DIYbio] Red-tide and dinoflagellate

1:19 PM |

So to summarize, you're interested in positive applications for the ammonia H2S and phosphorus that dinoflagellates produce, and which are harmful for other life.

I'm not a chemist, but it seems likely to me that the concentrations of these substances would be too small for it to be economical to do extract them and do something with them, even though the concentrations are large enough to be problematic for other wildlife.

Of course it's possible that just cleaning the seawater is valuable enough, so maybe the important question is simply how to do that in a scalable way?

On Sat, Nov 29, 2014 at 8:51 PM, 陳彥吟 <kyo05012000@gmail.com> wrote:

red- tide is the biggest disaster to the ocean. Red- tide means the booming of the algal. When algal booms, it floating on the surface of water, fishes and sea mammals suffers low oxygen and die gradually. Some algal not only makes sea creatures die, but also generate poisonous. The poisonous substance such as ammonia, H2S and phosphorus those could change the acidity of water. It brings the great impact for the food chain and poison human being indirectly.

The phenomenon always happens in the developing countries and coast area. Especially in China. In the recent year, this problem is getting seriously. My hometown is very close to China, we suffer the red-tide more frequently year by year. Lucky, the spices be found in my hometown is bioiluminiscent. The accidental beauty attracts tons of tourist come to this remote city.
Base on the research, dino generate ammonia, H2S and phosphorus when it booming and die . I assume if I can find another substances to create chemical reaction with those substances.Then make something. Just like the principle of seashell generate is CaCO3＝CaO+CO2, it would bring some contributions for local.
Do any experts or chemist know about this area.
I'm not to raise Dino, but use the chemistry they generate to do something.

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Re: [DIYbio] O'Reilly BioHacker Issue 4: Open Source Biotech Consumables

12:24 PM |

On Sat, Nov 29, 2014 at 6:07 AM, Aizan Fahri <vilafrantez@gmail.com> wrote:
> Hi there, Aizan's here from Rochester NY. Couple things I want to say here,
> and let me hear your thoughts.
>

I see you're at RIT (and studying biotech)! Glad to have another RIT
alum posting here on DIYbio (the open qPCR guy Josh is also an
Alum!!!).

Patents seem to work better for things that take longer to change, and
with the rapid pace of biotech these days it seems they are not best
suited for the task. If there was more collaboration, more money and
more progress would be being made.

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Re: [DIYbio] Re: update on the liquid handler

12:20 PM |

John, for Otto's design you are offering a projection out of the relatively 2D frame to navigate about a series of cascading shelves. Is that correct?

Guillotine design could probably use the same belt with the added Z axis projection. It would need a suspension bridge support or a brace.

>I don't now if it will be light and slim (to easily pass through the levels), we want a pipette car really light and tight.

Make a smaller but broader pipetter w/ autoclavable parts. What are you losing if the pipette goes in at an angle and then swivels upright into action? Or dare I propose adding some distance between shelves? ;)

Level buildings: I doubt DIYbio community is going to have trouble with a level and a right angle or a string with a load on it. But in case they are, a circular multi tier (typical wedding cake type) workstation on a turnable platform (equidistantly spaced ball bearings needed here for support) could be used. This would make the handler X and Y axis dependent whereas Z for the major part would be left to the cake. Holding containers would have to be custom made. Shouldn't be issue with additive manufacturing.

>It could go blind most of the time, but home in on some targets to calibrate position on each shelf.

Sure, let the apparatus dry run on high speed with [food coloring] or color turning [pH] sensetive liquids. You'd probably even work out kinks in the system that way.

As far as accuracy goes, laser guided (Kinect maybe on a stationary platform) realignment could be implemented for auto alignment, once level.

---

I just looked at the YouTube video again. In case I didn't mention it before, that's an impressive piece of machinery, Tom. How will you go about actual pipetter handling? Will it be modeled after commercially available machines?

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Re: [DIYbio] [diybio-eu] Indie.bio - Any interest in a "curated call" list?

12:12 PM |

On Sat, Nov 29, 2014 at 6:13 AM, Cathal (Phone)
<cathalgarvey@cathalgarvey.me> wrote:
> Sounds duplicative. Easy to post to this or other lists, or reddits, or just
> search on linkedin. If we made a ning or craigslist, we'd also have to spend
> time bringing candidate traffic there, for little gain over what's already
> out there.

It really should just be another part of some incubator/accelerator's
vetting process, not something totally new. There are tons of
motivated people out there without a project of their own, just
waiting to hear about some interesting project that they could make
enough $$ to eat without worry for a few months. I would probably say
in my opinion most of the bachelors-level biotech graduates are
willing to be put to work, but don't have (and haven't ever
considered) a project of their own. These smart people need a way to
be skimmed.

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Re: [DIYbio] Need some help starting a project (Agrobacteria-mediated transformation of a dicot via floral dip)

12:11 PM |

Sorry forgot to add that agro inserts into the genome randomly and can do so multiple times. The binary vector has a t-dna region delineated with a left and right border motif. You will see articles citing circuits that read like LB-MCS-Pnos-kanR-Tnos-RB. Your gene of interest along with appropriate promoter and terminator goes in the mcs like any ecoli plasmid. The tdna region always has those borders and a preassembled circuit for expressing a selection marker typically an herbicide resistance gene. That way you can kill off any non-transformed tissue and regenerate from only the transformed cells. If you are doing a transformation experiment you may want to regenerate a few plants to account for multiple insertions which may or may not get silence in the next generation. Multiple inserts can be considered as viral load and it will get cut out altogether. To check for insert count, grow transgenic plant until it makes seeds, then plate seeds in vitro onto media containing the selection herbicide and allow to germinate. You'd want around 50 seeds Per plate.

Once the seeds sprout, you'll notice some didnt germinate, some are happy and green, and if you are lucky, some are pale or white. If all germinated seeds are green, you have two or more inserts. You basically want a mendelian segregation of 75% resistant and 25% susceptible. At that point you know its just one insert.

Sent from my iPad

On Nov 27, 2014, at 6:03 AM, antomicblitz <amlamb@ucsc.edu> wrote:

I'm currently an undergrad studying molecular biology, and I recently joined a community lab after taking biochemistry lab at my school. In my class, we transformed a colony of E. coli using egfp and I thought it was really cool, and I've kind of been obsessed with trying it with other organisms as well, so I wanted to see if maybe I could do the same thing with a plant. After spending a few days at the library and searching through a couple of scientific journals, I found that I could do a similar procedure with agrobacteria, which can use a disarmed tumor-inducing plasmid to inject a segment of tDNA from another binary plasmid into a plant genome (I'm still not 100% sure how that works or where in the genome it gets incorporated, but I know it works at least). I would like to try and put egfp into a plant and have it expressed at detectable levels. I've had people tell me it's not too difficult to do. If any of you have done it before, or if you know what is involved, could you possibly give me some pointers on how/where I can order the appropriate plasmids, and which strain of agrobacteria I can use? I found a couple of protocols, so I have a general idea of what I'm gonna do (floral dip), but I'm still a bit iffy on how to select the right plasmids and bacteria, and where exactly on the binary plasmid I should ligate my gene of interest. Any help is much appreciated :).

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Re: [DIYbio] [diybio-eu] Indie.bio - Any interest in a "curated call" list?

12:08 PM |

On Sat, Nov 29, 2014 at 5:08 AM, Dakota Hamill <dkotes@gmail.com> wrote:
> I'd be more in line with what Brian was saying, as I'd be more interested in
> a place where you can list your skills or current projects, and either
> recruit talent to the project, or advertise yourself and skills for someone
> else to look at. A craigslist of science.

Exactly, I have a few ideas/projects that I would love to farm out to
the right/interested team. A platform for this would probably allow an
idea-poster to choose what license/business-model (trade-secret,
patents, open-source). For these such projects, I've done lots and
lots of research but am too busy with other things currently, so I
would really just want to be an adviser. Open-source projects would
obviously be easier to get going and develop trust, I think... but I
do think non-open projects could gain from this sort of system.

Basically it would like posting your idea to indie.bio's list of
'project ideas' (with their approval) and then choosing a team from
the people who showed up saying it was interesting to them.

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Re: [DIYbio] Need some help starting a project (Agrobacteria-mediated transformation of a dicot via floral dip)

12:02 PM |

I use agro strain GV3101 pmk90. You could probably have it shipped to you if you write to Stan Gelvin's lab over at perdue. My go to transformation plasmid is pPZP-200 series that confers kanamycin resistance as a selection marker. Floral dip sucks in my oppinion and youll be limited to arabidopsis only. Most important part of plant genetic engineering is tissue culture. You can build a laminar hood for cheap using a hepa air purifier, giant clear plastic storage bin, and some ducting. That way you could readily transform any plant (YMMV).

Just put a plant promoter like corn ubiquitin or CaMV in the mcs, them your egfp, then a terminator like the nopaline synthase one already in your plasmid downstream in the selection marker region. Then transform agro with the plasmid. Strain gv3101 is aggressive but a little hard to get rid of. It has genomic gentamycin resistance and spectinomycin in the plasmid if you are using pzp. I can send u my plasmid if you cant get it elsewhere. I transform tobacco on a daily basis and its my goto model organism. I can also send you seeds if you want to join the cult of nicotiana. Ive made some fluoroplasmids to shoot with my gene gun and results were fair. I use non optimized cometgfp and could never get my hands on egfp. Ill trade you my agro vector for yours with egfp. 😃 also feel free to ask whatever you want. I like helping plant newbies. I post all my lab stuff on fb and twitter. More than welcome to follow if you'd like. Good luck!

-Sebastian
Sent from my iPad

On Nov 27, 2014, at 6:03 AM, antomicblitz <amlamb@ucsc.edu> wrote:

I'm currently an undergrad studying molecular biology, and I recently joined a community lab after taking biochemistry lab at my school. In my class, we transformed a colony of E. coli using egfp and I thought it was really cool, and I've kind of been obsessed with trying it with other organisms as well, so I wanted to see if maybe I could do the same thing with a plant. After spending a few days at the library and searching through a couple of scientific journals, I found that I could do a similar procedure with agrobacteria, which can use a disarmed tumor-inducing plasmid to inject a segment of tDNA from another binary plasmid into a plant genome (I'm still not 100% sure how that works or where in the genome it gets incorporated, but I know it works at least). I would like to try and put egfp into a plant and have it expressed at detectable levels. I've had people tell me it's not too difficult to do. If any of you have done it before, or if you know what is involved, could you possibly give me some pointers on how/where I can order the appropriate plasmids, and which strain of agrobacteria I can use? I found a couple of protocols, so I have a general idea of what I'm gonna do (floral dip), but I'm still a bit iffy on how to select the right plasmids and bacteria, and where exactly on the binary plasmid I should ligate my gene of interest. Any help is much appreciated :).

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