Transcriptome of the deep-sea black scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae) : tissue-specific expression patterns and candidate genes associated to depth adaptation

Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.Publisher PDFPeer reviewe

Coronal properties of active G-type stars in different evolutionary phases

We report on the analysis of XMM-Newton observations of three G-type stars in very different evolutionary phases: the "weak-line" T Tauri star HD 283572, the Zero Age Main Sequence star EK Dra and the Hertzsprung-gap giant star 31 Corn. The X-ray luminosities of the three stars are all in the range 10(30) - 10(31) erg/s. We compare the Emission Measure Distributions of these bright sources, derived from high-resolution X-ray spectra, as well as the pattern of elemental abundances vs. First Ionization Potential (FIP). The results of our analysis suggest that the coronae of these stars are very similar in terms of dominant coronal magnetic structures, in spite of differences in their evolutionary phases, surface gravities and metallicities

The Discovery of a Companion to the Very Cool Dwarf Gl~569~B with the Keck Adaptive Optics Facility

We report observations obtained with the Keck adaptive optics facility of the nearby (d=9.8 pc) binary Gl~569. The system was known to be composed of a cool primary (dM2) and a very cool secondary (dM8.5) with a separation of 5" (49 Astronomical Units). We have found that Gl~569~B is itself double with a separation of only 0".101$\pm$0".002 (1 Astronomical Unit). This detection demonstrates the superb spatial resolution that can be achieved with adaptive optics at Keck. The difference in brightness between Gl~569~B and the companion is $\sim$0.5 magnitudes in the J, H and K' bands. Thus, both objects have similarly red colors and very likely constitute a very low-mass binary system. For reasonable assumptions about the age (0.12~Gyr--1.0~Gyr) and total mass of the system (0.09~M$_\odot$--0.15~M$_\odot$), we estimate that the orbital period is $\sim$3 years. Follow-up observations will allow us to obtain an astrometric orbit solution and will yield direct dynamical masses that can constrain evolutionary models of very low-mass stars and brown dwarfs

Element abundances of unevolved stars in the open cluster M 67

We determined the metallicity ([Fe/H]), together with O, Na, Mg, Al, Si, Ca, Ti, Cr and Ni abundances for a sample of 10 unevolved or slightly evolved stars belonging to the open cluster M 67. We find an average metallicity [Fe/H]=0.03 +/- 0.01, in very good agreement with previous determinations. All the [X/Fe] abundance ratios are very close to solar. The star-to-star scatter in [Fe/H] and [X/Fe] ratios for all elements, including oxygen, is lower than 0.05 dex, implying that the large dispersion in lithium reported in previous studies is not due to differences in these element abundances. We also find that, when using a homogeneous scale, the abundance pattern of unevolved stars in our sample is very similar to that of evolved stars, suggesting that, at least in this cluster, RGB and clump stars have not undergone any chemical processing. Finally, our results show that M 67 has a chemical composition that is representative of the solar neighborhood.Comment: 18 pages, 5 figures, accepted for publication in A&

Tannins-Based Extracts: Effects on Gut Chicken Spontaneous Contractility

The impossibility of using drugs for the health of farm animals leads to the search for alternative strategies with two purposes: to maintain animal health and safeguard human health. In this perspective, tannins have shown great promises. These phytocomplexes obtained from natural matrices with multiple health properties may be used as a feed supplement in chicken farms. In this work, we studied two tannin-based extracts (from Castanea sativa Mill. wood and from Schinopsis balansae Engl. Quebracho Colorado hardwood) with different chemical compositions on the spontaneous contractility on the isolated intestinal tissues of healthy chicken. The results showed that the chemical composition of the two phytocomplexes influenced the spontaneous intestinal contractility in different ways by regulating the tone and consequent progression of the food bolus. The chemical analysis of the two extracts revealed that Castanea sativa Mill. wood mainly contains hydrolysable tannins, while Schinopsis balansae Engl. hardwood mainly contains condensed tannins. The two phytocomplexes showed different effects towards gastrointestinal smooth muscle contractility, with Castanea sativa Mill. wood providing a better activity profile than Schinopsis balansae Engl. hardwood

Dual analysis of host and pathogen transcriptomes in ostreid herpesvirus 1-positive Crassostrea gigas

Ostreid herpesvirus type 1 (OsHV-1) has become a problematic infective agent for the Pacific oyster Crassostrea gigas. In particular, the OsHV-1 \u3bcVar subtype has been associated with severe mortality episodes in oyster spat and juvenile oysters in France and other regions of the world. Factors enhancing the infectivity of the virus and its interactions with susceptible and resistant bivalve hosts are still to be understood, and only few studies have explored the expression of oyster or viral genes during productive infections. In this work, we have performed a dual RNA sequencing analysis on an oyster sample with a high viral load. High sequence coverage allowed us to thoroughly explore the OsHV-1 transcriptome and identify the activated molecular pathways in C.gigas. The identification of several highly induced and defence-related oyster transcripts supports the crucial role played by the innate immune system against the virus and opportunistic microbes possibly contributing to subsequent spat mortality

Flaring Up All Over -- Radio Activity in Rapidly-Rotating Late-Type M and L Dwarfs

We present Very Large Array observations of twelve late M and L dwarfs in the Solar neighborhood. The observed sources were chosen to cover a wide range of physical characteristics - spectral type, rotation, age, binarity, and X-ray and H\alpha activity - to determine the role of these properties in the production of radio emission, and hence magnetic fields. Three of the twelve sources, TVLM513-46546, 2MASS J0036159+182110, and BRI0021-0214, were observed to flare and also exhibit persistent emission, indicating that magnetic activity is not quenched at the bottom of the main sequence. The radio emission extends to spectral type L3.5, and there is no apparent decrease in the ratio of flaring luminosities to bolometric luminosities between M8-L3.5. Moreover, contrary to the significant drop in persistent H\alpha activity beyond spectral type M7, the persistent radio activity appears to steadily increase between M3-L3.5. Similarly, the radio emission from BRI0021-0214 violates the phenomenological relations between the radio and X-ray luminosities of coronally active stars, hinting that radio and X-ray activity are also uncorrelated at the bottom of the main sequence. The radio active sources that have measured rotational velocities are rapid rotators, Vsin(i)>30 km/sec, while the upper limits on radio activity in slowly-rotating late M dwarfs (Vsin(i)<10 km/sec) are lower than these detections. These observations provide tantalizing evidence that rapidly-rotating late M and L dwarfs are more likely to be radio active. This possible correlation is puzzling given that the observed radio emission requires sustained magnetic fields of 10-1000 G and densities of 10^12 cm^-3, indicating that the active sources should have slowed down considerably due to magnetic braking.Comment: Accepted to ApJ; Two new figures; Minor text revision

PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called 'better clustering for QIIME' (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100\u2009224 sequences), PLANiTS2 (96\u2009771 sequences) and PLANiTS (97\u2009550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS