Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

BACKGROUND: Biological processes are carried out by coordinated modules of interacting molecules. As clustering methods demonstrate that genes with similar expression display increased likelihood of being associated with a common functional module, networks of coexpressed genes provide one framework for assigning gene function. This has informed the guilt-by-association (GBA) heuristic, widely invoked in functional genomics. Yet although the idea of GBA is accepted, the breadth of GBA applicability is uncertain. RESULTS: We developed methods to systematically explore the breadth of GBA across a large and varied corpus of expression data to answer the following question: To what extent is the GBA heuristic broadly applicable to the transcriptome and conversely how broadly is GBA captured by a priori knowledge represented in the Gene Ontology (GO)? Our study provides an investigation of the functional organization of five coexpression networks using data from three mammalian organisms. Our method calculates a probabilistic score between each gene and each Gene Ontology category that reflects coexpression enrichment of a GO module. For each GO category we use Receiver Operating Curves to assess whether these probabilistic scores reflect GBA. This methodology applied to five different coexpression networks demonstrates that the signature of guilt-by-association is ubiquitous and reproducible and that the GBA heuristic is broadly applicable across the population of nine hundred Gene Ontology categories. We also demonstrate the existence of highly reproducible patterns of coexpression between some pairs of GO categories. CONCLUSION: We conclude that GBA has universal value and that transcriptional control may be more modular than previously realized. Our analyses also suggest that methodologies combining coexpression measurements across multiple genes in a biologically-defined module can aid in characterizing gene function or in characterizing whether pairs of functions operate together

Double layering of a thermochemical plume in the upper mantle beneath Hawaii

According to classical plume theory, purely thermal upwellings rise through the mantle, pond in a thin layer beneath the lithosphere, and generate hotspot volcanism. Neglected by this theory, however, are the dynamical effects of compositional heterogeneity carried by mantle plumes even though this heterogeneity has been commonly identified in sources of hotspot magmas. Numerical models predict that a hot, compositionally heterogeneous mantle plume containing a denser eclogite component tends to pool at ∼300–410 km depth before rising to feed a shallower sublithospheric layer. This double-layered structure of a thermochemical plume is more consistent with seismic tomographic images at Hawaii than the classical plume model. The thermochemical structure as well as time dependence of plume material rising from the deeper into the shallower layer can further account for long-term fluctuations in volcanic activity and asymmetry in bathymetry, seismic structure, and magma chemistry across the hotspot track, as are observed

Seismic anisotropy and shear wave splitting associated with mantle plume-plate interaction

Geodynamic simulations of the development of lattice preferred orientation in the flowing mantle are used to characterize the seismic anisotropy and shear wave splitting (SWS) patterns expected for the interaction of mantle plumes and lithospheric plates. Models predict that in the deeper part of the plume layer ponding beneath the plate, olivine a axes tend to align perpendicular to the radially directed plume flow, forming a circular pattern reflecting circumferential stretching. In the shallower part of the plume layer, plate shear is more important and the a axes tend toward the direction of plate motion. Predicted SWS over intraplate plumes reflects the asymmetric influence of plate shear with fast S wave polarization directions forming a pattern of nested U shapes that open in the direction opposing both plate motion and the parabolic shape often used to describe the flow lines of the plume. Predictions explain SWS observations around the Eifel hot spot with an eastward, not westward, moving Eurasian plate, consistent with global studies that require relatively slow net (westward) rotation of all of the plates. SWS at the Hawaiian hot spot can be explained by the effects of plume-plate interaction, combined with fossil anisotropy in the Pacific lithosphere. In ridge-centered plume models, the fast polarization directions angle diagonally toward the ridge axis when the plume is simulated as having low viscosity beneath the thermal lithosphere. Such a model better explains SWS observations in northeast Iceland than a model that incorporates a high-viscosity layer due to dehydration of the shallow-most upper mantle

Shear wave splitting at the Hawaiian hot spot from the PLUME land and ocean bottom seismometer deployments

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 13 (2012): Q02007, doi:10.1029/2011GC003881.We examine upper mantle anisotropy across the Hawaiian Swell by analyzing shear wave splitting of teleseismic SKS waves recorded by the PLUME broadband land and ocean bottom seismometer deployments. Mantle anisotropy beneath the oceans is often attributed to flow-induced lattice-preferred orientation of olivine. Splitting observations may reflect a combination of both fossil lithospheric anisotropy and anisotropy due to present-day asthenospheric flow, and here we address the question whether splitting provides diagnostic information on possible asthenospheric plume flow at Hawaii. We find that the splitting fast directions are coherent and predominantly parallel to the fossil spreading direction, suggesting that shear wave splitting dominantly reflects fossil lithospheric anisotropy. The signature of anisotropy from asthenospheric flow is more subtle, although it could add some perturbation to lithospheric splitting. The measured delay times are typically 1 s or less, although a few stations display larger splitting delays of 1–2 s. The variability in the delay times across the different stations indicates differences in the degree of anisotropy or in the thickness of the anisotropic layer or in the effect of multilayer anisotropy. Regions with smaller splitting times may have experienced processes that modified the lithosphere and partially erased the fossil anisotropy; alternatively, asthenospheric splitting may either constructively add to or destructively subtract from lithospheric splitting to produce the observed variability in delay times.The PLUME project was supported by NSF.2012-08-1

Asymmetric shallow mantle structure beneath the Hawaiian Swell—evidence from Rayleigh waves recorded by the PLUME network

Author Posting. © The Author(s), 2011. This article is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 187 (2011): 1725–1742, doi:10.1111/j.1365-246X.2011.05238.x.We present models of the 3-D shear velocity structure of the lithosphere and asthenosphere beneath the Hawaiian hotspot and surrounding region. The models are derived from long-period Rayleigh-wave phase velocities that were obtained from the analysis of seismic recordings collected during two year-long deployments for the Hawaiian Plume-Lithosphere Undersea Mantle Experiment. For this experiment, broad-band seismic sensors were deployed at nearly 70 seafloor sites as well as 10 sites on the Hawaiian Islands. Our seismic images result from a two-step inversion of path-averaged dispersion curves using the two-station method. The images reveal an asymmetry in shear velocity structure with respect to the island chain, most notably in the lower lithosphere at depths of 60 km and greater, and in the asthenosphere. An elongated, 100-km-wide and 300-km-long low-velocity anomaly reaches to depths of at least 140 km. At depths of 60 km and shallower, the lowest velocities are found near the northern end of the island of Hawaii. No major velocity anomalies are found to the south or southeast of Hawaii, at any depth. The low-velocity anomaly in the asthenosphere is consistent with an excess temperature of 200–250 °C and partial melt at the level of a few percent by volume, if we assume that compositional variations as a result of melt extraction play a minor role. We also image small-scale low-velocity anomalies within the lithosphere that may be associated with the volcanic fields surrounding the Hawaiian Islands.This research was financed by the National Science Foundation under grants OCE-00-02470 and OCE-00-02819. Markee was partly sponsored by a SIO graduate student fellowship

Empirical Evidence for the Effect of Airline Travel on Inter-Regional Influenza Spread in the United States

BACKGROUND: The influence of air travel on influenza spread has been the subject of numerous investigations using simulation, but very little empirical evidence has been provided. Understanding the role of airline travel in large-scale influenza spread is especially important given the mounting threat of an influenza pandemic. Several recent simulation studies have concluded that air travel restrictions may not have a significant impact on the course of a pandemic. Here, we assess, with empirical data, the role of airline volume on the yearly inter-regional spread of influenza in the United States. METHODS AND FINDINGS: We measured rate of inter-regional spread and timing of influenza in the United States for nine seasons, from 1996 to 2005 using weekly influenza and pneumonia mortality from the Centers for Disease Control and Prevention. Seasonality was characterized by band-pass filtering. We found that domestic airline travel volume in November (mostly surrounding the Thanksgiving holiday) predicts the rate of influenza spread (r (2) = 0.60; p = 0.014). We also found that international airline travel influences the timing of influenza mortality (r (2) = 0.59; p = 0.016). The flight ban in the US after the terrorist attack on September 11, 2001, and the subsequent depression of the air travel market, provided a natural experiment for the evaluation of flight restrictions; the decrease in air travel was associated with a delayed and prolonged influenza season. CONCLUSIONS: We provide the first empirical evidence for the role of airline travel in long-range dissemination of influenza. Our results suggest an important influence of international air travel on the timing of influenza introduction, as well as an influence of domestic air travel on the rate of inter-regional influenza spread in the US. Pandemic preparedness strategies should account for a possible benefit of airline travel restrictions on influenza spread

Underplating of the Hawaiian Swell : evidence from teleseismic receiver functions

Author Posting. © The Authors, 2010. This article is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 183 (2010): 313-329, doi:10.1111/j.1365-246X.2010.04720.x.The Hawaiian Islands are the canonical example of an age-progressive island chain, formed by volcanism long thought to be fed from a hotspot source that is more or less fixed in the mantle. Geophysical data, however, have so far yielded contradictory evidence on subsurface structure. The substantial bathymetric swell is supportive of an anomalously hot upper mantle, yet seafloor heat flow in the region does not appear to be enhanced. The accumulation of magma beneath pre-existing crust (magmatic underplating) has been suggested to add chemical buoyancy to the swell, but to date the presence of underplating has been constrained only by local active-source experiments. In this study, teleseismic receiver functions derived from seismic events recorded during the PLUME project were analysed to obtain a regional map of crustal structure for the Hawaiian Swell. This method yields results that compare favourably with those from previous studies, but permits a much broader view than possible with active-source seismic experiments. Our results indicate that the crustal structure of the Hawaiian Islands is quite complicated and does not conform to the standard model of sills fed from a central source. We find that a shallow P-to-s conversion, previously hypothesized to result from the volcano-sediment interface, corresponds more closely to the boundary between subaerial and subaqueous extrusive material. Correlation between uplifted bathymetry at ocean-bottom-seismometer locations and presence of underplating suggests that much of the Hawaiian Swell is underplated, whereas a lack of underplating beneath the moat surrounding the island of Hawaii suggests that underplated crust outward of the moat has been fed from below by dykes through the lithosphere rather than by sills spreading from the island centre. Local differences in underplating may reflect focusing of magma-filled dykes in response to stress from volcanic loading. Finally, widespread underplating adds chemical buoyancy to the swell, reducing the amplitude of a mantle thermal anomaly needed to match bathymetry and supporting observations of normal heat flow.We are grateful to the Ocean Sciences Division of the U.S. National Science Foundation for their support of this project under grants OCE-0002470, OCE-0002552 and OCE-0002819

Seismic evidence for a lower-mantle origin of the Iceland plume

Iceland, one of the most thoroughly investigated hotspots1,2,3, is generally accepted to be the manifestation of an upwelling mantle plume4. Yet whether the plume originates from the lower mantle or from a convective instability at a thermal boundary layer between the upper and lower mantle near 660 km depth5,6 remains unconstrained. Tomographic inversions of body-wave delay times show that low seismic velocities extend to at least 400 km depth beneath central Iceland7,8, but cannot resolve structure at greater depth. Here we report lateral variations in the depths of compressional-to-shear wave conversions at the two seismic discontinuities marking the top and bottom of the mantle transition zone beneath Iceland. We find that the transition zone is 20 km thinner than in the average Earth9 beneath central and southern Iceland, but is of normal thickness beneath surrounding areas, a result indicative of a hot and narrow plume originating from the lower mantle.This work was supported by the US NSFPeer Reviewe