Cloning and Phylogenetic Analysis of Sid-1-Like Genes from Aphids

The sid-1 (systemic interference defective) gene encodes a transmembrane protein that is an important participator in the systemic RNAi pathway and has been reported in several organisms. In insects, sid-1-like genes were described from Tribolium castaneum, Apis mellifera, Bombyx mori and Schistocerca americana, but were not found in Drosophila melanogaster and Anopheles gambiae. To investigate whether this gene occurs in aphid species, RT-PCRs were performed using degenerate primers designed using the conserved motif of sid-1-like genes. An sid-1-like full-length transcript was amplified from the cotton/melon aphid, Aphis gossypii Glover (Homopera: Aphididae), and a fragment was amplified from the grain aphid, Sitobion avenae (F.). The trancript from A. gossypii was 3067 bp long, with an open reading frame encoding 766 amino acids. Sequence analysis indicated that this transcript shares highest similarity with the reported sid-1-like gene in Schistocerca americana (53%, fragment), followed by A. mellifera (44%), T. castaneum (32–44%), B. mori (38–42%) and Caenorhabditis elegans (25%). Analysis of the transmembrane protein topological structure indicated that the protein encoded by this gene has a similar structure to SID-1 of C. elegans. A phylogenetic tree with all available sid-1-like genes suggests that sid-1-like genes may have had a long evolutionary history. Considering its importance in the RNAi pathway, the absence of a sid-1-like gene in D. melanogaster and A. gambiae is worthy of further investigation

TreeRipper web application: towards a fully automated optical tree recognition software

Background: Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20(th) century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21(st) century. Results: TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/similar to jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Conclusions: Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v

Wikipedia as an encyclopaedia of life

In his 2003 essay E O Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although the “quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson's essay (e.g., "http://ispecies.org":http://ispecies.org, "http://www.eol.org":http://www.eol.org), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the efforts of biodiversity informatics and well-funded international efforts, Wikipedia ("http://en.wikipedia.org/wiki/Main_Page":http://en.wikipedia.org/wiki/Main_Page) has emerged as potentially the best platform for fulfilling E O Wilson’s vision

Spatially and genetically distinct African trypanosome virulence variants defined by host interferon-g response

We describe 2 spatially distinct foci of human African trypansomiasis in eastern Uganda. The Tororo and Soroti foci of <i>Trypanosoma brucei rhodesiense</i> infection were genetically distinct as characterized by 6 microsatellite and 1 minisatellite polymorphic markers and were characterized by differences in disease progression and host-immune response. In particular, infections with the Tororo genotype exhibited an increased frequency of progression to and severity of the meningoencephalitic stage and higher plasma interferon (IFN)–γ concentration, compared with those with the Soroti genotype. We propose that the magnitude of the systemic IFN-γ response determines the time at which infected individuals develop central nervous system infection and that this is consistent with the recently described role of IFN-γ in facilitating blood-brain barrier transmigration of trypanosomes in an experimental model of infection. The identification of trypanosome isolates with differing disease progression phenotypes provides the first field-based genetic evidence for virulence variants in T. <i>brucei rhodesiense</i>

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

<p>Abstract</p> <p>Background</p> <p>Evolutionary methods are increasingly challenged by the wealth of fast growing resources of genomic sequence information. Evolutionary events, like gene duplication, loss, and deep coalescence, account more then ever for incongruence between gene trees and the actual species tree. Gene tree reconciliation is addressing this fundamental problem by invoking the minimum number of gene duplication and losses that reconcile a rooted gene tree with a rooted species tree. However, the reconciliation process is highly sensitive to topological error or wrong rooting of the gene tree, a condition that is not met by most gene trees in practice. Thus, despite the promises of gene tree reconciliation, its applicability in practice is severely limited.</p> <p>Results</p> <p>We introduce the problem of reconciling unrooted and erroneous gene trees by simultaneously rooting and error-correcting them, and describe an efficient algorithm for this problem. Moreover, we introduce an error-corrected version of the gene duplication problem, a standard application of gene tree reconciliation. We introduce an effective heuristic for our error-corrected version of the gene duplication problem, given that the original version of this problem is NP-hard. Our experimental results suggest that our error-correcting approaches for unrooted input trees can significantly improve on the accuracy of gene tree reconciliation, and the species tree inference under the gene duplication problem. Furthermore, the efficiency of our algorithm for error-correcting reconciliation is capable of handling truly large-scale phylogenetic studies.</p> <p>Conclusions</p> <p>Our presented error-correction approach is a crucial step towards making gene tree reconciliation more robust, and thus to improve on the accuracy of applications that fundamentally rely on gene tree reconciliation, like the inference of gene-duplication supertrees.</p

Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library

Background: The Biodiversity Heritage Library (BHL) is a large digital archive of legacy biological literature, comprising over 31 million pages scanned from books, monographs, and journals. During the digitisation process basic metadata about the scanned items is recorded, but not article-level metadata. Given that the article is the standard unit of citation, this makes it difficult to locate cited literature in BHL. Adding the ability to easily find articles in BHL would greatly enhance the value of the archive. Description: A service was developed to locate articles in BHL based on matching article metadata to BHL metadata using approximate string matching, regular expressions, and string alignment. This article locating service is exposed as a standard OpenURL resolver on the BioStor web site http://biostor.org/openurl/. This resolver can be used on the web, or called by bibliographic tools that support OpenURL. Conclusions: BioStor provides tools for extracting, annotating, and visualising articles from the Biodiversity Heritage Library. BioStor is available from http://biostor.org

Towards a data publishing framework for primary biodiversity data: challenges and potentials for the biodiversity informatics community

Background: Currently primary scientific data, especially that dealing with biodiversity, is neither easily discoverable nor accessible. Amongst several impediments, one is a lack of professional recognition of scientific data publishing efforts. A possible solution is establishment of a ‘Data Publishing Framework’ which would encourage and recognise investments and efforts by institutions and individuals towards management, and publishing of primary scientific data potentially on a par with recognitions received for scholarly publications. Discussion: This paper reviews the state-of-the-art of primary biodiversity data publishing, and conceptualises a ‘Data Publishing Framework’ that would help incentivise efforts and investments by institutions and individuals in facilitating free and open access to biodiversity data. It further postulates the institutionalisation of a ‘Data Usage Index (DUI)’, that would attribute due recognition to multiple players in the data collection/creation, management and publishing cycle. Conclusion: We believe that institutionalisation of such a ‘Data Publishing Framework’ that offers socio-cultural, legal, technical, economic and policy environment conducive for data publishing will facilitate expedited discovery and mobilisation of an exponential increase in quantity of ‘fit-for-use’ primary biodiversity data, much of which is currently invisible