Working Together: Using protein networks of bacterial species to compare essentiality, centrality, and conservation in Escherichia coli.

Proteins in Escherichia coli were compared in terms of essentiality, centrality, and conservation. The hypotheses of this study are: for proteins in Escherichia coli, (1) there is a positive, measureable correlation between protein conservation and essentiality, (2) there is a positive relationship between conservation and degree centrality, and (3) essentiality and centrality also have a positive correlation. The third hypothesis was supported by a moderate correlation, the first with a weak correlation, and the second hypotheis was not supported. When proteins that did not map to orthologous groups and proteins that had no interactions were removed, the relationship between essentality and conservation increased to a strong relationship. This was due to the effect of proteins that did not map to orthologus groups and suggests that protein orthology represented by clusters of orthologus groups does not accurately dipict protein conservation among the species studied

Cataloging University Research Resources to Create DMPTool Templates and a LibGuide Research Portal

Objective Research data management plans require information about the resources used to create, store, and analyze the data. A table of resources in and outside the university was compiled for use when writing DMPTool templates for grants. The table was also used to create a LibGuide to help researchers learn about all the available resources. Methods Initially, resources directly related to data management such as storage availability, sharing options, and database programs available at the university were investigated to find boilerplate language to use in DMPTool data management plan templates. As the data librarian worked on more plans for grant applications, it became apparent that information about research resources related to the creation of data, and resources outside of the university would help provide more comprehensive data management plans, so further resources were investigated. Interviews with researchers had highlighted the lack of a centralized research resource catalogue at the university, so the information collected in spreadsheets by a graduate assistant was used to create a research portal LibGuide for all the documented resources. Plans are also underway to collaborate with the Coordinator for Research Development Services to create a boilerplate library for grants citing university resources

Protein Complexes in Bacteria

Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometrycharacterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies

Bacterial protein meta-interactomes predict cross-species interactions and protein function

Background Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactome studies while several more have had substantial segments of their proteomes screened for interactions. The protein interactomes of several bacterial species have been completed, including several from prominent human pathogens. The availability of interactome data has brought challenges, as these large data sets are difficult to compare across species, limiting their usefulness for broad studies of microbial genetics and evolution. Results In this study, we use more than 52,000 unique protein-protein interactions (PPIs) across 349 different bacterial species and strains to determine their conservation across data sets and taxonomic groups. When proteins are collapsed into orthologous groups (OGs) the resulting meta-interactome still includes more than 43,000 interactions, about 14,000 of which involve proteins of unknown function. While conserved interactions provide support for protein function in their respective species data, we found only 429 PPIs (~1% of the available data) conserved in two or more species, rendering any cross-species interactome comparison immediately useful. The meta-interactome serves as a model for predicting interactions, protein functions, and even full interactome sizes for species with limited to no experimentally observed PPI, including Bacillus subtilis and Salmonella enterica which are predicted to have up to 18,000 and 31,000 PPIs, respectively. Conclusions In the course of this work, we have assembled cross-species interactome comparisons that will allow interactomics researchers to anticipate the structures of yet-unexplored microbial interactomes and to focus on well-conserved yet uncharacterized interactors for further study. Such conserved interactions should provide evidence for important but yet-uncharacterized aspects of bacterial physiology and may provide targets for anti-microbial therapies

Pembagian Harta Warisan dalam Masyarakat Minangkabau di Kecamatan Medan Area Kelurahan Tegal Sari III Kota Medan

The change in the inheritance law of Minangkabau was identified by the agreement among ninik mamak (clan heads), cerdik pandai (the intellectuals), and generasi muda (the youth) in Bukittinggi in 1952. The agreement was strengthened by the seminar on the Minangkabau Customary Law in Padang in 1968. One of the clause was that joint property inherited by heirs had to comply with Faraid (religious obligation). The out-migrated Minangkabau community creates acculturation which influences their way of perception and thinking. Based on this background, the researcher studied the distribution of inheritance among the out-migrated Minangkabau community The Distribution of inheritance in the Minangkabau community at Kelurahan Tegal Sari III, Medan Area Subdistrict, Medan, is based on the Islamic Law. The factors of compliance and piety will cause customary law to be avoided. The change in heritance law can also accurs because of the factors of necessities of life

Applications to Aging Networks

This chapter introduces network concepts, and focuses on the application of the material in the previous chapter to the study of systems biology of aging. In particular, the study of aging networks in two sample species: Caenorhabditis elegans and Saccharomyces cerevisiae are used as an example of the method

Protein complexes are enriched for highly conserved components.

<p>Each point indicates a single genome and the average conservation of its loci or orthologous groups (OGs) as measured by its presence across 898 bacterial genomes. Representative genomes of the 8 species focused on in this study are indicated with vertical lines and the following labels: <i>M</i>. <i>g</i>., <i>Mycoplasma genitalium</i>; <i>M</i>. <i>p</i>., <i>Mycoplasma pneumoniae; H</i>. <i>p</i>., <i>Helicobacter pylori; S</i>. <i>s</i>., <i>Streptococcus sanguinis; C</i>. <i>c</i>., <i>Caulobacter crescentus; B</i>. <i>s</i>., <i>Bacillus subtilis; E</i>. <i>c</i>., <i>E</i>. <i>coli; P</i>. <i>a</i>., <i>Pseudomonas aeruginosa</i>. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004107#sec011" target="_blank">Materials and Methods</a> for specific genome identities. Average gene conservation is specified as a percentage. Average gene conservation values are reduced by the fraction of their predicted protein-coding genes not present in eggNOG v.3 to account for genes without predicted orthology. To produce OG conservation instead of locus conservation, all but one locus of a set of potential paralogs (in this case, genes sharing the same OG) was removed prior to calculating averages. A logarithmic regression is fitted to both sets of values. Average OG conservation values are also shown for subsets of protein-coding genes present within protein complexes from <i>E</i>. <i>coli</i> [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004107#pcbi.1004107.ref005" target="_blank">5</a>] and <i>M</i>. <i>pneumoniae</i> [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004107#pcbi.1004107.ref006" target="_blank">6</a>]. For these two species, values are representative of members in full complexomes while those for other species are predicted complexomes using each of the three data sets as models.</p

Examples of protein complex conservation across bacteria.

<p>Complexes are identified using a common name and an EcoCyc ID. Each complex subunit has been assigned a COG ID. Grey areas indicate OG presence, white areas indicate OG absence, and blue areas indicate essentiality in a species-specific screen (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004107#sec011" target="_blank">Materials and Methods</a> for references). Values within these spaces indicate the presence of potential paralogs in the corresponding species; proteins without specified values have no paralogs. Complex structures are available in PDB: ATP synthase F1, 3OAA; succinate dehydrogenase, 1NEN; Outer membrane protein assembly complex, (2KM7, 3TGO, 3TGO, 4K3C, 2YH3). Species are arranged by their taxonomy (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004107#sec011" target="_blank">Materials and Methods</a> for details) with <i>E</i>. <i>coli</i> and <i>Mycoplasma</i> serving as the most distant species.</p

Protein complexes are rich in highly-conserved proteins of unknown function.

<p><b>(A)</b> The list of EcoCyc <i>E</i>. <i>coli</i> protein complexes was compared on the basis of component presence vs. absence across seven other species in this study. Conserved complexes, in this figure, are those in which at least one orthologous component is present in the target species. Similarly, essential complexes include at least one component found to be essential in both <i>E</i>. <i>coli</i> and in the target species. <b>(B)</b> As in (A), but within the subset of EcoCyc complexes containing at least one protein of unknown or unclear function. In these instances, the complex itself may have a known function though the roles of its components may remain unclear. <b>(C)</b> Examples of experimentally-observed protein complexes containing proteins of unknown function. <i>E</i>. <i>coli</i> complex examples from Hu et al. are shown at left, <i>M</i>. <i>pneumoniae</i> complexes from Kühner et al. are shown at right. Complexes are labeled with the identifier used in their corresponding study.</p