Suggestions for beginner projects?

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MC

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Mar 4, 2017, 12:56:41 PM3/4/17
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Based on your experiences, what recommendations do you have for relatively simple beginner projects with good learning objectives that can be performed and verified without specialized equipment (like PCR)? Here are the ones I have in mind, any other ones you can suggest?
  • E. coli transformation with pVIB, GFP, pBLU, and other visually verifiable plasmids.
  • Agrobacterium mediated transformation of plants with GFP.
  • Isolation of V. phosphoreum from seafood.
Thanks!

Sebastian S Cocioba

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Mar 4, 2017, 1:58:41 PM3/4/17
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It depends on your goals. IMHO a beginner project should focus on learning about the organism, how to culture it, good experimental design practices, and a solid fundamental understanding of the theory that goes into this practice. I've seen many fall victim to the fetishization of equipment and the hype behind using cutting edge tools early on. Its fun at first but then fall into the common pitfall of "what can I do now that I made ecoli glow" and some remain there for a long time. If you have an understanding of the system under test or at least how these tools came about, you may find a plethora of questions you may want to pursue. 

If you want to do biology, Try something like documenting the effects of growth using various media formulations of your organism of choice. Learn your canvas before you paint!

If you just want to doodle with biotech, an ecoli transformation will give you a "yay me" moment and you can build upon that. As for plants, learn to tissue culture first. This is not trivial despite what people say and is absolutely crucial (i cant stress this enough) that you are capable of reliably regenerating plants from tissue BEFORE any engineering can take place. There is no cutting corners with plant biotech unfortunately and a bad foundation leads to an unstable building no matter how tall and fancy it may seem to be.

In summary: start with a question!

What do you want to know more about?

Science is all about generating new knowledge so having a tool set to pull knowledge from the ether is vital.

Book recommendations:
Experimental Design for Biologists, 2nd edition
Plants from Test Tubes, 4th edition
Philosophy of Science, A Very Short Introduction

Websites for chems and plasmids:
Edvotek
Bio-world
Phytotechlabs
Markergene
Bulldogbio

Good luck and don't be shy to ask questions frequently! 

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC

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MC

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Mar 4, 2017, 10:55:49 PM3/4/17
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Thanks Sebastian, those are really good points you bring up. My main interest is plants (where I started with TC) and has slowly evolved into bio, though I have a general interest in life science already. I've been doing a lot of reading (I'll check those books out as well) but it's hard for me to comprehend the reading and maintain interest without seeing the text on the page in action and get some hands on. I'd love to eventually try protoplast fusion, but looks like that's not quite novice-level.

Sebastian S Cocioba

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Mar 4, 2017, 11:07:07 PM3/4/17
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If you can source some agrobacterium why not try a hello world transformation using pCambia2301 from markergene.com in tobacco. It has a GUS gene so the assay if its gmo or not is really clear (blue on white). 


Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC


On Mar 4, 2017, at 10:55 PM, MC <marky...@gmail.com> wrote:

Thanks Sebastian, those are really good points you bring up. My main interest is plants (where I started with TC) and has slowly evolved into bio, though I have a general interest in life science already. I've been doing a lot of reading (I'll check those books out as well) but it's hard for me to comprehend the reading and maintain interest without seeing the text on the page in action and get some hands on. I'd love to eventually try protoplast fusion, but looks like that's not quite novice-level.

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MC

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Mar 4, 2017, 11:17:26 PM3/4/17
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I've never heard of that plasmid, but now I have something new to research. Thanks!

Mega [Andreas Stuermer]

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Mar 7, 2017, 2:36:12 AM3/7/17
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It's something spiritual. You don't find a project, your project finds you. You'll stumble upon it and immediately know that this is what you want to spend the next years of your life on.

If you are not that passionate about a project, motivation will fade when facing the first barriers

Lisa Thalheim

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Mar 7, 2017, 3:27:49 AM3/7/17
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I personally like the last one on your list of ideas as a beginner
project (isolation of V. phosphoerum or V. fischeri from seafood), for
the following reasons:

* Lets you get started cheaply, with no need to order fancy stuff or
reagents
* Gives you some hands-on experience with bread&butter skills - pouring
agar plates, sterile technique etc
* Opportunities to dive deeper into questions about quorum sensing, or
culture media and conditions (e.g. by measuring the light output of a
colony over time with different culture media, temperature, oxygen
concentration, ...)

I also like the general approach of building skills on top of each other
- so, starting out with simple culturing of bacteria, and then moving on
to transformation. This gives you some confidence and competence to
figure out what's going on when you run into problems. You know, rather
than having to disentangle a ton of sources of error all at once with no
experience in any of them to guide you...

If you haven't come across it yet, also have a look at "I,
Microbiologist"
(https://www.amazon.de/Microbiologist-Discovery-Based-Undergraduate-Microbial-Molecular/dp/1555814700)

On 04.03.2017 18:56, MC wrote:
> Based on your experiences, what recommendations do you have for
> relatively simple beginner projects with good learning objectives that
> can be performed and verified without specialized equipment (like PCR)?
> Here are the ones I have in mind, any other ones you can suggest?
>
> * E. coli transformation with pVIB, GFP, pBLU, and other visually
> verifiable plasmids.
> * Agrobacterium mediated transformation of plants with GFP.
> * Isolation of V. phosphoreum from seafood.
>
> Thanks!
>
> --
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MC

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Mar 7, 2017, 10:01:34 AM3/7/17
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I just took a look at the table of contents of that book and it looks like the perfect read for my level, thanks! And you've echoed my thoughts exactly, I've cultured a few strains and played with pVIB, but now I want to take it to the next step.
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