K.D. Smith | USGS Science

USGS2006

Conservation of Toll-like receptor signaling pathways in teleost fish

In mammals, toll-like receptors (TLR) recognize ligands, including pathogen-associated molecular patterns (PAMPs), and respond with ligand-specific induction of genes. In this study, we establish evolutionary conservation in teleost fish of key components of the TLR-signaling pathway that act as switches for differential gene induction, including MYD88, TIRAP, TRIF, TRAF6, IRF3, and IRF7. We further explore this conservation with a molecular phylogenetic analysis of MYD88. To the extent that current genomic analysis can establish, each vertebrate has one ortholog to each of these genes. For molecular tree construction and phylogeny inference, we demonstrate a methodology for including genes with only partial primary sequences without disrupting the topology provided by the high-confidence full-length sequences. Conservation of the TLR-signaling molecules suggests that the basic program of gene regulation by the TLR-signaling pathway is conserved across vertebrates. To test this hypothesis, leukocytes from a model fish, rainbow trout ( Oncorhynchus mykiss ), were stimulated with known mammalian TLR agonists including: diacylated and triacylated forms of lipoprotein, flagellin, two forms of LPS, synthetic double-stranded RNA, and two imidazoquinoline compounds (loxoribine and R848). Trout leukocytes responded in vitro to a number of these agonists with distinct patterns of cytokine expression that correspond to mammalian responses. Our results support the key prediction from our phylogenetic analyses that strong selective pressure of pathogenic microbes has preserved both TLR recognition and signaling functions during vertebrate evolution.

Comparative Biochemistry and Physiology, Part D: G↗

USGS2004

Transtensional deformation in the Lake Tahoe region, California and Nevada, USA

Dextral transtensional deformation is occurring along the Sierra Nevada–Great Basin boundary zone (SNGBBZ) at the eastern edge of the Sierra Nevada microplate. In the Lake Tahoe region of the SNGBBZ, transtension is partitioned spatially and temporally into domains of north–south striking normal faults and transitional domains with conjugate strike-slip faults. The normal fault domains, which have had large Holocene earthquakes but account only for background seismicity in the historic period, primarily accommodate east–west extension, while the transitional domains, which have had moderate Holocene and historic earthquakes and are currently seismically active, primarily record north–south shortening. Through partitioned slip, the upper crust in this region undergoes overall constrictional strain. Major fault zones within the Lake Tahoe basin include two normal fault zones: the northwest-trending Tahoe–Sierra frontal fault zone (TSFFZ) and the north-trending West Tahoe–Dollar Point fault zone. Most faults in these zones show eastside down displacements. Both of these fault zones show evidence of Holocene earthquakes but are relatively quiet seismically through the historic record. The northeast-trending North Tahoe–Incline Village fault zone is a major normal to sinistral-oblique fault zone. This fault zone shows evidence for large Holocene earthquakes and based on the historic record is seismically active at the microearthquake level. The zone forms the boundary between the Lake Tahoe normal fault domain to the south and the Truckee transition zone to the north. Several lines of evidence, including both geology and historic seismicity, indicate that the seismically active Truckee and Gardnerville transition zones, north and southeast of Lake Tahoe basin, respectively, are undergoing north–south shortening. In addition, the central Carson Range, a major north-trending range block between two large normal fault zones, shows internal fault patterns that suggest the range is undergoing north–south shortening in addition to east–west extension. A model capable of explaining the spatial and temporal partitioning of slip suggests that seismic behavior in the region alternates between two modes, one mode characterized by an east–west minimum principal stress and a north–south maximum principal stress as at present. In this mode, seismicity and small-scale faulting reflecting north–south shortening concentrate in mechanically weak transition zones with primarily strike-slip faulting in relatively small-magnitude events, and domains with major normal faults are relatively quiet. A second mode occurs after sufficient north–south shortening reduces the north–south S hmax in magnitude until it is less than S v , at which point S v becomes the maximum principal stress. This second mode is then characterized by large earthquakes on major normal faults in the large normal fault domains, which dominate the overall moment release in the region, producing significant east–west extension.

Tectonophysics↗

USGS2003

A methodology for probabilistic fault displacement hazard analysis (PFDHA)

We present a methodology for conducting a site-specific probabilistic analysis of fault displacement hazard. Two approaches are outlined. The first relates the occurrence of fault displacement at or near the ground surface to the occurrence of earthquakes in the same manner as is done in a standard probabilistic seismic hazard analysis (PSHA) for ground shaking. The methodology for this approach is taken directly from PSHA methodology with the ground-motion attenuation function replaced by a fault displacement attenuation function. In the second approach, the rate of displacement events and the distribution for fault displacement are derived directly from the characteristics of the faults or geologic features at the site of interest. The methodology for probabilistic fault displacement hazard analysis (PFDHA) was developed for a normal faulting environment and the probability distributions we present may have general application in similar tectonic regions. In addition, the general methodology is applicable to any region and we indicate the type of data needed to apply the methodology elsewhere.

Earthquake Spectra↗