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

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

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

Limpet feeding rate and the consistency of physiological response to temperature

Thermal reaction norms are fundamental relationships for geographic comparisons of organism response to temperature. They are shaped by an organism’s environmental history and provide insights into both the global patterns of thermal sensitivity and the physiological mechanisms underlying temperature response. In this study we conducted the first measure of the thermal reaction norm for feeding, comparing the radula rasping rate of two tropical and one polar limpet species. The consistency of thermal response was tested through comparisons with limpet duration tenacity. Feeding and duration tenacity of limpets are ecologically important muscular mechanisms that rely on very different aspects of muscle physiology, repeated concentric (shortening) and isometric (fixed length) contraction of muscles, respectively. In these limpets the thermal reaction norms of feeding limpets were best described by a single break point at a maximum temperature with linear declines at higher (Siphonaria atra) or lower temperatures (Nacella concinna and Cellana radiata) rather than a bell-shaped curve. The thermal reaction norms for duration tenacity were similar in the two tropical limpets. However, the rasping rate in Antarctic N. concinna increased linearly with temperature up to a maximum at 12.3 °C (maximal range 8.5–12.3 °C) when feeding stopped. In contrast, duration tenacity in N. concinna was maximal at 1.0 °C (−0.6 to 3.8 °C) and linearly decreased with increasing temperature. The thermal reaction norms of muscular activity were, therefore, inconsistent within and between species, indicating that different mechanisms likely underlie different aspects of species sensitivities to temperature

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

Characterisation of the mantle transcriptome and biomineralisation genes in the blunt-gaper clam, Mya truncata

Members of the Myidae family are ecologically and economically important, but there is currently very little molecular data on these species. The present study sequenced and assembled the mantle transcriptome of Mya truncata from the North West coast of Scotland and identified candidate biomineralisation genes. RNA-Seq reads were assembled to create 20,106 contigs in a de novo transciptome, 18.81% of which were assigned putative functions using BLAST sequence similarity searching (cuttoff E-value 1E − 10). The most highly expressed genes were compared to the Antarctic clam (Laternula elliptica) and showed that many of the dominant biological functions (muscle contraction, energy production, biomineralisation) in the mantle were conserved. There were however, differences in the constitutive expression of heat shock proteins, which were possibly due to the M. truncata sampling location being at a relatively low latitude, and hence relatively warm, in terms of the global distribution of the species. Phylogenetic analyses of the Tyrosinase proteins from M. truncata showed a gene expansion which was absent in L. elliptica. The tissue distribution expression patterns of putative biomineralisation genes were investigated using quantitative PCR, all genes showed a mantle specific expression pattern supporting their hypothesised role in shell secretion. The present study provides some preliminary insights into how clams from different environments – temperate versus polar – build their shells. In addition, the transcriptome data provides a valuable resource for future comparative studies investigating biomineralisation

Treatment of Heavy Quarks in Deeply Inelastic Scattering

We investigate a simplified version of the ACOT prescription for calculating deeply inelastic scattering from Q^2 values near the squared mass M_H^2 of a heavy quark to Q^2 much larger than M_H^2.Comment: 14 pages, 5 figure

Adult acclimation to combined temperature and pH stressors significantly enhances reproductive outcomes compared to short-term exposures

1.This study examined the effects of long-term culture under altered conditions on the Antarctic sea urchin, Sterechinus neumayeri. 2.Sterechinus neumayeri was cultured under the combined environmental stressors of lowered pH (−0·3 and −0·5 pH units) and increased temperature (+2 °C) for 2 years. This time-scale covered two full reproductive cycles in this species and analyses included studies on both adult metabolism and larval development. 3.Adults took at least 6–8 months to acclimate to the altered conditions, but beyond this, there was no detectable effect of temperature or pH. 4.Animals were spawned after 6 and 17 months exposure to altered conditions, with markedly different outcomes. At 6 months, the percentage hatching and larval survival rates were greatest in the animals kept at 0 °C under current pH conditions, whilst those under lowered pH and +2 °C performed significantly less well. After 17 months, performance was not significantly different across treatments, including controls. However, under the altered conditions urchins produced larger eggs compared with control animals. 5.These data show that under long-term culture adult S. neumayeri appear to acclimate their metabolic and reproductive physiology to the combined stressors of altered pH and increased temperature, with relatively little measureable effect. They also emphasize the importance of long-term studies in evaluating effects of altered pH, particularly in slow developing marine species with long gonad maturation times, as the effects of altered conditions cannot be accurately evaluated unless gonads have fully matured under the new conditions

Identification of molecular and physiological responses to chronic environmental challenge in an invasive species: the Pacific oyster, Crassostrea gigas

Understanding the environmental responses of an invasive species is critical in predicting how ecosystem composition may be transformed in the future, especially under climate change. In this study, Crassostrea gigas, a species well adapted to the highly variable intertidal environment, was exposed to the chronic environmental challenges of temperature (19 and 24°C) and pH (ambient seawater and a reduction of 0.4 pH units) in an extended 3-month laboratory-based study. Physiological parameters were measured (condition index, shell growth, respiration, excretion rates, O:N ratios, and ability to repair shell damage) alongside molecular analyses. Temperature was by far the most important stressor, as demonstrated by reduced condition indexes and shell growth at 24°C, with relatively little effect detected for pH. Transcriptional profiling using candidate genes and SOLiD sequencing of mantle tissue revealed that classical “stress” genes, previously reported to be upregulated under acute temperature challenges, were not significantly expressed in any of the treatments, emphasizing the different response between acute and longer term chronic stress. The transcriptional profiling also elaborated on the cellular responses underpinning the physiological results, including the identification of the PI3K/AKT/mTOR pathway as a potentially novel marker for chronic environmental challenge. This study represents a first attempt to understand the energetic consequences of cumulative thermal stress on the intertidal C. gigas which could significantly impact on coastal ecosystem biodiversity and function in the future