Perfect harmony

Ridiculed by some, Gaia theory - the idea that all living and non-living components on earth work together to promote life - is gaining support.

Earth is a perfect planet for life but, according to Gaia theory, this is no coincidence. From the moment life first appeared on Earth it has worked hard to make Earth a more comfortable place to live. Gaia theory suggests that the Earth and its natural cycles can be thought of like a living organism. When one natural cycle starts to go out of kilter other cycles work to bring it back, continually optimising the conditions for life on Earth. Named after the Greek Earth goddess, Gaia, the theory was developed in the 1960s by scientist Dr James Lovelock. At the time, Lovelock was working for Nasa, looking at methods of detecting life on Mars. The theory came about as a way of explaining why the Earth's atmosphere contains high levels of nitrogen and oxygen.

Initially, Gaia theory was ignored, and then later ridiculed by scientists such as Richard Dawkins and Stephen J Gould. However, in recent times stronger evidence for the theory has emerged and Gaia has started to gain support. The theory helps to explain some of the more unusual features of planet Earth, such as why the atmosphere isn't mostly carbon dioxide, and why the oceans aren't more salty. In its early years Earth's atmosphere was mostly carbon dioxide - the product of multiple volcanic burps. It wasn't until life arrived that the balance began to change. Bacteria produced nitrogen, an inert gas, and photosynthesising plants produced oxygen, a very reactive gas. Ever since that time, about 2,500m years ago, Earth's atmosphere has contained significant amounts of nitrogen and oxygen, supporting life on this planet. The nitrogen helps to keep things stable, preventing oxygen levels from climbing too high and fuelling runaway fires. Meanwhile, the oxygen supports complex life.

Gaia also helps to explain how the oceans are kept in balance. Rivers dissolve salt from rocks and carry it to the ocean, yet ocean salinity has remained at about 3.4% for a very long time. It appears that the salt is removed again when water is cycled through cracks on the ocean floor. This process keeps the oceans' salinity in balance and at a level that most lifeforms can tolerate. These processes are not thought to be conscious ones, or to favour any one life form over another. Gaia theory simply maintains that Earth's natural cycles work together to keep the Earth healthy and support life on Earth. Lovelock argues that humans have now pushed Gaia to her limit. In addition to filling the atmosphere with carbon dioxide, we have hacked our way through the "lungs" of the planet (the rainforests) and driven many species to extinction. He thinks we are heading for a very warm world, where only polar regions are comfortable for most life forms. Eventually, he suspects, Gaia will pull things back into check, but it may be too late for the human race.

Explainer: Feedback loops

Feedback loops often appear to keep the planet in balance. One good example of this is the way in which atmospheric carbon dioxide is kept in check. Carbon dioxide is pumped into the atmosphere by volcanoes, and removed by the weathering of rocks (encouraged by bacteria and plant roots in the soil). When it reaches the sea, the dissolved carbon dioxide is used by tiny organisms, known as coccolithophores (algae), to make their shells. When coccolithophores die they release a gas - dimethyl sulphate - which encourages the formation of clouds in the atmosphere. When atmospheric carbon dioxide levels become too high, coccolithophores get busy, locking up more carbon dioxide in their shells and pumping dimethyl sulphate into the atmosphere when they die - producing clouds which reflect back sunlight and help the Earth to cool. Conversely, if atmospheric carbon dioxide levels become low, coccolithophores reduce their activity.

Over the past 200 years mankind has greatly increased atmospheric carbon dioxide levels, and recently there has been evidence that algal blooms in the ocean are increasing. Could Gaia be trying to correct our mistake?

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Putting That Bioinformatics 101 Class to Work

In a paper called "Metagenome Annotation Using a Distributed Grid of Undergraduate Students" I just love this title! It's nerdy and cute, all at the same time. Says Sandra Porter.

The paper describes a class where students from Marseilles University investigate the function of unidentified genes from a Global Ocean Sampling experiment. All the sequences are obtained from the environmental sequence division at the NCBI.

French researchers describe their strategy for teaching undergraduate-level bioinformatics using cutting-edge genomic data and a Web-based learning tool. The students then annotated real metagenomic sequences from the Global Ocean Sampling experiment. "In return for their much-needed help sorting out oodles of DNA data, the undergrads gain a practical knowledge of the work involved in doing bioinformatics and metagenomics, and, most importantly of all, they get to experience what it's like to do real research," says Karen James at the Beagle Project. Jonathan Eisen's a fan of the work, too, not only because it was metagenomics and published in a PLoS journal, but also because the software is open source.

Pascal Hingamp et al discuss in detail the Open Source, Open Science system for metagenome annotation (see PLoS Biology - Metagenome Annotation Using a Distributed Grid of Undergraduate Students).

They do this as part of a course on metagenome annotation. And the software for running this is all Open Source and available. They say in a way this is a metagenomics version of the Undergraduate Genomics Research Initiative (UGRI) which was described in a PLoS Biology paper previously.

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Systems Biology Can Uncover Signatures of Vaccination Immune Response

A team of American and French researchers used systems biology to identify gene signatures predicting human immune responses to the yellow fever vaccine, YF-17D. The work appeared in an advanced online publication in Nature Immunology yesterday.

Using high-throughput gene expression measurements, multiplex analysis of cytokines and chemokines, and multi-parameter flow cytometry, investigators tested samples taken from more than a dozen individuals in the days and weeks following their yellow fever vaccination. Computational modeling allowed them to come up with signatures predicting CD8+ T-cell and neutralizing antibody responses to YF-17D — insights into vaccine immunogenicity that may inform future vaccine research and development.

“The identification of gene signatures that correlate with, and are capable of predicting, the magnitudes of the antigen-specific CD8+ T-cell and neutralizing antibody responses provides the first methodological evidence that vaccine-induced immune responses can indeed be predicted,” senior author Bali Pulendran, an immunologist and virologist at the Emory Vaccine Center in Atlanta, and his colleagues wrote.

The yellow fever vaccine, which was developed in the 1930s, has been administered to more than 600 million people around the world. Because it is among the most effective vaccines to date — protecting 80 to 90 percent of the individuals who receive it — the researchers reasoned that YF-17D could serve as a good model for studying the early immune response to vaccination.

Do you want to know more?

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Position open Group Leader - Bioinformatics/Systems Biology

The Computational Biology Unit (CBU) has been established to conduct top-level European research in bioinformatics, and to serve functional genomics research in Norway with relevant training and services.

CBU is searching for an additional group leader. The group leader will carry out research in the field of computational biology/bioinformatics and contribute to the overall objectives of CBU. The group leader should have a PhD and post-doctoral experience including a solid publication record in a relevant subject. Candidates will be evaluated with emphasis on their ability to raise external funding and to supervise and carry out research projects. The research profile of the candidate should be within a relevant area for CBU. Candidates with profiles in direction of systems biology will be preferred. The group leader will direct a research group consisting of Ph.D. and post-doctoral scientists.

The CBU and its partners currently have bioinformatics research activities in the fields of protein biophysics, molecular modeling and protein dynamics, transcriptional regulation microarray and proteomics bioinformatics, and genome assembly and annotation. Activity has been initiated towards integrative bioinformatics and systems biology. There are excellent opportunities for collaboration with the molecular biological and biomedical as well as mathematical and informatics research groups in Bergen.

CBU is part of Bergen Center for Computational Science (BCCS) and located together with the Department for Informatics, the Molecular Biology Department and the SARS Centre for Marine Molecular Biology, a partner of EMBL. BCCS owns and operates large scale computing facilities that provide an excellent computational environment. CBU is partner in the Molecular and Computational Biology research school (http://www.mcb.uib.no). CBU is coordinating the bioinformatics technology platform for the national functional genomics programme (FUGE) in Norway.

Salary and professional resources are internationally competitive. Please send your CV, your ten most relevant publications, and a detailed statement of research interests to Professor Inge Jonassen (Inge.Jonassen@bccs.uib.no), head of the CBU. Evaluation of applications will commence January 4th 2009 and continue until a suitable candidate has been identified. For more information about CBU, please refer to http://www.cbu.uib.no/, or contact Inge Jonassen.

Courtesy:

Inge Jonassen, PhD

Department of Informatics and

Computational Biology Unit, BCCS

University of Bergen

HiB

No5020 Bergen

Norway

email: inge.jonassen@ii.uib.no

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Leukemia Genome Project Highlights Second-Gen Sequencing Software Needs

The first effort to sequence a complete cancer genome has underscored the power of second-generation sequencing while further establishing the lack of a “killer software app” in the field.

In the study, published this week in Nature, a team of 48 scientists at the Genome Center of Washington University and elsewhere sequenced a female patient’s acute myeloid leukemia genome and compared it to the genome of her biopsied skin as well as reference genomes to uncover 10 cancer-associated mutations — eight of which were previously unknown.

The team used two high-throughput sequencing platforms — the Illumina Genome Analyzer and the Roche/454 FLX platform — and software tools such as Maq, Cross_Match, BLAT, and Decision Tree analysis. The team also did its own scripting and algorithm development in the course of the project, Rick Wilson, director of the Genome Sequencing Center at Washington University School of Medicine, said.

The AML sequencing team applied several established software tools and algorithms as well as those developed specifically for the project, underscoring the fact that second-generation sequencing projects are not taking place in a one-pipeline-fits-all world.

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