Long and short range multi-locus QTL interactions in a complex trait of yeast

We analyse interactions of Quantitative Trait Loci (QTL) in heat selected yeast by comparing them to an unselected pool of random individuals. Here we re-examine data on individual F12 progeny selected for heat tolerance, which have been genotyped at 25 locations identified by sequencing a selected pool [Parts, L., Cubillos, F. A., Warringer, J., Jain, K., Salinas, F., Bumpstead, S. J., Molin, M., Zia, A., Simpson, J. T., Quail, M. A., Moses, A., Louis, E. J., Durbin, R., and Liti, G. (2011). Genome research, 21(7), 1131-1138]. 960 individuals were genotyped at these locations and multi-locus genotype frequencies were compared to 172 sequenced individuals from the original unselected pool (a control group). Various non-random associations were found across the genome, both within chromosomes and between chromosomes. Some of the non-random associations are likely due to retention of linkage disequilibrium in the F12 population, however many, including the inter-chromosomal interactions, must be due to genetic interactions in heat tolerance. One region of particular interest involves 3 linked loci on chromosome IV where the central variant responsible for heat tolerance is antagonistic, coming from the heat sensitive parent and the flanking ones are from the more heat tolerant parent. The 3-locus haplotypes in the selected individuals represent a highly biased sample of the population haplotypes with rare double recombinants in high frequency. These were missed in the original analysis and would never be seen without the multigenerational approach. We show that a statistical analysis of entropy and information gain in genotypes of a selected population can reveal further interactions than previously seen. Importantly this must be done in comparison to the unselected population's genotypes to account for inherent biases in the original population

Discrimination of Individual Tigers (\u3cem\u3ePanthera tigris\u3c/em\u3e) from Long Distance Roars

This paper investigates the extent of tiger (Panthera tigris) vocal individuality through both qualitative and quantitative approaches using long distance roars from six individual tigers at Omaha\u27s Henry Doorly Zoo in Omaha, NE. The framework for comparison across individuals includes statistical and discriminant function analysis across whole vocalization measures and statistical pattern classification using a hidden Markov model (HMM) with frame-based spectral features comprised of Greenwood frequency cepstral coefficients. Individual discrimination accuracy is evaluated as a function of spectral model complexity, represented by the number of mixtures in the underlying Gaussian mixture model (GMM), and temporal model complexity, represented by the number of sequential states in the HMM. Results indicate that the temporal pattern of the vocalization is the most significant factor in accurate discrimination. Overall baseline discrimination accuracy for this data set is about 70% using high level features without complex spectral or temporal models. Accuracy increases to about 80% when more complex spectral models (multiple mixture GMMs) are incorporated, and increases to a final accuracy of 90% when more detailed temporal models (10-state HMMs) are used. Classification accuracy is stable across a relatively wide range of configurations in terms of spectral and temporal model resolution

Input-output curves of low and high spontaneous rate auditory nerve fibers are exponential near threshold

Input-output (IO) properties of cochlear transduction are frequently determined by analyzing the average discharge rates of auditory nerve fibers (ANFs) in response to relatively long tonal stimulation. The ANFs in cats have spontaneous discharge rates (SRs) that are bimodally distributed, peaking at low (<0.5 spikes/s) and high (∼60 spikes/s) rates, and rate-level characteristics differ depending upon SR. In an effort to assess the instantaneous IO properties of ANFs having different SRs, static IO-curves were constructed from period histograms based on phase-locking of spikes to the stimulus waveform. These curves provide information unavailable in conventional average rate-level curves. We find that all IO curves follow an exponential trajectory. It is argued that the exponential behavior represents the transduction in the IHC and that the difference among ANFs having different SRs is predominantly a difference in gain attributed most likely to synaptic drive

Observations of Steep Wave Statistics in Open Ocean Waters

A new wavelet analysis methodology is proposed to estimate the statistics of steep waves. The method is applied to open ocean wave height data from the Southern Ocean Waves Experiment (1992) and from a field experiment conducted at Duck, North Carolina (1997). Results show that high wave slope crests appear over a wide range of wavenumbers, with a large amount being much shorter than the dominant wave. At low wave slope thresholds, all wave fields have roughly the same amount of wave crests regardless of wind forcing. The steep wave statistic decays exponentially with the square of the wave slope threshold, with a decay rate that is larger for the low wind cases than the high wind cases. Comparison of the steep wave statistic with independent measurements of the breaking wave statistic suggests a breaking wave slope threshold of about 0.12. The steep wave statistic does not scale with the cube of the wind speed, suggesting that other factors besides the wind speed also affect its level. Comparison of the steep wave statistic to the saturation spectrum reveals a reasonable correlation at moderate wave slope thresholds

Numerical Simulations and Observations of Surface Wave Fields under an Extreme Tropical Cyclone

The performance of the wave model WAVEWATCH III under a very strong, category 5, tropical cyclone wind forcing is investigated with different drag coefficient parameterizations and ocean current inputs. The model results are compared with field observations of the surface wave spectra from an airborne scanning radar altimeter, National Data Buoy Center (NDBC) time series, and satellite altimeter measurements in Hurricane Ivan (2004). The results suggest that the model with the original drag coefficient parameterization tends to overestimate the significant wave height and the dominant wavelength and produces a wave spectrum with narrower directional spreading. When an improved drag parameterization is introduced and the wave–current interaction is included, the model yields an improved forecast of significant wave height, but underestimates the dominant wavelength. When the hurricane moves over a preexisting mesoscale ocean feature, such as the Loop Current in the Gulf of Mexico or a warm- and cold-core ring, the current associated with the feature can accelerate or decelerate the wave propagation and significantly modulate the wave spectrum

The very large G-protein coupled receptor VLGR1: a component of the ankle link complex required for the normal development of auditory hair bundles

Sensory hair bundles in the inner ear are composed of stereocilia that can be interconnected by a variety of different link types, including tip links, horizontal top connectors, shaft connectors, and ankle links. The ankle link antigen is an epitope specifically associated with ankle links and the calycal processes of photoreceptors in chicks. Mass spectrometry and immunoblotting were used to identify this antigen as the avian ortholog of the very large G-protein-coupled receptor VLGR1, the product of the Usher syndrome USH2C (Mass1) locus. Like ankle links, Vlgr1 is expressed transiently around the base of developing hair bundles in mice. Ankle links fail to form in the cochleae of mice carrying a targeted mutation in Vlgr1 (Vlgr1/del7TM), and the bundles become disorganized just after birth. FM1-43 [N-(3-triethylammonium)propyl)-4-(4-(dibutylamino)styryl) pyridinium dibromide] dye loading and whole-cell recordings indicate mechanotransduction is impaired in cochlear, but not vestibular, hair cells of early postnatal Vlgr1/del7TM mutant mice. Auditory brainstem recordings and distortion product measurements indicate that these mice are severely deaf by the third week of life. Hair cells from the basal half of the cochlea are lost in 2-month-old Vlgr1/del7TM mice, and retinal function is mildly abnormal in aged mutants. Our results indicate that Vlgr1 is required for formation of the ankle link complex and the normal development of cochlear hair bundles

Acoustic Characteristics of Lekking Male Greater Prairie-Chicken (\u3ci\u3eTympanuchus cupido pinnatus\u3c/i\u3e) Vocalizations (Supplement)

Boom Cackle Whine Whoo

The CBLAST-Hurricane program and the next-generation fully coupled atmosphere–wave–ocean models for hurricane research and prediction

Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 88 (2007): 311-317, doi:10.1175/bams-88-3-311.The record-setting 2005 hurricane season has highlighted the urgent need for a better understanding of the factors that contribute to hurricane intensity, and for the development of corresponding advanced hurricane prediction models to improve intensity forecasts. The lack of skill in present forecasts of hurricane intensity may be attributed, in part, to deficiencies in the current prediction models—insufficient grid resolution, inadequate surface and boundary-layer formulations, and the lack of full coupling to a dynamic ocean. The extreme high winds, intense rainfall, large ocean waves, and copious sea spray in hurricanes push the surface-exchange parameters for temperature, water vapor, and momentum into untested regimes. The Coupled Boundary Layer Air–Sea Transfer (CBLAST)-Hurricane program is aimed at developing improved parameterizations using observations from the CBLAST-Hurricane field program that will be suitable for the next generation of hurricane-prediction models. The most innovative aspect of the CBLAST-Hurricane modeling effort is the development and testing of a fully coupled atmosphere–wave–ocean modeling system that is capable of resolving the eye and eyewall at ~1-km grid resolution, which is consistent with a key recommendation for the next-generation hurricane-prediction models by the NOAA Science Advisor Board Hurricane Intensity Research Working Group. It is also the National Centers for Environmental Prediction (NCEP) plan for the new Hurricane Weather Research and Forecasting (HWRF) model to be implemented operationally in 2007–08.The CBLAST-Hurricane is a research program supported by a departmental research initiative at the Office of Naval Research (ONR). The research is supported by ONR Research Grants N00014-01-1-0156, N00014-04-1-0109, N00014-01-F-0052, and SBIR for the EM-APEX development and deployment

Kaneohe Bay Sewage Diversion Experiment: Perspectives on Ecosystem Responses to Nutritional Perturbation

Kaneohe Bay, Hawaii, received increasing amounts of sewage from the 1950s through 1977. Most sewage was diverted from the bay in 1977 and early 1978. This investigation, begun in January 1976 and continued through August 1979, described the bay over that period, with particular reference to the responses of the ecosystem to sewage diversion. The sewage was a nutritional subsidy. All of the inorganic nitrogen and most of the inorganic phosphorus introduced into the ecosystem were taken up biologically before being advected from the bay. The major uptake was by phytoplankton, and the internal water-column cycle between dissolved nutrients, phytoplankton, zooplankton, microheterotrophs, and detritus supported a rate of productivity far exceeding the rate of nutrient loading. These water-column particles were partly washed out of the ecosystem and partly sedimented and became available to the benthos. The primary benthic response to nutrient loading was a large buildup of detritivorous heterotrophic biomass. Cycling of nutrients among heterotrophs, autotrophs, detritus, and inorganic nutrients was important. With sewage diversion, the biomass of both plankton and benthos decreased rapidly. Benthic biological composition has not yet returned to presewage conditions, partly because some key organisms are long-lived and partly because the bay substratum has been perturbed by both the sewage and other human influences