I’ve been studying different types of phytoremediation lately and here’s a new form I’d never heard much about: The riparian buffer. Named after the riparian zone, A riparian buffer is the assemblage of plants and organisms lining the bank of a water body, be it a marsh, lake, stream, etc. These are naturally occurring zones that form the transition between the aquatic habitat and that on land.

Natural riparian buffers help filter water and remove non-point source contamination. In phytoremediation, riparian buffers are designed and maintained with specific vegetation to treat a specific contaminant(s) in the surface water or in shallow ground water entering the waterway. According to the University of Florida webpage on riparian buffers, the application of this biotechnology has not traditionally been common in the USA, but is gaining popularity as a sustainable way to protect waterways, particularly from agricultural runoff containing pesticides or excessive amounts of nitrogen or phosphate fertilizers.

Phytoremediation is a form of bioremediation that makes use of plants to degrade or sequester contaminants in soil and groundwater. While the technology is not new, it seems current trends suggest its popularity is growing. This may be due to several factors. One is that the technology has seen some significant developments and a variety of different types of phytoremediation now exist. Genetic studies and cloning technologies have helped us learn more about plant physiology and how to improve uptake or degradation rates, and the use of genetically engineered plants, better suited to the environments to which they are subjected, has improved the phytoremediation process.

The increasing popularity of this technology might also be due to a number of economic and societal factors. For example, phytoremediation for sequestering metals in soil can be a much less expensive, and aesthetically pleasing option than "dig and dump" (i.e.carting the soil off to a landfill). The downside is how long it takes (you have wait for the plants to grow and mature before harvesting) but I think the payoffs are worth it, since phyto, or any bioremediation, when designed well, can be model examples of green biotechnologies.

Antibiotic resistant bacteria, sometimes called "Superbugs" are becoming a widespread problem particularly in hospitals where immunocompromised patients can become very susceptible to infection. For example, we all have the bacterium Staphylococcus aureus growing on our skin at all times. This is a healthy state of being for humans, but during surgery, some of the microorganisms can enter the wound and cause infection. Unless the patient can be treated with antibiotics, infection can become a serious complication to what might otherwise be a routine surgery.

The means by which bacteria become superbugs are largely unknown. The bacteria in question are not those that typically carry the antibiotic resistance genes used in gene cloning techniques, but are usually susceptible to antibiotic treatments. A new clue to the puzzle was reported in Science Magazine by Schumacher et al. (2009) who found a biochemical explanation for antibiotic resistance in Escherichia coli (E. coli). These bacteria have been found to produce a protein, now dubbed HipA (high persistence A). Hip A is a kinase (a type of enzyme) that phosphorylates translation factor EF-TU, sending the cell into a state of stasis. While antibiotics mainly target growing cells, the cells in stasis are able to survive until the antibiotic has worn out, at which time they continue to grow and flourish, at the expense of their human host.

_Source:

Schumacher et al. (2009). Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science 323(5912):396-401. doi:10.1126/science.1163806.

A new link between the protease activity of an enzyme called scrawny (scny), chromatin modification and cell differentiation, has been described in Science Magazine. Scientists from Howard Hugh Medical Institute Research Laboratories used drosophila (fruit flies) to study a type of histone modification called ubiquitylation. Histones are proteins around which chromosomes coil, comprising part of the system for controlling which genes are expressed and which ones aren't.

Ubiquitin is a very widespread eukaryotic protein, found in so many cell processes that, after its discovery, it was named after the word "ubiquitous". Protein degradation, cell signalling and membrane trafficking are among its many roles in cellular processes, in addition to its role in controlling transcription. In their research on gene expression, Buszczak et al. (2009) found that scny silenced gene expression by deubiquitinylating histone H2B.

In different types of pluripotent stem cells, chromatin modifications are usually under the control of different enzymes, but the enzyme scny was found to play a major role in repressing expression of genes that begin the process of cell differentiation in three different types of stem cells.

_Source:

Buszczak et al. 2009. Drosophila stem cells share a common requirement for the histone H2B ubiquitin protease scrawny. Science 323(5911):248-251. doi:10.1126/science.1165678.

A large number of transcription factors in humans belong to a superfamily that shares a similar motif known as the zinc finger. Among these, a large proportion have multiple tandem repeats, and are known as poly zinc finger (polyZF) proteins. These proteins can have anywhere from 4 to 30 repeating units, existing mainly in tandem and highly homologous in terms of spacing and size. The human genome encodes nearly 700 of these type of transcriptional repressors, but their main functions are largely undeciphered. What's more, evolutionary analysis has revealed that these hundreds of similarly structured proteins evolved from a very small pool of ancestors. Over the years, repeated duplications of the zinc finger region have lead to gene diversity, and differences in protein structure suggest a multitude of diverging roles in several lineages of different species, including fish, humans and other primates, and mice.

_Source:

Emerson, R. and Thomas, J. 2009. Adaptive evolution in zinc finger transcription factors. PLOS Genetics 5(1) e1000325, doi:10.1371/journal.pgen.1000325.

How does a weak patent system affect ordinary people? There's more to IP laws than protecting companies so they can make a profit. Of course part of building a strong intellectual property rights (IPR) system is supporting businesses within your jurisdiction (i.e. country) but that doesn't necessarily apply if the business in question of part of big pharma. So how does protecting the interests of even the big companies help us?

Startup Financing – Smaller companies benefit from ood IPR legislation because, if their discoveries are protected, they are more likely to have one of the key criteria among what venture investors are looking for, security for the future. This makes it easier to obtain venture funding to take their products to market.

Legal Empowerment – Why create laws that border officials and law enforcement officers can't enforce? This is part of having a strong IPR system that might be easily overlooked. The laws protecting IP need to come hand-in-hand with strong enforcement practices and adequate consequences to deter non-compliance.

Public Safety – How many of us wouldn't buy the "generic" brand to save a little cash? Counterfeit drugs are everywhere. Preventing knock-off drugs, whether imported or domestic, that might not contain the proper ingredients, or have the right stuff mixed in the wrong amounts is important to public protection.

In a previous blog, I pointed out how genetic polymorphisms can complicate the testing of new drugs on animals, despite the fact that we have some enzymes in common with rats, mice and other test organisms. Over the years, as gene sequencing methods have been perfected and whole genomes sequenced, scientists have come up with creative ways to improve drug fate studies. One solution is to develop mouse lines expressing human genes. According to Powley et al. (2009) the benefits are three-fold: better scientific relevance of the animal study, decreased costs and a possible decrease in the number of test subjects (i.e. mice) needed per study. In another laboratory, chimeric mice with humanized livers, generated by xenotransplantation of human hepatocytes into the mice, have been created, and the properties of the enzymes (such as specific activity, Vmax and Km values) compared to the donor humans with promising results (Katoh et al. 2008).

No matter what the technique though, the mouse models remain just that – models. Many other factors including the expression of other enzymes and minor metabolites, and relative concentrations of each, will affect the outcome of a pharmacogenetic study.

_Sources:

Powley, MW et al. 2009. Safety assessment of drug metabolites: implications of regulatory guidance and potential application of genetically engineered mouse models that express human P450s. Chem. Res. Toxicol. 22(2):257-62.

Katoh, M. et al. 2008. Chimeric mice with humanized liver. Toxicology 246(1):9-17.

Just when I was about to provide an update on progress in developing a Swine Flu (H1N1 virus) vaccine, Novartis, Germany made their big announcement that the first batch of vaccine has been produced, weeks ahead of schedule. Ten litres of the vaccine were made using cell-based techniques, instead of the traditional chicken egg technique that I described in a previous blog. According to their press release, the company will be able to produce millions of doses of vaccine per week, and order have been flooding in from all over the world. Unfortunately, the vaccine still needs testing, and is only at the pre-clinical stage. The 10 L batch will be used for testing, possibly including clinical trials on humans. Other Novartis labs are working on vaccine production using the egg-based technique.

The good news comes the day after the World Health Organization declared this flu outbreak a Level 6 Pandemic. Novartis stocks have jumped by over 4% today.

The city of Hamilton, Ontario (Canada) is embarking on a new Green Biotech project that will utilize human waste to make methane gas for fueling it’s fleet of 110 vehicles. Thanks to a $30 million infrastructure grant, the city will invest in a biofuel technology that has been used in Europe for years, to generate methane from wastewater treatment plant sludge. According to the Hamilton Spectator, the city is the first in Canada to use this technology. Part of the funding will be used to retrofit the vehicles, invest in new technologies for energy recovery from biodegrading microorganisms, and purification of the methane.

Hamilton made headlines in 2005 for a project to convert sludge to electricity that is now used to heat the wastewater treatment plant from which it came, saving the city about $450K per year on natural gas costs, and creating revenue as excess electricity is sold.

Meanwhile, Canada has also jumped on the bioethanol bandwagon as Shell announced today that an Ottawa station has begun selling gasoline containing 10% bioethanol made from wheat straw. According to Shell, this is the first commercial use of bioethanol from straw. Other companies, such as Genencor, are trying to find ways to improve the efficiency of bioethanol production from traditional sources such as corn or sugarcane. The Ottawa technology is the result of a collaborative project between Royal Dutch Shell and the Ottawa-based biotech company Iogen Energy Corporation.

_Sources:

AM 680 News Radio, News Headlines, June 10, 2009. Rogers Broadcasting Ltd.

Environment Canada Pollution Prevention: Canadian Success Stories: Hamilton Renewable Power Incorporated.

MacIntyre, N. Human waste will fuel city fleet. The Hamilton Spectator, June 10, 2009 online at thespec.com.

When it comes to testing the pharmacokinetics of drugs, pesticides or other xenobiotics (man-made compounds), we often turn to other animal species such as rats and mice. However, when interpreting the data we collect, it’s very important to remember that, while there are many similarities in terms of the metabolic pathways in mammalian cells, there are also many differences in the enzymes that execute those pathways. The cytochrome P450 enzyme group is the predominant class of enzymes in the liver for dealing with foreign chemicals. Not only are there species differences at the genetic level of these enzymes (polymorphisms) that result in slight differences in their activities and specificities for certain compounds, there are also differences at the level of transcription (caused by polymorphisms in transcriptional machinery), dictating how much of each enzyme we may produce in our bodies.

One enzyme responsible for much of the conversion of pro-carcinogens to their carcinogenic form in our bodies, P450 1A2, is known to be 75% identical between rats and humans. However, depending on the substrate, N-hydroxylation activities can vary by an order of magnitude between the species. Add to that the fact that there are considerable differences among species themselves such as humans of different family lineages or races, and genders. N-hydroxylation by P450 1A2 has been found to vary by as much as 40% between human individuals. Gene polymorphisms, or these differences between individuals, is the basis of RFLP analysis (think DNA fingerprinting). This is why interpreting the data from drug, or other metabolism studies, is much more complex than it may appear on the surface.

_Sources:

Uno S. et al. 2009. CYP1A1 and CYP1A2 expression: comparing ‘humanized’ mouse line and wild-type mice: comparing human and mouse hepatoma-derived cell lines. Toxicol. appl Pharmacol. 237(1):119-26.

Kirchheiner et al. 2005. Effect of genetic polymorphisms in cytochrome P450 (CYP) 2C9 and CYP2C8 on the pharmacokinetics of oral antidiabetic drugs: clinical relevance. Clin Pharmacokinet. 44(12):1209-25.

Kuribayashi et al. 2009. Human cytochrome P450 1A2 involvement in the formation of reactive metaoblites from a species-specific hepatotoxic pyrazolopyrimidine derivative, 5-n-butyl-7-(3,4,5-trimethoxybenzoylamino)pyrazolo[1,5-a]pyrimidine. Chem Res Toxicol. 22(2):323-31.

Guengerich FP. et al. 1999. Inter-individual differences in the metabolism of environmental toxicants: cytochrome P450 1A2 as a prototype. Mutat Res. 428(1-2):115-24.

Anzenbacher P. and Anzenbacherova E. 2001. Cytochromes P450 and metabolism of xenobiotics. Cell Mol Life Sci. 58(5-6):737-47.