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Nanobiopsy: the beauty in the very small is a big deal

The ability to study the living without destroying it has been the goal of many scientists for decades. A new article in ACS Nano has paved the road towards noninvasive cellular-level examination. The only true way to study cellular dynamics is to study a single cell over time (temporally). The reason for this is the heterogeneous nature of any cell culture because no two cells are identical spatially and temporally. Each individual cell has its own set of experiences that has generated its current molecular inventory, ie. RNA molecules, metabolites, proteins, sugars, lipids, etc. Studying a community of cells gives rise to noise that makes finding significant differences incredibly difficult.

In the article entitled Compartmental Genomics in Living Cells Revealed by Single-Cell Nanobiopsy, the authors used a kind of microscopy called scanning ion conductance microscopy, or SICM, that allows for continuous sampling of a single cell over time. The authors used a nanopipette as part of the SICM and combined this with sensitive sequencing techniques resulting in a high resolution look at what genes are being expressed over time into RNA molecules. Furthermore, this technique was used to study the genomic information of individual mitochondria within a single cell without also studying the nuclear material. In other words, this new technique has resulted in the ability to not only study cellular dynamics, but go beyond that and study subcellular dynamics.

This breakthrough will have impacts across many fields from cancer biology to improving climate models.

Paolo Actis, Michelle M. Maalouf, Hyunsung John Kim, Akshar Lohith, Boaz Vilozny, R. Adam Seger, & Nader Pourmand (2013). Compartmental Genomics in Living Cells Revealed by Single-Cell Nanobiopsy ACS Nano DOI: 10.1021/nn405097u

The Tree of (the Study of) Life

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American Renaisscience: Bioengineering stem cells for targeted drug delivery

The field of stem cell research promises to deliver truly amazing medical breakthroughs in the coming decades. However, the fundamental research needed must first provide the proof-of-principle necessary for private industry to take note. That is happening according to a recent article published in the journal Blood. Researchers at Brigham and Women’s HospitalHarvard‘s Stem Cell Institute, in collaboration with MIT and Mass General have successfully reprogrammed a type of connective tissue stem cell line, known as mesenchymal stem cells, to produce specific surface proteins and the anti-inflammatory molecule interleukin-10.

To accomplish this, researchers injected a modified form of messenger RNA, the blueprint for protein synthesis in cells. The modified stem cells were injected into mice. Once in the mouse bloodstream, the stem cells successfully targeted sites of inflammation and reduced swelling.

This approach is promising because it targets the site in need of therapeutics and can deliver the needed drug at a level high enough to provide results. This approach is attracting attention from large pharmaceutical companies because of the capability to target the disease site itself.


Oren Levy, Weian Zhao, Luke J. Mortensen, Sarah LeBlanc, Kyle Tsang, Moyu Fu, Joseph A. Phillips, Vinay Sagar, Priya Anandakumaran, Jessica Ngai, Cheryl H. Cui, Peter Eimon, Matthew Angel, Charles P. Lin, Mehmet Fatih Yanik, & Jeffrey M. Karp (2013). mRNA-engineered mesenchymal stem cells for targeted delivery of interleukin-10 to sites of inflammation Blood DOI: 10.1182/blood-2013-04-495119

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Useful Products Engineered into E. coli “Poop” (Thank Goodness)

I can’t sit back and let the internet become saturated with misleading phrasing regarding by-products genetically engineered into E. coli metabolism. The latest sensation stems from the commercial production of the artificial sweetener aspartame. It was reported this week, well…read it for yourself (notice the language used):

This scientific jargon obfuscates (perhaps deliberately) a truly disturbing process:
1.) ‘Cloned microorganisms’ (which the patent later reveals to be genetically modified E. coli) are cultivated in tanks whose environments are tailored to help them thrive.
2.) The well-fed E. coli cultures defecate the proteins that contain the aspartic acid-phenylalanine amino acid segment needed to make aspartame.
3.) The proteins containing the Asp-Phe segments are ‘harvested’ (i.e. lab assistants collect the bacteria’s feces).
4.) The feces are then treated. This includes a process of methylation (adding an excess of the toxic alcohol, methanol, to the protected dipeptide).

While common sense dictates that this abomination doesn’t belong anywhere near our bodies, the patent’s authors made no secret about their belief that aspartame constitutes a safe and nutritious sweetener:


It was picked up on the UPI under “Science News” with a headline reading:

The use of the words ‘poop’, ‘feces’, ‘defecate’, and ‘excrement’ is truly unfortunate and used to sensationalize the process. Natural News has an agenda, or several agendas. First they are against genetic modifications to living organisms even though almost all discoveries and breakthroughs in modern medicine can be contributed to some form of genetic modification. Second, they are publicly against the use of aspartame in commercial products.

The truth about E. coli ‘poop’

First, E. coli do not ‘poop’ in the sense a human can relate. These are single-celled organisms and are rather leaky to certain molecules naturally. E. coli produce by-products, not poop. Metabolic end products are considered waste to the E. coli cell, but these natural end products include carbon dioxide, hydrogen gas, acetate (vinegar), and water. Their poop doesn’t sound so bad now does it?

The evolution of E. coli ‘poop’

E. coli has been the organism of choice for decades in myriad research areas. Simple genetic modifications like gene deletion and gene insertion are the norm and can easily be performed in a lab. Scientists and doctors have used this technique to engineer novel strains of E. coli that tweaks their metabolism to produce useful products for the general public. One great example occurred in 1978 by Herbert Boyer who inserted the gene for human insulin into E. coli. Recombinant insulin was approved by the FDA in 1982 and is now the source of 70% of the insulin sold today.

Human growth factor is another by-product engineered into E. coli to treat different forms of dwarfism. For hemophiliacs, E. coli are utilized to produce missing clotting factors like tissue plasminogen activator and factor VIII. It should be noted that before producing these therapeutics in E. coli, they were harvested from cadavers. Patients with immunodeficiency can receive recombinant interferon, used to treat viral infections, produced in bacteria.

E. coli and other bacteria are used in other industries as well. They have been modified to produce large amounts of succinate, a precursor for the solvent 1,4-butanediol. It can then be used to make some plastics and even Spandex. E. coli are also used in the production of polyhydroxybutyrate, or PHB, for the production of plastics. E. coli is also used for production of polyamines for synthesis of polyamide plastics.

Over the past decade, a lot of research has taken place in the field of renewable energy. One approach to lessen our dependence on foreign oil is the microbial conversion of cellulosic (non-food) plant material into viable fuels like ethanol and butanol. This task has given E. coli and other microbes ‘poop potential’. Through genetic engineering and synthetic biology techniques, E. coli can produce large amounts of free fatty acids which are one catalytic step away from the same diesel fuel derived from petroleum. E. coli is also engineered to produce precursors for jet fuel.

In this post, I have focused on only one microbe, E. coli, since this was the bacterium sensationalized this week in the press.

Bacteria; They’re not only for biofuel anymore. Unsung heroes for bioplastics

illustrated bacteria, microbiology, bioplastic, bioenergy, environment
Illustration of PHB within bacterial cells

I spend a lot of time on this blog illustrating and promoting the benefits of the things we can’t see, however, we can’t live without and finding new ways they can help us out. To focus on bacteria along for now, they are beneficial overwhelmingly more than they are hazardous. Lots of research is going into utilizing them in new arenas from ethanol to diesel and jet fuels.

Helping solve the forthcoming energy/climate crisis is not the only area these guys can help. Lots of bacteria, under certain environmental conditions, can and will produce huge internal polymers as carbon stores, especially when nitrogen supplies are limited. Think of this polymer like starch in plants and glycogen in mammals. Research is still ongoing into the mechanisms that regulate polymer synthesis and degradation.

The bacterial polymer is special, unlike the molecular make-up of starch or glycogen, this polymer is a class of polyhydroxyalkanoate (PHA).

Structure of poly-(R)-3-hydroxybutyrate (P3HB)
Structure of poly-(R)-3-hydroxybutyrate (P3HB) (Photo credit: Wikipedia)

One of the most prevalent forms of PHA is polyhydroxybutyrate, or PHB. Speaking from experience, PHB is an interesting macromolecule to study and observe under the microscope with cells treated with a fluorescent dye that stains PHB. PHB can account for up to 75%  of the total cell weight. PHB, and PHAs in general, can be used to make plastic thus replacing the need for petroleum based plastics.

Living at the Boiling Point: What we can learn from extreme heat-loving microbes

Thanks to the decreasing costs of sequencing genomic DNA, finding novel microorganisms that add to our understanding of metabolism in myriad environments is becoming common place. Not only are we learning about the diversity of life in extreme environments, like heat, cold, pressure, and altitude, but we are also learning what life on other planets may be like. With each additional genome added into ‘the cloud’, our synthetic biology toolbox gets a little bit bigger and our ability to manipulate tiny organisms to produce novel compounds is possible. Enter the “rushing fireball”.

Pyrococcus furiosus is an archeal species that thrives near deep-sea thermal vents where temperatures are between 90 and 100 degrees Celsius (or 194 to 212 degrees F). P. furiosus can grow at temperatures as low as 70 degrees C (158 deg F). To live in such conditions, this organism’s proteins must be tolerant to what we would consider harsh conditions. This organism’s ambient conditions makes wild-type proteins well-suited for industrial processes where temperatures are near boiling.

So far, P. furiosus has been utilized to produce 3-hydroxypropionic acid, a common industrial chemical used to make various products including acrylics. The kicker is that these cells were wired to make this chemical from atmospheric carbon dioxide. It is not crazy to think of what other useful products can be produced by P. furiosus with small modifications within the genome; products like ethanol or butanol as biofuels.

Pyrococcus furiosus, bacteria, archea, illustration, microbiology
My illustration of Pyrococcus furiosus


Keller, M., Schut, G. J., Lipscomb, G. L., Menon, A., Iwuchukwu, I., Leuko, T., Thorgersen, M. P., Nixon, W. J., Hawkins, A., Kelly, R. M. and Adams, M. W. W. (2013) “Exploiting microbial hyperthermophilicity to produce an industrial chemical using hydrogen and carbon dioxide”Proc. Natl. Acad. Sci. U.S.A. (in press).