Biology Direct

Community annotation in biology.

Publication Date: 2010 Feb 18 PMID: 20167071
Authors: Mazumder, R. - Natale, D. A. - Julio, J. A. - Yeh, L. S. - Wu, C. H.
Journal: Biol Direct

ABSTRACT: Attempts to engage the scientific community to annotate biological data (such as protein/gene function) stored in databases have not been overly successful. There are several hypotheses on why this has not been successful but it is not clear which of these hypotheses are correct. In this study we have surveyed 50 biologists (who have recently published a paper characterizing a gene or protein) to better understand what would make them interested in providing input/contributions to biological databases. Based on our survey two things become clear: a) database managers need to proactively contact biologists to solicit contributions; and b) potential contributors need to be provided with an easy-to-use interface and clear instructions on what to annotate. Other factors such as 'reward' and 'employer/funding agency recognition' previously perceived as motivators was found to be less important. Based on this study we propose community annotation projects should devote resources to direct solicitation for input and streamlining of the processes or interfaces used to collect this input. Reviewers: This article was reviewed by I. King Jordan, Daniel Haft and Yuriy Gusev.

post to: CiteULike

Proteome changes of Caenorhabditis elegans upon a Staphylococcus aureus infection.

Publication Date: 2010 Feb 17 PMID: 20163716
Authors: Bogaerts, A. - Beets, I. - Temmerman, L. - Schoofs, L. - Verleyen, P.
Journal: Biol Direct

ABSTRACT: BACKGROUND: The success of invertebrates throughout evolution is an excellent illustration of the efficiency of their defence strategies. Caenorhabditis elegans has proven to be an appropriate model for transcriptome studies of host-pathogen interactions. The aim of this paper is to complement this knowledge by investigating the worm's response to a Staphylococcus aureus infection through a 2-dimensional differential proteomics approach. RESULTS: Different types of growth media in combination with either E. coli OP50 or Staphylococcus aureus were tested for an effect on the worm's lifespan. LB agar was chosen and C. elegans samples were collected 1h, 4h, 8h and 24h post S. aureus infection or E. coli incubation. Proteomics analyses resulted in the identification of 130 spots corresponding to a total of 108 differentially expressed proteins. CONCLUSIONS: Exploring four time-points discloses a dynamic insight of the reaction against a gram-positive infection at the level of the whole organism. The remarkable upregulation after 8h and 24h of many enzymes involved in the citric acid cycle might illustrate the cost of fighting off an infection. Intriguing is the downregulation of chaperone molecules, which are presumed to serve a protective role. A comparison with a similar experiment in which C. elegans was infected with the gram-negative Aeromonas hydrophila reveals that merely 9% of the identified spots, some of which even exhibiting an opposite regulation, are present in both studies. Hence, our findings emphasise the complexity and pathogen-specificity of the worm's immune response and form a firm basis for future functional research. Reviewers This article was reviewed by Itai Yanai, Dieter Wolf and Torben Luebke (nominated by Walter Lutz).

post to: CiteULike

'Genome order index' should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve.

Publication Date: 2010 Feb 17 PMID: 20158921
Authors: Elhaik, E. - Graur, D. - Josic, K.
Journal: Biol Direct

ABSTRACT: BACKGROUND: The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gene transfer detection, and sequence analysis. Based on the Z-curve, a "genome order index," was proposed, which is defined as , where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively. This index was found to be smaller than for almost all tested genomes, which was taken as support for the existence of a constraint on genome composition. A geometric explanation for this constraint has been suggested. Each genome was represented by a point P whose distance from the four faces of a regular tetrahedron was given by the frequencies a, c, t, and g. They claimed that an inscribed sphere of radius contains almost all points corresponding to various genomes, implying that . The distribution of the points P obtained by S was studied using the Z-curve. RESULTS: In this work, we studied the basic properties of the Z-curve using the "genome order index" as a case study. We show that (1) the calculation of the radius of the inscribed sphere of a regular tetrahedron is incorrect, (2) the S index is narrowly distributed, (3) based on the second parity rule, the S index can be derived directly from the Shannon entropy and is, therefore, redundant, and (4) the Z-curve suffers from over dimensionality, and the dimension stands for GC content alone suffices to represent any given genome. CONCLUSION: The "genome order index" S does not represent a constraint on nucleotide composition. Moreover, S can be easily computed from the Gini-Simpson index and be directly derived from entropy and is redundant. Overall, the Z-curve and S are over-complicated measures to GC content and Shannon H index, respectively. Reviewers: This article was reviewed by Claus Wilke, Joel Bader, Marek Kimmel and Uladzislau Hryshkevich( nominated by Itai Yanai).

post to: CiteULike