European sea bass (Dicentrarchus labrax) skin and scale transcriptomes

Fish skin and their appendages, the mineralized scales, are important organs for protection and homeostasis, but little is known about their specific transcript or protein repertoire. This study used RNA-seq to generate transcriptome data for skin and scales in the European sea bass (Dicentrarchus labrax), an important species for fisheries and aquaculture. RNA was extracted from the pectoral skin and from scales collected above the midline of immature one-year old sea bass. More than 20 x 10(6) reads were obtained for each tissue, using RNA-seq Illumina technology. De novo assembly resulted in 31,842 transcripts (of 500 base pairs or greater) for skin and 20,423 transcripts for scale. This dataset provides a useful resource for both aquaculture and fish conservation studies and for research into the physiology and molecular biology of fish skin and scales. (C) 2017 Elsevier B.V. All rights reserved.Foundation for Science and Technology of Portugal (FCT) [PTDC/AAG-GLO/4003/2012, CCMAR/Multi/04326/2013, SFRH/BPD/84033/2012

Viterbi sparse spike detection

pre-printAccurate interpretation of seismic traveltimes and amplitudes in the exploration and global scales is complicated by the band-limited nature of seismic data. We discovered a stochastic method to reduce a seismic waveform into a most probable constituent spike train. Model waveforms were constructed from a set of candidate spike trains convolved with a source wavelet estimate. For each model waveform, a profile hidden Markov model (HMM) was constructed to represent the waveform as a stochastic generative model with a linear topology corresponding to a sequence of samples. Each match state in the HMM represented a sample in the model waveform, in which the amplitude was represented by a Gaussian distribution. Insert and delete states allowed the underlying source wavelet to dilate or contract, accounting for nonstationarity in the seismic data and errors in the source wavelet estimate. The Gaussian distribution characterizing each sample's amplitude accounted for random noise. The Viterbi algorithm was employed to simultaneously find the optimal nonlinear alignment between a model waveform and the seismic data and to assign a score to each candidate spike train. The most probable traveltimes and amplitudes were inferred from the alignments of the highest scoring models. The method required no implicit assumptions regarding the distribution of traveltimes and amplitudes; however, in practice, the solution set may be limited to mitigate the nonuniqueness of solutions and to reduce the computational effort. Our analyses found that the method can resolve closely spaced arrivals below traditional resolution limits and that traveltime estimates are robust in the presence of random noise and source wavelet errors. The method was particularly well suited to fine-scale interpretation problems such as thin bed interpretation, tying seismic images to well logs, and the analysis of anomalous waveforms in global seismology

Valuing the risk associated with willow and miscanthus relative to conventional agricultural systems

The agronomic characteristics of willow and miscanthus make these crops highly susceptible to risk. This is particularly true in a country such as Ireland which has limited experience in the production of these crops. Issues such as soil and climate suitability have as yet to be resolved. The lengthy production lifespan of energy crops only serve to heighten the level of risk that affects key variables. The uncertainty surrounding the risk variables involved in producing willow and miscanthus, such as the annual yield level and the energy price, make it difficult to accurately calculate the returns of such a project. The returns from willow and miscanthus are compared with those of conventional agricultural enterprises using Stochastic Efficiency with Respect to a Function (SERF). A risk premium is calculated which farmers would need to be compensated with in order for them to be indifferent between their current enterprise and switching to biomass crop production. With the exception of spring barley, a risk premium is required if farmers are to be indifferent between their current enterprise and willow or miscanthus. The value of the risk premium required to entice farmers to switch to miscanthus production is significantly less than that required for willow. This suggests that a greater level of risk is associated with willow than with miscanthus.Biomass, SERF, Risk Premium, Resource /Energy Economics and Policy, Risk and Uncertainty,

Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish

Abstract Background Calcium ion is tightly regulated in body fluids and for euryhaline fish, which are exposed to rapid changes in environmental [Ca2+], homeostasis is especially challenging. The gill is the main organ of active calcium uptake and therefore plays a crucial role in the maintenance of calcium ion homeostasis. To study the molecular basis of the short-term responses to changing calcium availability, the whole gill transcriptome obtained by Super Serial Analysis of Gene Expression (SuperSAGE) of the euryhaline teleost green spotted puffer fish, Tetraodon nigroviridis, exposed to water with altered [Ca2+] was analysed. Results Transfer of T. nigroviridis from 10 ppt water salinity containing 2.9 mM Ca2+ to high (10 mM Ca2+ ) and low (0.01 mM Ca2+) calcium water of similar salinity for 2-12 h resulted in 1,339 differentially expressed SuperSAGE tags (26-bp transcript identifiers) in gills. Of these 869 tags (65%) were mapped to T. nigroviridis cDNAs or genomic DNA and 497 (57%) were assigned to known proteins. Thirteen percent of the genes matched multiple tags indicating alternative RNA transcripts. The main enriched gene ontology groups belong to Ca2+ signaling/homeostasis but also muscle contraction, cytoskeleton, energy production/homeostasis and tissue remodeling. K-means clustering identified co-expressed transcripts with distinct patterns in response to water [Ca2+] and exposure time. Conclusions The generated transcript expression patterns provide a framework of novel water calcium-responsive genes in the gill during the initial response after transfer to different [Ca2+]. This molecular response entails initial perception of alterations, activation of signaling networks and effectors and suggests active remodeling of cytoskeletal proteins during the initial acclimation process. Genes related to energy production and energy homeostasis are also up-regulated, probably reflecting the increased energetic needs of the acclimation response. This study is the first genome-wide transcriptome analysis of fish gills and is an important resource for future research on the short-term mechanisms involved in the gill acclimation responses to environmental Ca2+ changes and osmoregulation.Peer Reviewe

Estimate of the Rigidity of Eclogite in the Lower Mantle From Waveform Modeling of Broadband S‐to‐P Wave Conversions

Broadband USArray recordings of the 21 July 2007 western Brazil earthquake (Mw=6.0; depth = 633 km) include high‐amplitude signals about 40 s, 75 s, and 100 s after the P wave arrival. They are consistent with S wave to P wave conversions in the mantle beneath northwestern South America. The signal at 100 s, denoted as S1750P, has the highest amplitude and is formed at 1,750 km depth based on slant‐stacking and semblance analysis. Waveform modeling using axisymmetric, finite difference synthetics indicates that S1750P is generated by a 10 km thick heterogeneity, presumably a fragment of subducted mid‐ocean ridge basalt in the lower mantle. The negative polarity of S1750P is a robust observation and constrains the shear velocity anomaly δVS of the heterogeneity to be negative. The amplitude of S1750P indicates that δVS is in the range from −1.6% to −12.4%. The large uncertainty in δVS is due to the large variability in the recorded S1750P amplitude and simplifications in the modeling of S1750P waveforms. The lower end of our estimate for δVS is consistent with ab initio calculations by Tsuchiya (2011), who estimated that δVS of eclogite at lower mantle pressure is between 0 and −2% due to shear softening from the poststishovite phase transition.Key PointsBroadband recordings of S‐P conversions allow for constraining compositional properties of deep Earth materialsStishovite is present in subducted eclogite and contributes to shear velocity softeningFragments of subducted oceanic crust are entrained in mantle flow and can be preserved at depths approaching 2,000 kmPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141104/1/grl56669_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141104/2/grl56642-sup-0002-supplementary.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141104/3/grl56642-sup-0001-supplementary.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141104/4/grl56669.pd

Minimum Length from Quantum Mechanics and Classical General Relativity

We derive fundamental limits on measurements of position, arising from quantum mechanics and classical general relativity. First, we show that any primitive probe or target used in an experiment must be larger than the Planck length, $l_P$. This suggests a Planck-size {\it minimum ball} of uncertainty in any measurement. Next, we study interferometers (such as LIGO) whose precision is much finer than the size of any individual components and hence are not obviously limited by the minimum ball. Nevertheless, we deduce a fundamental limit on their accuracy of order $l_P$. Our results imply a {\it device independent} limit on possible position measurements.Comment: 8 pages, latex, to appear in the Physical Review Letter

Thermal reaction norms and the scale of temperature variation: latitudinal vulnerability of intertidal Nacellid limpets to climate change

The thermal reaction norms of 4 closely related intertidal Nacellid limpets, Antarctic (Nacella concinna), New Zealand (Cellana ornata), Australia (C. tramoserica) and Singapore (C. radiata), were compared across environments with different temperature magnitude, variability and predictability, to test their relative vulnerability to different scales of climate warming. Lethal limits were measured alongside a newly developed metric of “duration tenacity”, which was tested at different temperatures to calculate the thermal reaction norm of limpet adductor muscle fatigue. Except in C. tramoserica which had a wide optimum range with two break points, duration tenacity did not follow a typical aerobic capacity curve but was best described by a single break point at an optimum temperature. Thermal reaction norms were shifted to warmer temperatures in warmer environments; the optimum temperature for tenacity (Topt) increased from 1.0°C (N. concinna) to 14.3°C (C. ornata) to 18.0°C (an average for the optimum range of C. tramoserica) to 27.6°C (C. radiata). The temperature limits for duration tenacity of the 4 species were most consistently correlated with both maximum sea surface temperature and summer maximum in situ habitat logger temperature. Tropical C. radiata, which lives in the least variable and most predictable environment, generally had the lowest warming tolerance and thermal safety margin (WT and TSM; respectively the thermal buffer of CTmax and Topt over habitat temperature). However, the two temperate species, C. ornata and C. tramoserica, which live in a variable and seasonally unpredictable microhabitat, had the lowest TSM relative to in situ logger temperature. N. concinna which lives in the most variable, but seasonally predictable microhabitat, generally had the highest TSMs. Intertidal animals live at the highly variable interface between terrestrial and marine biomes and even small changes in the magnitude and predictability of their environment could markedly influence their future distributions

Molecular analysis of the cold tolerant Antarctic nematode, Panagrolaimus davidi

Isolated and established in culture from the Antarctic in 1988, the nematode Panagrolaimus davidi has proven to be an ideal model for the study of adaptation to the cold. Not only is it the best-documented example of an organism surviving intracellular freezing but it is also able to undergo cryoprotective dehydration. As part of an ongoing effort to develop a molecular understanding of this remarkable organism, we have assembled both a transcriptome and a set of genomic scaffolds. We provide an overview of the transcriptome and a survey of genes involved in temperature stress. We also explore, in silico, the possibility that P. davidi will be susceptible to an environmental RNAi response, important for further functional studies

Wormholes, time machines, and the weak energy condition

It is argued that, if the laws of physics permit an advanced civilization to create and maintain a wormhole in space for interstellar travel, then that wormhole can be converted into a time machine with which causality might be violatable. Whether wormholes can be created and maintained entails deep, ill-understood issues about cosmic censorship, quantum gravity, and quantum field theory, including the question of whether field theory enforces an averaged version of the weak energy condition