787 research outputs found
Termites in the woodwork
Termites eat and digest wood, but how do they do it? Combining advanced genomics and proteomics techniques, researchers have now shown that microbes found in the termites' hindguts possess just the right tools.
Most animals, from insects to mammals, carry complex communities of microbes in their digestive tracts. In the case of wood-eating termites, these gut microbes are particularly important: they are thought to provide most of the capabilities needed for efficient digestion of wood, which is otherwise a largely inaccessible food source. They also help to compensate for the paucity of some nutrients in wood, for example by fixing atmospheric nitrogen, and they synthesize essential amino acids and other compounds for their hosts [1, 2].
Despite their importance, relatively little is known about gut microbes in termites. This is partly because gut microbes are often difficult to grow in pure culture (as is the case for most microbes sampled from natural environments). Furthermore, a single termite can harbor a very complex assemblage of hundreds of different microbial lineages, whose members may vary widely in terms of abundance and growth rates. Without access to cultivated strains, researchers have to rely on so-called 'cultivation-independent' molecular techniques to analyze such communities. A clever combination of these techniques has now been applied to a section of the termite hindgut, aiming to identify molecular tools used by the microbes in this compartment to degrade wood [3]. Here, we review the procedures and results of this study, and discuss insights into the biological system as well as implications for the generation of biofuels
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
Three integrated genomic context methods were used to annotate uncharacterized proteins in 102 bacterial genomes. Of 7853 orthologous groups with unknown function containing 45,110 proteins, 1738 groups could be linked to functionally associated partners. In many cases, those partners are uncharacterized themselves (hinting at newly identified modules) or have been described in general terms only. However, we were able to assign pathways, cellular processes or physical complexes for 273 groups (encompassing 3624 previously functionally uncharacterized proteins)
STITCH: interaction networks of chemicals and proteins
The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely dispersed across numerous databases and the literature. To facilitate access to this data, STITCH (āsearch tool for interactions of chemicalsā) integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drugātarget relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. Our database contains interaction information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de
Spectral Measures of Bipartivity in Complex Networks
We introduce a quantitative measure of network bipartivity as a proportion of
even to total number of closed walks in the network. Spectral graph theory is
used to quantify how close to bipartite a network is and the extent to which
individual nodes and edges contribute to the global network bipartivity. It is
shown that the bipartivity characterizes the network structure and can be
related to the efficiency of semantic or communication networks, trophic
interactions in food webs, construction principles in metabolic networks, or
communities in social networks.Comment: 16 pages, 1 figure, 1 tabl
Preferential attachment in the protein network evolution
The Saccharomyces cerevisiae protein-protein interaction map, as well as many
natural and man-made networks, shares the scale-free topology. The preferential
attachment model was suggested as a generic network evolution model that yields
this universal topology. However, it is not clear that the model assumptions
hold for the protein interaction network. Using a cross genome comparison we
show that (a) the older a protein, the better connected it is, and (b) The
number of interactions a protein gains during its evolution is proportional to
its connectivity. Therefore, preferential attachment governs the protein
network evolution. The evolutionary mechanism leading to such preference and
some implications are discussed.Comment: Minor changes per referees requests; to appear in PR
Distance, dissimilarity index, and network community structure
We address the question of finding the community structure of a complex
network. In an earlier effort [H. Zhou, {\em Phys. Rev. E} (2003)], the concept
of network random walking is introduced and a distance measure defined. Here we
calculate, based on this distance measure, the dissimilarity index between
nearest-neighboring vertices of a network and design an algorithm to partition
these vertices into communities that are hierarchically organized. Each
community is characterized by an upper and a lower dissimilarity threshold. The
algorithm is applied to several artificial and real-world networks, and
excellent results are obtained. In the case of artificially generated random
modular networks, this method outperforms the algorithm based on the concept of
edge betweenness centrality. For yeast's protein-protein interaction network,
we are able to identify many clusters that have well defined biological
functions.Comment: 10 pages, 7 figures, REVTeX4 forma
eggNOG: automated construction and annotation of orthologous groups of genes
The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes. Here we present the eggNOG database ('evolutionary genealogy of genes: Non-supervised Orthologous Groups'), which contains orthologous groups constructed from Smith-Waterman alignments through identification of reciprocal best matches and triangular linkage clustering. Applying this procedure to 312 bacterial, 26 archaeal and 35 eukaryotic genomes yielded 43 582 course-grained orthologous groups of which 9724 are extended versions of those from the original COG/KOG database. We also constructed more fine-grained groups for selected subsets of organisms, such as the 19 914 mammalian orthologous groups. We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them. Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.d
Sampling properties of random graphs: the degree distribution
We discuss two sampling schemes for selecting random subnets from a network:
Random sampling and connectivity dependent sampling, and investigate how the
degree distribution of a node in the network is affected by the two types of
sampling. Here we derive a necessary and sufficient condition that guarantees
that the degree distribution of the subnet and the true network belong to the
same family of probability distributions. For completely random sampling of
nodes we find that this condition is fulfilled by classical random graphs; for
the vast majority of networks this condition will, however, not be met. We
furthermore discuss the case where the probability of sampling a node depends
on the degree of a node and we find that even classical random graphs are no
longer closed under this sampling regime. We conclude by relating the results
to real {\it E.coli} protein interaction network data.Comment: accepted for publication in Phys.Rev.
STITCH 4: integration of protein-chemical interactions with user data
STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions. Available at http://stitch.embl.de, the resulting interaction network includes 390 000 chemicals and 3.6 million proteins from 1133 organisms. Compared with the previous version, the number of high-confidence protein-chemical interactions in human has increased by 45%, to 367 000. In this version, we added features for users to upload their own data to STITCH in the form of internal identifiers, chemical structures or quantitative data. For example, a user can now upload a spreadsheet with screening hits to easily check which interactions are already known. To increase the coverage of STITCH, we expanded the text mining to include full-text articles and added a prediction method based on chemical structures. We further changed our scheme for transferring interactions between species to rely on orthology rather than protein similarity. This improves the performance within protein families, where scores are now transferred only to orthologous proteins, but not to paralogous proteins. STITCH can be accessed with a web-interface, an API and downloadable files
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