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)

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

Analisis Musik Dendo Dayak Kanayatn di Kecamatan Mandor Kabupaten Landak

The purpose of this research is to analysis of composition of Gadobong was patterns, Agukng and Tawak-tawak as well as an analysis of Dau melody in Dendo music of Kanayatn tribe Mandor Subdistrict Landak District of West Kalimantan. Data were analyzed qualitatively. Dendo music is a music that be functioning as a companion in a traditional rituals for healing the sick (Babore) and Nyaru\u27 Sumangat. Wasp on Dendo music composition includes three instruments are Gadobong instrument amounted to one player, Agukng and Tawak-tawak amounted to one player, and Dau amounted two player. Dendo musical composition analysis includes the element of music, the rhythm patterns, melody, tone, time signatures, notation, and tempo. This Dendo music can be used as a lesson plan in teaching and learning activities and teaching theory and also the practical work in Culture and Skill Art (Seni Budaya dan Keterampilan) lesson

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

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 (‘search tool for interactions of chemicals’) integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug–target 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

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

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.