Bioreactors

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Contents

[edit]

Sata Growth Chamber & Bioreactor subgroups

Meeting times:

  • Growth chamber group - Fridays - 230 pm
  • Brackenridge Lab / Bioreactor group - Thursdays - 200 pm.

Paper repository: http://heybryan.org/~bbishop/docs/bioreactor/ and you can download the zip file to get everything at once. This way, you don't have to individually click each one.

  • Please email Bryan ( kanzure@gmail.com ) if you want to add anything to the directory. Editing this page too wouldn't be a bad idea.


Small-scale papers:

Slightly larger:

Other:


Unprocessed papers (Dr. Sata acquired these and handed out stacks):

  • High quality biodiesel production from a microalga Chlorella protothecoides by heterotrophic growth in fermenters
  • Ultrahigh bioproductivity from algae
  • Growth medium recycling in Nannochloropsis sp. mass cultivation
  • Development of a ground-based space micro-algae photo-bioreactor
  • Supersized algae bioreactors - http://biodieselmagazine.com/article-print.jsp?article_id=1910
  • AlgaeWay algae photobioreactor - http://www.algaelink.com/algaeway_photobioreactor_system.html
  • Second generation biofuels: high-efficiency microalgae for biodiesel production
  • Use of Chlorella vulgaris for CO2 mitigation in a photobioreactor
  • Photosynthetic biomass and H2 production by green algae: from bioengineering to bioreactor scale-up
  • Biodiesel from microalgae beats bioethanol
  • Culture of microalgae using interstitial water extracted from shrimp pond bottom sediments
  • Biodiesel from microalgae (Yusuf Christi, 2007)

Fetching digital copies is on the todo list somewhere.


Feel free to add papers or notes on to the wiki.

Growing algae on fiber optic cables. What's an optimal fiber optic surface area to light to algae surface area equation going to look like? Also, fiber optics aren't really cheap, what about the terahertz-level acrylamide biolenses for the transmission of light throughout the structure instead of just using typical glass processes?



[edit]

Computational biology software packages

  • List of software packages (open source / free)
    • Anything for bioreactor simulation, optimization and design for modular/easy scale-up?
      • commercial: Aspen BPS™; SuperPro designer® (according to [1])
  • There's a handful of papers that suggest using CFD (computational fluid dynamics) and Finite Element Analysis methods to optimize the design of bioreactors. I'm not entirely convinced yet of the improvements of going into such detail, but if it there's significant fluid flows then it might be useful for double checking the internal curvature of piping and tanks if we opt for a tubular design. Open surface ponds, not so much. Software packages like OpenFOAM can be freely used to simulate fluid flow dynamics. (There was an old page I had on CFD over at scramjets I think.) -- Kanzure 17:22, 17 September 2008 (CDT)




Nobuyoshi Ishii, Martin Robert, Yoichi Nakayama, Akio Kanai and Masaru Tomita, Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata 997-0017, Japan Received 5 September 2003; revised 30 March 2004; accepted 1 April 2004. Available online 7 August 2004. Abstract

In the post-genomic era, the large-scale, systematic, and functional analysis of all cellular components using transcriptomics, proteomics, and metabolomics, together with bioinformatics for the analysis of the massive amount of data generated by these “omics” methods are the focus of intensive research activities. As a consequence of these developments, systems biology, whose goal is to comprehend the organism as a complex system arising from interactions between its multiple elements, becomes a more tangible objective. Mathematical modeling of microorganisms and subsequent computer simulations are effective tools for systems biology, which will lead to a better understanding of the microbial cell and will have immense ramifications for biological, medical, environmental sciences, and the pharmaceutical industry.

In this review, we describe various types of mathematical models (structured, unstructured, static, dynamic, etc.), of microorganisms that have been in use for a while, and others that are emerging. Several biochemical/cellular simulation platforms to manipulate such models are summarized and the E-Cell system1 developed in our laboratory is introduced. Finally, our strategy for building a “whole cell metabolism model”, including the experimental approach, is presented.


E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.

[edit]

Review of different geometries and types of bioreactors

  1. Open/closed/hybrid
  2. Closed geometries
    1. Tubular
    2. Box/tank
  3. Open geometries
    1. Pond surfaces?
[edit]

Other / old stuff

Everything below this is from before 2008-09-17, mostly from Bryan's other projects / stuff.



[edit]

Todo

[edit]

2008-05-29 email

Hi all,


[edit]

Todo

[edit]

2008-05-29 email

Hi all,

You might know about

And one of the biggest problems with a simple collection of notes and
documents is mainly that you can't really do anything with it except
read, which is fine, if you have the time, but it's just not "up to
date" and it never can be due to the intense amount of effort that it
would take to make sure you have everything covered, that a rewritten
and new version is scientifically accurate, etc.

So, simultaneously, there are other 'problems' in diy tech. A few days
ago I was going through some neurosci papers on GABAergic and ACh

circuits in the prefrontal and visual cortices:

To do experimentation on biopsied organotypical neuron slices would
require the neurochemicals. And if you go look up on Sigma-Aldrich, the
neurotransmitters, agonists, antagonists and related substances are
prohibitively expensive. $1/mg. That's ridiculous. We *know* that we
can have bacteria/algal bioreactor tanks that will produce it for free.

So let's do it.

http://heybryan.org/mediawiki/index.php/Neurochem_kit
http://heybryan.org/mediawiki/index.php/Bioreactors
^ this last page is where I'm centralizing most of the notes. But please
excuse the current state of the page, it's mostly just a link to an IRC
log, and at the moment I fail to recall the other documents on the wiki
that are of relevant note.

The idea is to build a biroeactor tank out of scrap parts. There are
lots of problems to be solved like contamination, piping, purification
of substances, cloning and making new versions for friends (or
yourself), reprogramming the ecoli farms, etc. But I'm certain it can
work, and once it's able to produce the reactants for PCR and the
chemicals necessary to do oligonucleotide synthesis in the DNA
synthesizer, it's basically self-supporting except for the metals that
would be required to make a new bioreactor over all. That's pretty good
results, if it ever gets that far.

And on top of that, if you're incorporating an entire DNA synthesizer
(which is really just a giant, over-sized inkjet printer that uses
phosphodiesters if I recall correctly), you can connect it to a cheap
PIC or microcontroller and download genes from the internet, perhaps
from GenBank or Entrez or something, get new biobricks, incorporate
synthesis reaction pathways from other species (i.e., integrate
dopmaine synthesis).

There are other possible uses of a biotan. Tissue engineering, biofuels,
organ farms, the PETA in vitro meat prize, which I happen to have notes
on here:

It could also be used in neural tissue experimentation, longevity
experiments, but as a first step ecoli or algal farming is excellent.

I'm still outlining the overall protocols that could be used, but I'm
optimal so far. The main problem seems to be the tens of thousands of
RPMs in common protocols for using plasmids. Purification of
synthesized neurotransmitters would /normally/ be painful because I
frankly have no ideas on synthesizing filtration membranes, however an
interesting alternative is to use aptamers:

.. which have the added bonus of having a synthesis largely dependent on
a DNA synthesizer in the first place. So that's good news, killing (or
giving life to?) a few birds with one stone.

What's needed:

  • cheap, but effective protocols (as 'biologically-dependent' as

possible) for cloning, cultures, subcloning, PCR, expression
experiments, and selection experiments (ampicillin, etc.)

  • ideas on the physical setup of the bioreactor, i.e. how to do piping

with glassware, PVC pipes, or catching produced materials via simple
things like balloons tied to faucets, etc.

information as a git repository. I'd offer my server space, but I'm
quickly approaching zero available space, although the cheap 12 cents
per GB announced on some websites today has me scouting for the $64 500
GB steals. So that might change soo
You might know about

And one of the biggest problems with a simple collection of notes and
documents is mainly that you can't really do anything with it except
read, which is fine, if you have the time, but it's just not "up to
date" and it never can be due to the intense amount of effort that it
would take to make sure you have everything covered, that a rewritten
and new version is scientifically accurate, etc.

So, simultaneously, there are other 'problems' in diy tech. A few days
ago I was going through some neurosci papers on GABAergic and ACh

circuits in the prefrontal and visual cortices:

To do experimentation on biopsied organotypical neuron slices would
require the neurochemicals. And if you go look up on Sigma-Aldrich, the
neurotransmitters, agonists, antagonists and related substances are
prohibitively expensive. $1/mg. That's ridiculous. We *know* that we
can have bacteria/algal bioreactor tanks that will produce it for free.

So let's do it.

http://heybryan.org/mediawiki/index.php/Neurochem_kit
http://heybryan.org/mediawiki/index.php/Bioreactors
^ this last page is where I'm centralizing most of the notes. But please
excuse the current state of the page, it's mostly just a link to an IRC
log, and at the moment I fail to recall the other documents on the wiki
that are of relevant note.

The idea is to build a biroeactor tank out of scrap parts. There are
lots of problems to be solved like contamination, piping, purification
of substances, cloning and making new versions for friends (or
yourself), reprogramming the ecoli farms, etc. But I'm certain it can
work, and once it's able to produce the reactants for PCR and the
chemicals necessary to do oligonucleotide synthesis in the DNA
synthesizer, it's basically self-supporting except for the metals that
would be required to make a new bioreactor over all. That's pretty good
results, if it ever gets that far.

And on top of that, if you're incorporating an entire DNA synthesizer
(which is really just a giant, over-sized inkjet printer that uses
phosphodiesters if I recall correctly), you can connect it to a cheap
PIC or microcontroller and download genes from the internet, perhaps
from GenBank or Entrez or something, get new biobricks, incorporate
synthesis reaction pathways from other species (i.e., integrate
dopmaine synthesis).

There are other possible uses of a biotan. Tissue engineering, biofuels,
organ farms, the PETA in vitro meat prize, which I happen to have notes
on here:

It could also be used in neural tissue experimentation, longevity
experiments, but as a first step ecoli or algal farming is excellent.

I'm still outlining the overall protocols that could be used, but I'm
optimal so far. The main problem seems to be the tens of thousands of
RPMs in common protocols for using plasmids. Purification of
synthesized neurotransmitters would /normally/ be painful because I
frankly have no ideas on synthesizing filtration membranes, however an
interesting alternative is to use aptamers:

.. which have the added bonus of having a synthesis largely dependent on
a DNA synthesizer in the first place. So that's good news, killing (or
giving life to?) a few birds with one stone.

What's needed:

  • cheap, but effective protocols (as 'biologically-dependent' as

possible) for cloning, cultures, subcloning, PCR, expression
experiments, and selection experiments (ampicillin, etc.)

  • ideas on the physical setup of the bioreactor, i.e. how to do piping

with glassware, PVC pipes, or catching produced materials via simple
things like balloons tied to faucets, etc.

information as a git repository. I'd offer my server space, but I'm
quickly approaching zero available space, although the cheap 12 cents
per GB announced on some websites today has me scouting for the $64 500
GB steals. So that might change soon. :)

I'd like to hear some ideas.

- Bryan
________________________________________
http://heybryan.org/

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