Tuesday, February 16, 2016

New Research Shines Light on Historical Skin Blight

by KS

“Ringworm” is a common infection that has plagued humans for centuries. It lives on the skin of humans and our domesticated animals, causing a distinctive oozy, red, ring-shaped sore (1). This infection has an interesting history that starts in the early 1800s, though disease was present in human populations well before that. The 1800s brought great societal changes for the inhabitants of Western Europe where the industrial revolution was in full force. Many people left behind their small village agricultural lifestyle in search of prosperity in the growing cities. This was great for development but it had one massive unintended consequence: disease. One disease that became a public nuisance during this time was ringworm. People originally thought that the ringworm infection was caused by a worm that you could contract via everything from having bad hygiene to associating with the poor (2). The late 19th century saw a shift in the perception of the disease. Instead of being seen as a fact of life, it was starting to be seen as a highly contagious pathogen. In fact, many immigrants were turned away at Ellis Island due to this infection (2). A breakthrough was finally made during this time period that identified the causative agent of ringworm infection as a fungus, Trichophyton rubrum that is neither a worm nor associated with the poor (3).
False color image of Trichophyton growing
on human skin cells
 
  
Trichophyton is part of a group of fungal pathogens called dermatophytes, which live and feed on the skin of humans and mammals. These eukaryotic microbes have a very specialized way in which they go about eating human skin; they feed on keratin, the main protein component of skin and hair. Feeding on keratin is a very interesting survival strategy because keratin is a rigid protein that is very hard breakdown and extract nutrients from (4). On the other hand, it is one of the most abundant proteins on the planet, so the ability to feed on it is a clear advantage for Trichophyton. This raises an interesting question for researchers, what allows Trichophyton to use keratin as a food source and is this ability the reason it so readily infects humans?
Recently researchers have aimed to explore the infectiousness of Trichophyton by looking at virulence factors (5). Virulence factors are proteins or molecules that are produced by the pathogen that help it to infect the host. Virulence factors play an important role in Trichophyton infection because the fungus must adhere to your skin and start breaking down keratin, a process that is likely mediated by proteins or molecules that the fungus secretes. A group of researchers decided to explore in the role that virulence factors play in Trichophyton’s ability to adhere to and devour human skin cells by looking at what genes were overexpressed during growth on keratin. This experiment was done ex vivo, outside of actual host infection but with attempts made to recreate some of the natural environment. Trichophyton cells were grown on either keratin or glucose and their gene expression was evaluated at several time points (5). The authors used a really interesting method called subtractive suppression that uses messenger RNA levels to look at how much a gene is being transcribed and comparing that with library DNA measurements to identify only genes that differing in expression. Using this method they found 238 genes that appeared to be overexpressed in Trichophyton grown on keratin. They investigated further 28 of these genes and found that several of them encoded virulence factors that help Trichophyton infect skin cells. The most significant virulence factors they found were subtilisins, which are proteins that digest and breakdown other proteins (5). Some of the subtilisins that are overexpressed are specific for keratin. This data shows Trichophyton has genes that encode keratin specific subtilisins which give a glimpse into how they are able to breakdown and feed on keratin.
Another group of researchers took a different approach in hopes of answering the same question, what makes Trichophyton so infectious? Martinez et al conducted a full genome comparison between different Trichophyton species, T. rubrum, T.tonsurans, T. equinum, and the non-dermatophyte species Microsporum canis and Microsporum gypseum (6). They sequenced the complete genomes of each species and then compared the genome composition and gene between the Trichophyton species as well as the non-dermatophyte fungi. They found some interesting and significant results. The data shows Trichophyton species do in fact have unique genes that are not found in other pathogenic fungi and may give them the ability to live and fed on human skin. A group of unique genes in Trichophyton encode for distinct proteases that are not found in other fungi. These proteases are very similar to the subtilisins identified in the other paper, as they are used by cells to breakdown proteins. Similarly these proteases where shown to be specific for keratin (6). These results further support idea that Trichophyton has unique genes that produce proteins that allow the parasite to effectively break down keratin. However, the breakdown of keratin is not the only thing that enables the fungi to survive. This research also discovered some genes that do not code for virulence factors but are unique to the Trichophyton genus (6). Genes encoding novel kinases were common to only the Trichophyton fungi. Interestingly, they discovered many non-functional pseudokinases that, instead of turning on signaling pathways and activating proteins like normal kinases, they actually interfere with those processes due to competition. This may seem like something that wouldn’t be helpful to a pathogen but here it actually gives them a nontraditional way of regulating signaling and gene expression. This extra method for controlling cell processes may contribute to their ability to switch their metabolism to keratin digestion. Thus, this paper identified genes that are unique to Trichophyton that play an important role in keratin breakdown and cell process regulation, allowing Trichophyton to effectively infect and feed on human skin cells.
            Recent research has shed new light on an old and irritating pathogen, the causative agent of ringworm that definitely isn’t a worm; Trichophyton. The information gained from the papers above show that this pathogen’s genome does contain unique genes that encode novel proteases and pseudokinases that seem to function during infection of human skin cell. These proteins allow Trichophyton to disassemble the tough structure of keratin and then use cellular metabolic pathways to digest it, allowing this fungal pathogen to survive in the challenging environment that is the human skin. In the end, new research has shown that novel genes and proteins that enable Trichophyton to breakdown and digest keratin are part of what make Trichophyton such a prolific human pathogen.



1. Degreef, H. (2008). Clinical forms of dermatophytosis (ringworm infection).Mycopathologia166(5-6), 257-265.

2. Unna, P. G. (1896). The Histopathology of the Diseases of the Skin. WF Clay.

3. Morris, M., & Henderson, G. C. (1883). The Cultivation and Life‐History of the Ringworm Fungus (Trichophyton tonsurans). Journal of the Royal Microscopical Society3(3), 329-337.

4. Tombolato, L., Novitskaya, E. E., Chen, P. Y., Sheppard, F. A., & McKittrick, J. (2010). Microstructure, elastic properties and deformation mechanisms of horn keratin. Acta biomaterialia,6(2), 319-330.

5. Maranhão, F. C., Paião, F. G., & Martinez-Rossi, N. M. (2007). Isolation of transcripts over-expressed in human pathogen Trichophyton rubrum during growth in keratin. Microbial pathogenesis43(4), 166-172.

6. Martinez, D. A., Oliver, B. G., Gräser, Y., Goldberg, J. M., Li, W., Martinez-Rossi, N. M., ... & White, T. C. (2012). Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. MBio, 3(5), e00259-12.


Friday, February 12, 2016

Eliminating Nuclear Pollution Using Algae - Coccomyxa actinabiotis

When you imagine a pool of water filled with high concentrations of toxic metal debris and uranium from a nuclear power plant, what do you think of?  Do you think lethal, deadly or completely inhospitable?  If so, you would be, for the most part, correct.  Such conditions are fatal to nearly every living cell on the planet.  However, a recently-isolated algae found in a nuclear material storage site named Coccomyxa actinabiotis is able to not only survive in such conditions, but can even thrive.  Such an organism can prove a useful tool in slowing the increasing levels of nuclear waste due to the development of nuclear power.

In our current situation of constantly increasing demand for energy, nuclear power presents a valuable source of electricity: nuclear reactors currently supply the world with 13% of its total electricity, and nuclear energy processes produce virtually no greenhouse gases.  With carbon emissions becoming an increasing threat to global temperatures by the year, nuclear power is likely to become a popular alternative to more air-polluting energy production tactics such as coal-burning plants.  However, with this revolution in energy will come a different pollutant in the form of particles known as radionuclides.  Radionuclides are high-energy, unstable atoms that are an inevitable product of nuclear fission that takes place in energy-producing nuclear plants1.

Many nuclear power plants utilize a water-based system in which water is run by a reactor to harness the heat energy of the nuclear reactions.  In this way, radionuclides leak into the water, which must be removed before the water is reused1.  The methods by which this is done (such as precipitation, evaporation, ion-exchange, etc.) are energy-intensive and expensive2.  Additionally, any leaks of radioactive material, such as the explosion of the Fukushima power plant in 2011, are dealt with via blunt and inefficient methods, such as manual washing and concrete isolation of contaminated surfaces3.  Therefore, a radionuclide-cleaning technique such as bioremediation presents an appealing alternative to current detoxification processes.
Bioremediation is the use of microorganisms to render hazardous materials harmless.  Such a strategy is cost-effective, allows decontamination of large areas such as bodies of water, and is generally gentle on the environment.  This technique is already used in the nuclear industry using organisms such as genetically-modified yeasts, though these microbes require a significant amount of nutrients and are not as efficient at concentrating radionuclides as certain cells that are naturally resistant to radioactivity.  Examples of these promising specimens with high natural radiation resistance are mostly cells without nuclei, such as Pyrococcus furiosus or Deinococcus radiodurans.  However, the nucleated algae Coccomyxa actinabiotis presents one of the most convenient specimens for bioremediation deployment for a multitude of factors: it has demonstrated extreme resistance to both radionuclides and heavy metals, it has natural mechanisms to turn radionuclides into inert substances, and it is photosynthetic2.

cells. Note the bright green coloration
indicative of the photosynthetic
chloroplasts in the algae.
First, what makes environments filled with radionuclides so hostile?  In high levels of radiation, very small particles such as gamma or beta rays are emitted from decaying radionuclides.  These rays are able to penetrate cells and nuclei where they can fragment and mutate the cell's DNA.  Excessive levels of genetic destruction are fatal for the cell.  Amazingly, C. actinabiotis is capable of surviving and reproducing in radioactivity of up to 20,000 Gy - a concentration of radionuclides that can shatter glass and plastics2.  As a more relatable point of comparison, a full-body dose of radiation that is internally measured at only 5 Gy is lethal to 50% of humans after one month of the initial exposure4. 

The methods by which C. actinabiotis and other cells survive this harsh environment are varied, but all depend on maintaining the integrity of the organism's DNA.  It is known that C. actinabiotis actively accumulates deadly radionuclides and uses them in certain biochemical pathways, partially detoxifying them and concentrating them within the cell membrane.  Currently, however, there is little thorough research on the specific mechanisms by which this resistant algae lives in such intense radiation.  Studies on the non-nucleated, radiation-resistant organism D. radiodurans indicate that microbes can use techniques such as enhanced gene repair mechanisms and maintaining multiple genome copies to combat radioactive gene damage.  Additionally, supplementary experiments have suggested that C. actinabiotis is capable of restoring its entire genome in the event of severe radioactive mutation, allowing continued growth and multiplication2.

In addition to radionuclides, C. actinabiotis can also withstand extremely high concentrations of toxic metals such as cobalt and silver.  Using a high-resolution imaging technique, it was found that cobalt ions become highly concentrated outside of C. actinabiotis chloroplasts, suggesting that cobalt is possibly used within the chloroplasts to produce nutrients.  The imaging also revealed that silver ions are spread evenly throughout the inside of the cell.  Silver may or may not be used in C. actinabiotis biochemical reactions, but it is, at the very least, highly isolated from compartments in which it can interfere.  Alternatively, silver ions may be bound to other molecules that render it harmless to vital biochemical pathways5.

These properties, when uniquely combined in a single organism, make for a relatively superior tool for cleaning hazardous environments.  While species such as D. radiodurans are capable of surviving in high concentrations of radionuclides, they are heterotrophic microbes.  This means that they require other microorganisms to feed upon, which is difficult for these cells to accomplish in bioremediation environments when nuclear material kills most, if not all, D. radiodurans prey species6.  C. actinabiotis, on the other hand, is a photosynthetic algae.  Thus, all it requires to clean toxic substances is light and a carbon source, making it far more applicable in situations in which bioremediation is necessary.  Additionally, most microbes that are resistant to either radioactivity or heavy metals are not resistant to the other: D. radiodurans, while highly radionuclide-resistant, cannot tolerate high toxic metal concentrations.  C. actinabiotis is capable of handling high concentrations of both types of substances simultaneously, giving the organism unparalleled versatility in the detoxification of dangerous materials7.  Lastly, most currently used bioremediation species require intensive genetic manipulation in order to possess traits such as detoxification and resistance6.  C. actinabiotis is capable of performing these actions naturally, requiring less lengthy and expensive manipulations of DNA2.

So, finally, how would C. actinabiotis actually be used as a bioremediation tool?  Upon being placed on a contaminated surface or in a contaminated body of water, C. actinabiotis will begin absorbing radionuclides and heavy metals at a rapid pace, concentrating and purifying them to a certain extent.  Eventually, most of the contaminants will be contained within cell bodies, which can then be gathered and disposed of by incineration or other such disposal methods.  Alternatively, trapped heavy metals can be recycled from these algae cells to be reused in various industries2.

In conclusion, the process of using C. actinabiotis as a nuclear decontamination tool can occur without genetic manipulation and with only a source of light energy and carbon atoms.  Thus, the end result of such a treatment is an area cleansed of both dangerous radionuclides and toxic metals with relatively little energy investment and minimal environmental harm2.  No other microorganisms currently known, nucleated or not, can equal the versatility, resilience and simplicity by which this novel algae absorbs and concentrates deadly atoms.  Acquiring such an efficient technique of resolving radionuclide pollution can allow nuclear power to completely meet world energy demands without suffering the consequences of radioactive contamination.


References:

1. Zinkle, S.J. (2013). Materials challenges in nuclear energy. Acta Materialia. 61(3). Pgs. 735-758. Retrieved from http://www.sciencedirect.com/science/article/pii/S1359645412007987

2. Rivasseau, Corinne, et. al. (2012). An extremely radioresistant green eukaryote for radionuclide bio-decontamination in the nuclear industry. Energy and Environmental Science. 6. Pgs. 1230-1239. Retrieved from https://hal-agrocampus-ouest.archives-ouvertes.fr/hal-00796855/document

3. Brumfiel, Jeff. (2011). Fukushima set for epic clean-up. Nature. 472. Pgs. 146-147. Retrieved from http://www.nature.com/news/2011/110411/full/472146a.html

4. Caso, C. et. al. (1999). Section 5.4 Radioactivity and Radiation Protection. Review of Particle Physics. Retrieved from http://xdb.lbl.gov/Section5/Sec_5-4.pdf

5. Leonardo, T. et. al. (2014). Determination of elemental distribution in green micro-algae using synchrotron radiation nano X-ray fluorescence (SR-nXRF) and electron microscopy techniques – subcellular localization and quantitative imaging of silver and cobalt uptake by Coccomyxa actinabiotis. Metallomics. 6. Pgs. 316-329. Retrieved from http://pubs.rsc.org.ezp1.lib.umn.edu/en/content/articlepdf/2014/mt/c3mt00281k

6. Misra, Chitra Seetharam et. al. (2012). Recombinant D. radiodurans cells for bioremediation of heavy metals from acidic/neutral aqueous wastes. Bioengineered. 3(1). Pgs. 2165-5979. Retrieved from http://www.tandfonline.com/doi/full/10.4161/bbug.3.1.18878

7. Rivasseau, Corinne et. al. (2011). U.S. Patent No. 20130078707. Retrieved from http://www.google.com/patents/US20130078707

8. Associated Press. (Mar. 10, 2013). Japan struggles to clean up after tsunami, nuclear disaster. The Oregonian.  Retrieved from http://www.oregonlive.com/today/index.ssf/2013/03/japan_struggles_to_clean_up_af.html