Month: October 2008

Witch Hazel? Triclosan? Horsetail Extract? Camellia Sinesis Leaf?

Posted by JonathanCline – October 29, 2008

Breeze by the cosmetics section of the department store next time. There is a 1+ billion-dollar market being bought and sold right under, and on top of, everyone’s noses, using mostly experimental organic chemistry, wrapped up in advertisements of sexualizing, anti-aging, softening, cleansing, wrinkle-reducing, organic, non-animal tested, oil-free, oil-reducing, oil-enhancing, whitening, darkening, clarifying, and most of all, “all natural”.

The cosmetics industry seems ripe for synthetic biology chemical factory creation. A short list of ingredients in skin care products, as some examples, are below (disclaimer: quoted from wikipedia).  Many of these ingredients do have supposed medicinal properties.. some are questionable.

Witch Hazel

Witch hazel is an astringent produced from the leaves and bark of the North American Witch Hazel shrub (Hamamelis virginiana) which ranges from Nova Scotia west to Ontario, and south to Florida, and Texas[1]. This plant, native to Canada and the United States was widely used for medicinal purposes by American Natives. The witch hazel extract was obtained by steaming the twigs of the shrub.

The essential oil of witch hazel is not sold separately as a consumer product. The plant does not produce enough essential oil to make production viable. However, there are various distillates of witch hazel (called hydrosols or hydrolats) that are gentler than the “drug store” witch hazel and contain alcohol.

Now for a PubMed article:

Highly galloylated tannin fractions from witch hazel (Hamamelis virginiana) bark: electron transfer capacity, in vitro antioxidant activity, and effects on skin-related cells, Touriño S, Lizárraga D, Carreras A, Lorenzo S, Ugartondo V, Mitjans M, Vinardell MP, Juliá L, Cascante M, Torres JL. Chem Res Toxicol. 2008 Mar; 21(3):696-704. Epub 2008 Mar 1.

Institute for Chemical and Environmental Research (IIQAB-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.    PMID: 18311930

Witch hazel ( Hammamelis virginiana) bark is a rich source of both condensed and hydrolizable oligomeric tannins. From a polyphenolic extract soluble in both ethyl acetate and water, we have generated fractions rich in pyrogallol-containing polyphenols (proanthocyanidins, gallotannins, and gallates). The mixtures were highly active as free radical scavengers against ABTS, DPPH (hydrogen donation and electron transfer), and HNTTM (electron transfer). They were also able to reduce the newly introduced TNPTM radical, meaning that they included some highly reactive components. Witch hazel phenolics protected red blood cells from free radical-induced hemolysis and were mildly cytotoxic to 3T3 fibroblasts and HaCat keratinocytes. They also inhibited the proliferation of tumoral SK-Mel 28 melanoma cells at lower concentrations than grape and pine procyanidins. The high content in pyrogallol moieties may be behind the effect of witch hazel phenolics on skin cells. Because the most cytotoxic and antiproliferative mixtures were also the most efficient as electron transfer agents, we hypothesize that the final putative antioxidant effect of polyphenols may be in part attributed to the stimulation of defense systems by mild prooxidant challenges provided by reactive oxygen species generated through redox cycling.

That doesn’t mean everyone should go rubbing witch hazel all over themselves..  though it does show that witch hazel does “something.”

Triclosan

Triclosan (IUPAC name: 5-chloro-2-(2,4-dichlorophenoxy)phenol) is a potent wide spectrum antibacterial and antifungal agent. Triclosan is found in soaps (0.15-0.30%), deodorants, toothpastes, shaving creams, mouth washes, and cleaning supplies and is infused in an increasing number of consumer products, such as kitchen utensils, toys, bedding, socks, trash bags, and some Microban treatments. Triclosan has been shown to be effective in reducing and controlling bacterial contamination on the hands and on treated products. More recently, showering or bathing with 2% triclosan has become a recommended regimen for the decolonization of patients whose skin is carrying methicillin resistant Staphylococcus aureus (MRSA)[1] following the successful control of MRSA outbreaks in several clinical settings.

Horsetail Extract

What! Yes, it says “Horsetail Extract” on the container. Though I didn’t find this as a real ingredient in wikipedia, I found it in the following patent.

United States Patent 5415861

Abstract: A method for reducing the visible size of facial skin pores by applying a novel composition which comprises an oil absorbing powder, a botanical astringent and a biological compound that alters the structure of the skin and/or the function of the sebaceous glands. […]

Horsetail extract (Equisetum arvense) is a preferred compound because it contains significant amounts (>8%) of organic silicones. These silicones are known to regulate collagen cross linking and improve the structural framework of connective tissues in the skin. Like the alternative compositions, Horsetail extract functions on and below the skin surface to reduce pore size with regular application.

Camellia Sinensis Leaf

Camellia sinensis is the tea plant, the plant species whose leaves and leaf buds are used to produce tea. It is of the genus Camellia (Chinese: 茶花; pinyin: Cháhuā), a genus of flowering plants in the family Theaceae. White tea, green tea, oolong and black tea are all harvested from this species, but are processed differently to attain different levels of oxidation. Kukicha (twig tea) is also harvested from camellia sinensis, but uses twigs and stems rather than leaves.

Tea extracts have become field of interest, due to their notional antibacterial activity. Especially the preservation of processed organic food and the treatment of persistent bacterial infections are being investigated.

  • Green tea leaves and extracts have shown to be effective against bacteria responsible for bad breath.
  • The tea component epicatechin gallate is being researched because in-vitro experiments showed that it can reverse methicillin resistance in bacteria like Staphylococcus aureus. If confirmed, this means that the combined intake of a tea extract containing this component will enhance the effectiveness of methicillin treatment against some resistant bacteria.

An amazing aspect of cosmetics is the historical basis for many of the ingredients, many of them in use for hundreds or thousands of years.

  • Category: Notes
  • Comments Closed

Next Generation Tech for DNA Sequencing

Posted by JonathanCline – October 24, 2008

Let’s say an organism is successfully modified and seems to be performing a portion of it’s synthetically designed biological tasks.  Several questions are raised:  has the organism evolved, during replication, from it’s original design?  Is the organism’s DNA actually the same as the desired engineered DNA?  Is there some mistake in the new organism’s DNA which could be improved?  If the organism doesn’t function properly, is it because of the designers’ mistake, or is it because of the random chance in nature?

These questions are usually answered by verifying the DNA of the organism — sequencing.  Today, verifying the organism’s sequence in a normal lab is done by a long process of diffusing the DNA through a gel and taking a UV picture of the result.  This is rather old (and annoying) technology.  Yet DNA sequencing is difficult because working with DNA poses several big technical problems.  What is the next generation technology for DNA sequencing which could improve this?

Here are some examples and some cool videos as well:

More→

“SynBioSS: The Synthetic Biology Modeling Suite”

Posted by JonathanCline – October 20, 2008

SynBioSS (Synthetic Biology Software Suite) is a suite of software for the modeling and simulation of synthetic genetic constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale simulation algorithms. SynBioSS is available under the GNU General Public License. — Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios Sotiropoulos, and Yiannis N. Kaznessis, Bioinformatics 2008 24(21):2551-2553; doi:10.1093/bioinformatics/btn468

Sounds neat, let’s try it. Interestingly, the iGEM participants and biologists, in discussions of modeling, have thrown their hands in the air & state that it is difficult or impossible to model biology. Maybe SynBioSS can do the impossible?  Except: There is no specific installer available for OS/X (as of this writing) and it seems there are many assorted packages required.

Here are my install summary/notes/fixes for getting SynBioSS (version 1.0.1) running on OS/X (Leopard 10.5.5):
More→

Creating beneficial biological systems without cells

Posted by JonathanCline – October 19, 2008

In general terms, synthetic biology brings to mind using “BioBricks”, which are engineered genetic parts used to modify an organism, such as bacteria or yeast. The idea is to modify the organism to work to our advantage; for example, to eat sugar and produce biofuel — a pretty good tradeoff, considering the cost of gasoline and the cost of sugar. This is a top-down methodology: take an existing organism, modify it’s DNA, measure it’s behavior, and repeat the modification process until the desired “behavior” is measured.

Some synthetic biology research, however, doesn’t use traditional organisms at all. In fact, doesn’t even use “cells”. This might be called cell-free synthetic biology, or in vitro synthetic biology. This is a bottom-up approach: create the desired “behavior” from scratch. The idea has existed for some time; a good summary is Synthetic biology projects in vitro, Anthony C. Forster and George M. Church, Genome Res. 17:1-6, 2007: “Many biopolymer syntheses are already better scaled up in cell-free systems, such as linear DNAs by oligo synthesis and PCR, unmodified RNAs by in vitro transcription, and peptide libraries by in vitro transcription/translation. And engineering flexibility is much greater in vitro, unshackled from cellular viability, complexity, and walls.”

Synthetic Life

“How can I hack biology without using cellular organisms?”, you’re probably asking.

One proposed method for creating such cell-free synthetic biology projects (meaning: no bacteria, no yeast…  just… chemistry) is An integrated cell-free metabolic platform for protein production and synthetic biology, Michael C Jewett, Kara A Calhoun, Alexei Voloshin, Jessica J Wuu & James R Swartz, Molecular Systems Biology 4:220. These fully synthetic systems have significant environmental interactions in common with traditional bacteria:

It is striking to note that the Cytomim system closely mimics E. coli cellular metabolism. It is homeostatic in pH and [Pi], uses natural, non-phosphorylated energy substrates, provides a long-lasting ATP source, and fuels highly productive protein synthesis (up to 600 mg protein/l/h). In addition, each ribosome can polymerize approximately 10 500 amino acids (42 copies of chloramphenicol acetyl transferase, CAT), indicating that the Cytomim system is not limited by enzyme turnover (e.g. only one protein, or fraction of a protein, produced per ribosome). Furthermore, the specific oxygen uptake rate in the Cytomim system is on the same order as for intact E. coli cells.

As can be seen from the date of this publication (2008), this research is cutting edge. Prior work by the same primary author established this Cytomim system.

Digital-logic-like bistable circuit using synthetic biology without using organisms has previously been described in Construction of an in vitro bistable circuit from synthetic transcriptional switches, Jongmin Kim, Kristin S White & Erik Winfree, Molecular Systems Biology 2:68

The question by now might have changed.  Maybe at this point, you are asking, “Why should I use extensive trial-and-error while attempting to modify existing bacteria, when I can create exactly the proteins I need, from the ground-up, instead?”

That’s a good question for further research.

Word on the Street @ Synthetic Biology 4.0 – Day 3

Posted by JonathanCline – October 12, 2008

Word on the street from Synthetic Biology 4.0..  take a word or leave a word.

  • Venture capitalists and private investors are very interested in synthetic biology.  Significant buzz in the Bay Area regarding the term.  Large capital is required when making the transition from proven concept to, for example, a pilot plant for biofuel production.  Venture capitalists love to get excited because it’s their job to both get themselves excited and get others excited (excited enough to give them loads of money).
  • As on day2, a laboratory-proven “built from the ground up” organism (a thing, separate from other things, that eats, replicates, grows, and divides) may only be years away.
  • Very innovative solution proposed to slow the rate of spreading HIV, using synthetic biology to create a “get-the-HIV-away” preventative medicine.  Seemed very well received as a different track than current antiviral cures.
  • No one really knows how to model cells or modified cells.  (Again)
  • An interesting group at Cal Tech has proposed a method of designing, or compiling the design by converting a hardware netlist into DNA sequences, combinatorial logic which has unique signal outputs, thus eliminating the cross-talk problem; theoretically modeled up to 1,000 gates, currently tested up to 4 gates.
  • A cynical undergrad says that engineering biology will never work and will never be able to be modeled; though he has an iGEM project.
  • A Hong Kong local university biology professor also mentions that engineering biology will never work; it is too unreasonable to expect biology to behave under known rules: “biology is not like that.”
    • The word “never” in both cases might be very surprising to some, especially coming from two people in the field, one of whom has built Biobrick device(s).
  • “DIY Bio is real!  Bio can be done as a hobby!  We want to let amateurs hack biology just like scientists do!  We need to apply rules to make it non-biohazard, and then just do it.”
    • Strongly contrasting opinion to the “it will never work” biologists.
  • Cells can be made to change shape dramatically with specific (laser) light input.  Very freakily amazing video.
  • Which opinion is more correct, that engineering biology will work or that it doesn’t or where we fall as of right now?
    • Drew Endy:  “The truth is somewhere in the middle.  Years ago, we had a lot of iGEM teams, and nothing worked.  Last year, we had let’s say 100 iGEM teams, and 10 teams had working devices.”  I conclude, the engineering process is improving through lab experience and raw data feedback.  Engineers eventually make nearly anything work (just ask Scotty).
    • Reshma Shetty (now at Ginko BioWorks): “It takes about 3 years to ‘get it’ [collect enough experience to be successful at creating biological devices].  Everyone seems to struggle until then.”
  • More back & forth related to the licensing issues of an “open source” biological library.
  • The Bay Area may have an accessible “Bio Fab Lab” in the years ahead, funded by public sources and aimed at improving the “open source” biological library.
  • Even the venture capitalists and synthetic biology company owners get history wrong; mistakenly stating facts.  “This is like the IBM PC architecture, completely open, and enabling things like the open source movement later”.. Wrong!; in fact, the IBM PC was completely locked down and very proprietary and backed by lawyers from the huge deep pockets of IBM — it was Compaq who, through a legal process of reverse engineering to work around the patent and intellectual property process, completely cloned the IBM PC firmware to a compatible version, thus inventing the clone-PC market (while IBM vehemently objected and litigated against).  Please read the history books (I would suggest Hackers, by Steven Levy, as a starting point). Most of the “this is like open source with computers” analogies are.. well.. off by a factor of two. At least a factor of two.
All quotes above are not to be taken literally.  Any resemblance to actual persons is entirely coincidental.  The contents of this article and this web site (web log) are Copyright with All Rights Reserved.  No content may be used without explicit written permission.  (This is to prevent quoting out of context.)

For those who aren’t familiar with synthetic biology, I will quote the Synthetic Biology 4.0 web site:

What are the applications of Synthetic Biology?

BioEnergy. Cells are being engineered to consume agricultural products and produce liquid fuels. British Petroleum and the US DOE granted $650 million dollars for research in the San Francisco Bay Area.

Drug Production. Bacteria and yeast can be re-engineered for the low cost production of drugs. Examples include the anti-malarial drug Artemisinin and the cholesterol-lowering drug Lipitor.

Materials. Recombinant cells have been constructed that can build chemical precursors for the production of plastics and textiles, such as Bio-PDO and spider silk.

Medicine. Cells are being programmed for therapeutic purposes. Bacteria and T-cells can be rewired to circulate in the body and identify and treat diseased cells and tissues. One such research program is the NIH-funded Cell Propulsion Laboratory at UCSF.

Synthetic Biology is a new approach to engineering biology, with an emphasis on technologies to write DNA. Recent advances make the de novo chemical synthesis of long DNA polymers routine and precise. Foundational work, including the standardization of DNA-encoded parts and devices, enables them to be combined to create programs to control cells. With the development of this technology, there is a concurrent effort to address legal, social and ethical issues.

How is this different from genetic engineering?

Synthetic Biology builds on tools that have been developed over the last 30 years. Genetic engineering has focused on the use of molecular biology to build DNA (for example, cloning and PCR) and automated sequencing to read DNA. Synthetic Biology adds the automated synthesis of DNA, the setting of standards and the use of abstraction to simplify the design process.

Word on the Street @ Synthetic Biology 4.0 – Day 2

Posted by JonathanCline – October 11, 2008

Word on the street from Synthetic Biology 4.0..  take a word or leave a word.

  • Tom Knight mentions it will be another 10 years before an untrained hobbyist can order a BioBrick off the shelf, stir things up, and have them work like a can currently be done for a hobby electronics kit, noting they (the engineers! Applying proper engineering design rules!) have only been at system-level design biology for a couple years.  He suggests anyone interested should do iGEM, using borrowed or scrounged equipment if necessary, but doesn’t know about the startup costs involved.   (Budget would be good to know.)
  • Various MIT people again mention the way to get started from scratch in synthetic biology is through iGEM.
  • Big open questions (and significantly opposed views) regarding the licensing surrounding biobricks or “open source” parts libraries.
  • While everyone bandies about the phrase “open source,” it seems no one actually understands what open source means (or that there are two major camps in open source:  viral innovation-stifling copyleft GPL in which all your work must also be disclosed, and more open Apache/BSD which allows your work to remain private).  A point was made that the intellectual property could be released as public domain, yet authors rarely chose to do so, instead adopting a more complex license.
  • I didn’t realize this before, though apparently there is a “humanist” group which is reporting pseudo-scientific fluff regarding genetic engineering & synthetic biology.  I won’t name them as they don’t deserve air time based on the couple sensationalistic & skewed articles they’ve written.
  • A very small minority of specialists believe in just going skunk-works style, ignoring the assumed difficulty of engineering biology.  That means, setting up startup-like garage operations while maintaining control of everything.
  • Laboratory-created self-mobile molecular machines (aka: synthetic life) is closer to reality than anyone might guess.  Mix the right things into the right places and things which previously were inert will start to move on their own.
All quotes above are not to be taken literally.  Any resemblance to actual persons is entirely coincidental.  The contents of this article and this web site (web log) are Copyright with All Rights Reserved.  No content may be used without explicit written permission.  (This is to prevent quoting out of context.)

For those unfamiliar with synthetic biology, this video by Mac Cowell shows Drew Endy explaining the field:

Word on the Street @ SB 4.0 – Day 1

Posted by JonathanCline – October 10, 2008

Word on the street from Synthetic Biology 4.0..  take a word or leave a word.

  • DIY Bio such as Garage Hacking Biobricks – it’s not for grandma or the kids or even the DIY hackers.  It’s not an issue with access to tools, access to research, access to equipment, or access to a lab.  It’s lack of experience which will hamper any real results from the “I want to do DIY Bio”.  It could take an untrained bio hacker “years” to complete a simple new project since the design will be full of dead ends, whereas the trained (postdoc) scientist would complete similar tasks in a couple months.
  • Standard biological parts won’t solve everything, they could solve some things.
  • At least the belief that there’s a lot of doubt that standard biological parts could ever come to fruition, especially considering everyone sends everything to “the registry” which presumably can’t handle the burden of filling in all the gaps in everyone’s parts.
  • Hong Kong’s Ministry of Finance says he likes synthetic biology and believes in pledging lots of resources to the field even though he says he doesn’t really know what it is; the venture capitalists tell him it’s a good idea.
  • Free t-shirts.
  • Free Biobricks Foundation stickers.
  • Biologists are touchy about the “god” subject and about the “what is life?” subject.  Funny, I don’t know a single astrophysicist who is touchy about the “is the earth flat?” subject.
  • Some people adamantly believe that Biobricks are way too much baggage to be carrying around to solve an enzymatic problem (“we don’t need all these stinkin’ genes”).
  • Lots of software aided design tools for point-click-drag-drop-the-Biobrick-done!  Somehow, if it were really that easy, I would have expected the “grandma can DIY bio” argument to hold.
  • Students originating from foreign countries and heading to the U.S. to study biology have big visa issues.  Security level orange!  Banana-smelling e. coli detected!  We have an issue possibly brewing from the baker’s yeast!
  • Certain venture capitalists looove synthetic biology, and believe it is a far different capitalizing model than traditional genetic engineering or chemical engineering fields.
All quotes above are not to be taken literally.  Any resemblance to actual persons is entirely coincidental.  The contents of this article and this web site (web log) are Copyright with All Rights Reserved.  No content may be used without explicit written permission.  (This is to prevent quoting out of context.)

Happy Protein Families :-D

Posted by JonathanCline – October 10, 2008

A fun card deck from GeneArt at SB4.0.

Synthetic Biology Conference 4.0 (2008) Agenda

Posted by JonathanCline – October 8, 2008

The Synthetic Biology Conference for 2008 is in Hong Kong.

The agenda can be found here: Synthetic Biology Conference 4.0 Agenda