Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History

Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to inferring network evolution history from the topology of PPI networks and the duplication relationship among the paralogs. Simulations show that our approach outperforms the existing ones in terms of the accuracy of reconstruction. Moreover, the growth parameters of several real PPI networks estimated by our method are more consistent with the ones predicted in literature.Comment: 15 pages, 5 figures, submitted to ISBRA 201

Landscape context outweighs local habitat quality in its effects on herbivore dispersal and distribution

Past studies with spatially structured herbivore populations have emphasized the primacy of intrinsic factors (e.g., patch quality), patch geometry (e.g., patch size and isolation), and more recently landscape context (e.g., matrix composition) in affecting local population abundance and dispersal rate. However, few studies have examined the relative importance of each factor, or how they might interact to affect herbivore abundance or dispersal. Here, we performed a factorial field experiment to examine the independent and interactive effects of patch quality (plant biomass, leaf protein, leaf phenolics) and matrix composition [mudflat or non-host grass (Bromus inermis)] on planthopper (Prokelisia crocea) emigration from host-plant patches (prairie cordgrass, Spartina pectinata). In addition, a field survey was conducted to examine the relative importance of patch quality, geography, and matrix composition on planthopper occupancy and density. In the experiment, we found that rates of emigration from low and intermediate quality patches were, on average, 21% percent higher for patches embedded in brome than mudflat. In contrast, the emigration rate was unaffected by matrix composition in nutrient-rich patches. Within matrix types, plant quality had little effect on emigration. In the survey, planthopper density and the patch occupancy rate of planthoppers increased nonadditively with increasing patch size and the percentage of the surrounding matrix composed of mudflat. This study suggests that landscape-level factors, such as the matrix, may be more important than factors intrinsic to the patches. © 2006 Springer-Verlag

An overview of the Evaluation of Oxygen Interactions with Materials 3 experiment: Space Shuttle Mission 46, July-August 1992

The Evaluation of Oxygen Interactions with Materials 3 (EOIM-3) flight experiment was developed to obtain benchmark atomic oxygen reactivity data and was conducted during Space Transportation System Mission 46 (STS-46), July 31 to August 7, 1992. In this paper, we present an overview of EOIM-3 and the results of the Lyndon B. Johnson Space Center (JSC) materials reactivity and mass spectrometer/carousel experiments. Mass spectrometer calibration methods are discussed briefly, as a prelude to a detailed discussion of the mass spectrometric results produced during STS-46. Mass spectrometric measurements of ambient O-atom flux and fluence are in good agreement with the values calculated using the MSIS-86 model of the thermosphere as well as estimates based on the extent of O-atom reaction with Kapton polyimide. Mass spectrometric measurements of gaseous products formed by O-atom reaction with C(13) labeled Kapton revealed CO, CO2, H2O, NO, and NO2. Finally, by operating the mass spectrometer so as to detect naturally occurring ionospheric species, we characterized the ambient ionosphere at various times during EOIM-3 and detected the gaseous reaction products formed when ambient ions interacted with the C(13) Kapton carousel sector. By direct comparison of the results of on-orbit O-atom exposures with those conducted in ground-based laboratory systems, which provide known O-atom fluences and translational energies, we have demonstrated the strong translational energy dependence of O-atom reactions with a variety of polymers. A 'line-of-centers' reactive scattering model was shown to provide a reasonably accurate description of the translational energy dependence of polymer reactions with O atoms at high atom kinetic energies while a Beckerle-Ceyer model provided an accurate description of O-atom reactivity over a three order-of-magnitude range in translational energy and a four order-of-magnitude range in reaction efficiency. Postflight studies of the polymer samples by x-ray photoelectron spectroscopy and infrared spectroscopy demonstrate that O-atom attack is confined to the near-surface region of the sample, i.e. within 50 to 100 A of the surface

Evaluation of Oxygen Interactions with Materials 3: Mission and induced environments

The Evaluation of Oxygen Interactions with Materials 3 (EOIM-3) flight experiment was developed to obtain benchmark atomic oxygen/material reactivity data. The experiment was conducted during Space Shuttle mission 46 (STS-46), which flew July 31 to August 7, 1992. Quantitative interpretation of the materials reactivity measurements requires a complete and accurate definition of the space environment exposure, including the thermal history of the payload, the solar ultraviolet exposure, the atomic oxygen fluence, and any spacecraft outgassing contamination effects. The thermal history of the payload was measured using twelve thermocouple sensors placed behind selected samples and on the EOIM-3 payload structure. The solar ultraviolet exposure history of the EOIM-3 payload was determined by analysis of the as-flown orbit and vehicle attitude combined with daily average solar ultraviolet and vacuum ultraviolet (UV/VUV) fluxes. The atomic oxygen fluence was assessed in three different ways. First, the O-atom fluence was calculated using a program that incorporates the MSIS-86 atmospheric model, the as-flown Space Shuttle trajectory, and solar activity parameters. Second, the oxygen atom fluence was estimated directly from Kapton film erosion. Third, ambient oxygen atom measurements were made using the quadrupole mass spectrometer on the EOIM-3 payload. Our best estimate of the oxygen atom fluence as of this writing is 2.3 +/- 0.3 x 10(exp 20) atoms/sq cm. Finally, results of post-flight X-ray photoelectron spectroscopy (XPS) surface analyses of selected samples indicate low levels of contamination on the payload surface

The yeast open reading frame encoding a dual specificity phosphatase

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31016/1/0000691.pd

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

The idea of 'date' and 'party' hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. Thus, we suggest that a date/party dichotomy is not meaningful and it might be more useful to conceive of roles for protein-protein interactions rather than individual proteins. We find significant correlations between interaction centrality and the functional similarity of the interacting proteins.Comment: 27 pages, 5 main figures, 4 supplementary figure

Bridging topological and functional information in protein interaction networks by short loops profiling

Protein-protein interaction networks (PPINs) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. In this study we identify fundamental principles of PPIN topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. We compared 30 PPINs with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-validated high-confidence dataset of 622 human protein complexes. We demonstrate that loops are an intrinsic feature of PPINs and that specific cell functions are predominantly performed by loops of different lengths. Topologically, we find that loops are strongly related to the accuracy of PPINs and define a core of interactions with high resilience. The identification of this core and the analysis of loop composition are promising tools to assess PPIN quality and to uncover possible biases from experimental detection methods. More than 96% of loops share at least one biological function, with enrichment of cellular functions related to mRNA metabolic processing and the cell cycle. Our analyses suggest that these motifs can be used in the design of targeted experiments for functional phenotype detection.This research was supported by the Biotechnology and Biological Sciences Research Council (BB/H018409/1 to AP, ACCC and FF, and BB/J016284/1 to NSBT) and by the Leukaemia & Lymphoma Research (to NSBT and FF). SSC is funded by a Leukaemia & Lymphoma Research Gordon Piller PhD Studentship

Network Archaeology: Uncovering Ancient Networks from Present-day Interactions

Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been limited by the unavailability of past versions of networks. To overcome these limitations, we propose several algorithms for reconstructing a network's history of growth given only the network as it exists today and a generative model by which the network is believed to have evolved. Our likelihood-based method finds a probable previous state of the network by reversing the forward growth model. This approach retains node identities so that the history of individual nodes can be tracked. We apply these algorithms to uncover older, non-extant biological and social networks believed to have grown via several models, including duplication-mutation with complementarity, forest fire, and preferential attachment. Through experiments on both synthetic and real-world data, we find that our algorithms can estimate node arrival times, identify anchor nodes from which new nodes copy links, and can reveal significant features of networks that have long since disappeared.Comment: 16 pages, 10 figure

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

8 páginas, 3 figuras, 1 tabla.-- This is an open-access article distributed under the terms of the Creative Commons Attribution License.This work has been supported by funds provided by the Local Government Junta de Castilla y León (JCyL, ref. project: CSI07A09), by the Spanish Ministry of Science and Innovation (MICINN - ISCiii, ref. projects: PI061153 and PS09/00843) and by the European Commission Research Grant PSIMEx (ref. FP7-HEALTH-2007-223411).Peer Reviewe