25 mei 2010

An online publication in Euphytica reflects on the results of a workshop that focused on the role of molecular markers and marker assistedselection in breeding for organic agriculture.

Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular markers is not self-evident and is often debated.

Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture was the topic of a recent European plant breeding workshop. The participants evaluated strengths, weaknesses, opportunities, and threats of the use of molecular markers and we formalized their inputs into breeder’s perspectives and perspectives seen from the organic sector’s standpoint. Clear strengths were identified, e.g. better knowledge about gene pool of breeding material, more efficient introgression of new resistance genes from wild relatives and testing pyramided genes. There were also common concerns among breeders aiming at breeding for organic and/or conventional agriculture, such as the increasing competition and cost investments to get access to marker technology, and the need for bridging the gap between phenotyping and genotyping especially with complex and quantitative inherited traits such as nutrient-efficiency. A major conclusion of the authors is that more interaction and mutual understanding between organic and molecular oriented breeders is necessary and can benefit both research communities.

The full article can be downloaded here

The Proceedings of the workshop held on February 25-26, 2009 can be downloaded here

26 April 2010

One of the ambitions of synthetic biology is the design and construction of entirely novel, orthogonal life-forms. Their incompatibility with existing life-forms would not only make such orthogonal systems relatively safe to use, they could also be designed to produce new types of proteins that can be assessed for potential medical and industrial applications. From this perspective, the work of a research group from Cambridge University, in the UK is groundbreaking. They designed a novel system that can incorporate unnatural amino acids in biosynthesis of peptides and proteins far more efficiently than present technologies.

In natural living systems, the cell’s DNA is translated into proteins or peptides in three steps. First of all, the cell copies the genetic code from its DNA to  messenger RNA. The messenger RNA then takes this copy to the part of the cell that produces peptides, the ribosome. On the ribosome so-called triplets, codons of three nucleotides (i.e. the building blocks of the genetic code: A, C, U or G), are linked to an amino acid (see figure). Thus, the ribosome transcribes the genetic code step-by-step in a peptide chain or a protein. There is a total of 64 possible combinations of A, C, U and G in triplets (4³). One of the triplets is the so-called start codon, which makes the transcription process begin. Another three triplets are stop codons that make the process end. That leaves 60 remaining triplets encoding for linkage to amino acids. Most amino acids are encoded by several different triplets. Therefore, the natural system can link only 20 different amino acids instead of 60 (see the table at the bottom of the article).

Solid-phase peptide synthesis (SPPS) was developed in the 1960's as a chemical method for creating peptides and proteins in the lab. This technology can be used to synthesize natural peptides, which are difficult to express in bacteria and to incorporate unnatural amino acids. Although SPPS is relatively simple to apply, there remain some constraints concerning the yield, length of the peptides (a maximum of 70 – 100 amino acids) and the type of peptides and proteins that can be synthesized.

Jason Chin’s research group in Cambridge redesigned several pieces of the cell’s protein-building machinery to construct a so-called orthogonal ribosome. Based on transcription of quadruplets, the orthogonal ribosome contains codons of four bases, and uses the cell’s normal protein translation machinery. This raises the number of possible combinations of A, C, U and G to 256 (4⁴) allowing the system to produce peptides and proteins with unnatural amino acids without the constraints of SPPS.

Chin’s team took the gene that codes for the calcium binding protein calmodulin and synthesized pieces of DNA designed to enhance the capability of the ribosome system, to decode quadruplets. They put this synthesized DNA in the calmodulin gene and integrated unnatural amino acids. This resulted in a protein that is more condensed and stable, allowing the protein to survive in a much wider range of environments.

Chin’s research could lead to new drugs that can be swallowed without being destroyed by the acids in the digestive tract, and to polymers with entirely new characteristics for industrial uses.

Some scientists already warn that the synthesis of new proteins is not without risk. New polymers may interfere with existing cellular processes, and should therefore be carefully assessed before their use outside the lab.

Sources:

Guzman F, Barberis S, Illanes A. Peptide synthesis: chemical or enzymatic. Electronic Journal of Biotechnology [online] 2007; 10(2).

Chin, Jason W. Modular approaches to expanding the functions of living matter. Nature Chemical Biology Vol. 2, nr 6, p. 304-311

Heinz Neumann et al. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature Vol. 464, 441-444 (18 March 2010) | doi:10.1038

Life’s code rewritten in four-letter words, New Scientist 2748, 17 February 2010.

26 April 2010

During the last decade, governments have included the use of biomass for biofuel production as a serious option in their energy policies. However, biomass production and its conversion to bioethanol is a rather inefficient way of capturing and storing solar energy. Engineers from the University of Cincinnati have devised a far more efficient synthetic system: a foam that captures energy and removes excess carbon dioxide from the air — thanks to semi-tropical frogs.

In natural photosynthesis, plants absorb solar energy and carbon dioxide and then convert it to oxygen and sugars such as glucose and fructose. These plant sugars can be converted to ethanol as a renewable energy source. Unfortunately, this process of solar energy conversion is not very efficient. Due to limitations in wavelength sensitivities and extensive  cellular processes (including growth, repair, and maintenance), plants convert only 1-2% of usable energy into sugars. Moreover, the production of plant sugars requires that limited land and water resources be diverted, in part, to biomass production.

Now, thanks to a semi-tropical frog species, engineering researchers at the University of Cincinnati are finding ways to take energy from the sun and carbon from the air to create new forms of biofuels. To produce these sugars from sunlight and carbon dioxide, researchers developed a new artificial photosynthetic material which uses plant, bacterial, frog and fungal enzymes, by trapping them within a foam housing.

Foam was chosen because it can effectively concentrate the reactants, but allows considerable light and air penetration. The design was based on the foam nests of a semi-tropical frog called the Tungara frog, which creates very long-lived foams for its developing tadpoles.

The researchers first divided the entire photosynthetic system into three independent reactions: 1) the conversion of energy from the sunlight (photons) to the natural energy molecule ATP, 2) a RuBisCo carbon fixation assay, and 3) a glucose producing assay. After demonstrating the system as separate experiments, the three reactions were combined and an assessment of the full process was conducted. The peak chemical conversion efficiency was 96% (as compared to the 1-2% of plants prior).

The artificial system has several advantages over plants and algae. First of all, the system does not have to maintain life and reproduce, so it converts all captured energy to sugars. The foam also uses no soil, so food production will not be interrupted. In natural plant systems, excessive carbon dioxide shuts down photosynthesis, but the frog foam based system does not have this limitation due to the bacterial-based photo-capture strategy.  Thus, the frog foam based system can be used in highly enriched carbon dioxide environments, like the exhaust from coal-burning power plants. Finally, by designing the photosynthetic foam to synthesize sugar directly, biofuels like DMF (2,5-dimethylfuran) could be produced, which has advantages over ethanol because of its 40% higher energy density, higher boiling point and insolubility in water that makes it more suitable for pipeline transport.

Research groups all over the world are working on similar systems based on photosynthesis. Recently, a  consortium of Dutch research groups will focus received a government grant of 25 million Euros to establish a Center for Photosynthesis in the next five years. This Center will focus on three fields of research: 1) systems biology of photosynthesis processes, 2) re-engineering organisms for optimal photosynthetic energy conversion into biomass, and 3) energy-tapping before the energy is converted into biomass, resulting, for instance, in solar cells that yield methanol instead of electricity.

Although the next step for the Cincinnati team will be to try to make the technology feasible for large-scale applications like carbon capture at coal-burning power plants, it is unclear whether and when this type of promising research will result in commercial application of new energy production methods. For this to occur, there has to be sufficient proof that the technology is working in large-scale production facilities and outside the lab.  Perhaps even more important will be whether commercial incentives are developed for energy companies.

Sources:

Wendy Beckman, Frogs, Foam and Fuel: UC Researchers Convert Solar Energy to Sugars, University of Cincinnati, March 12, 2010.

David Wendell, Jacob Todd, and Carlo Montemagno. Artificial Photosynthesis in Ranaspumin-2 Based Foam. Nanoletters, March 5, 2010, DOI: 10.1021/nl100550k.

Center for Photosynthesis Research, Towards Biosolar Cells, Wageningen University Research Centre, Leiden University, VU University of Amsterdam and University of Groningen, May 2008.