De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis

BACKGROUND: Karenia brevis is a harmful algal species that blooms in the Gulf of Mexico and produces brevetoxins that cause neurotoxic shellfish poisoning. Elevated brevetoxin levels in K. brevis cells have been measured during laboratory hypo-osmotic stress treatments. To investigate mechanisms underlying K. brevis osmoacclimation and osmoregulation and establish a valuable resource for gene discovery, we assembled reference transcriptomes for three clones: Wilson-CCFWC268, SP3, and SP1 (a low-toxin producing variant). K. brevis transcriptomes were annotated with gene ontology terms and searched for putative transmembrane proteins that may elucidate cellular responses to hypo-osmotic stress. An analysis of single nucleotide polymorphisms among clones was used to characterize genetic divergence. RESULTS: K. brevis reference transcriptomes were assembled with 58.5 (Wilson), 78.0 (SP1), and 51.4 million (SP3) paired reads. Transcriptomes contained 86,580 (Wilson), 93,668 (SP1), and 84,309 (SP3) predicted transcripts. Approximately 40% of the transcripts were homologous to proteins in the BLAST nr database with an E value ≤ 1.00E-6. Greater than 80% of the highly conserved CEGMA core eukaryotic genes were identified in each transcriptome, which supports assembly completeness. Seven putative voltage-gated Na(+) or Ca(2+) channels, two aquaporin-like proteins, and twelve putative VATPase subunits were discovered in all clones using multiple bioinformatics approaches. Furthermore, 45% (Wilson) and 43% (SP1 and SP3) of the K. brevis putative peptides > 100 amino acids long produced significant hits to a sequence in the NCBI nr protein database. Of these, 77% (Wilson and SP1) and 73% (SP3) were successfully assigned gene ontology functional terms. The predicted single nucleotide polymorphism (SNP) frequencies between clones were 0.0028 (Wilson to SP1), 0.0030 (Wilson to SP3), and 0.0028 (SP1 to SP3). CONCLUSIONS: The K. brevis transcriptomes assembled here provide a foundational resource for gene discovery and future RNA-seq experiments. The identification of ion channels, VATPases, and aquaporins in all three transcriptomes indicates that K. brevis regulates cellular ion and water concentrations via transmembrane proteins. Additionally, > 40,000 unannotated loci may include potentially novel K. brevis genes. Ultimately, the SNPs identified among the three ecologically diverse clones with different toxin profiles may help to elucidate variations in K. brevis brevetoxin production. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-888) contains supplementary material, which is available to authorized users

Duplication, divergence and persistence in the Phytochrome photoreceptor gene family of cottons (Gossypium spp.)

<p>Abstract</p> <p>Background</p> <p>Phytochromes are a family of red/far-red photoreceptors that regulate a number of important developmental traits in cotton (<it>Gossypium </it>spp.), including plant architecture, fiber development, and photoperiodic flowering. Little is known about the composition and evolution of the phytochrome gene family in diploid (<it>G. herbaceum</it>, <it>G. raimondii</it>) or allotetraploid (<it>G. hirsutum</it>, <it>G. barbadense</it>) cotton species. The objective of this study was to obtain a preliminary inventory and molecular-evolutionary characterization of the phytochrome gene family in cotton.</p> <p>Results</p> <p>We used comparative sequence resources to design low-degeneracy PCR primers that amplify genomic sequence tags (GSTs) for members of the <it>PHYA</it>, <it>PHYB/D</it>, <it>PHYC </it>and <it>PHYE </it>gene sub-families from A- and D-genome diploid and AD-genome allotetraploid <it>Gossypium </it>species. We identified two paralogous <it>PHYA </it>genes (designated <it>PHYA1 </it>and <it>PHYA2</it>) in diploid cottons, the result of a Malvaceae-specific <it>PHYA </it>gene duplication that occurred approximately 14 million years ago (MYA), before the divergence of the A- and D-genome ancestors. We identified a single gene copy of <it>PHYB</it>, <it>PHYC</it>, and <it>PHYE </it>in diploid cottons. The allotetraploid genomes have largely retained the complete gene complements inherited from both of the diploid genome ancestors, with at least four <it>PHYA </it>genes and two genes encoding <it>PHYB</it>, <it>PHYC </it>and <it>PHYE </it>in the AD-genomes. We did not identify a <it>PHYD </it>gene in any cotton genomes examined.</p> <p>Conclusions</p> <p>Detailed sequence analysis suggests that phytochrome genes retained after duplication by segmental duplication and allopolyploidy appear to be evolving independently under a birth-and-death-process with strong purifying selection. Our study provides a preliminary phytochrome gene inventory that is necessary and sufficient for further characterization of the biological functions of each of the cotton phytochrome genes, and for the development of 'candidate gene' markers that are potentially useful for cotton improvement via modern marker-assisted selection strategies.</p

Establishment and Spread of a Single Parthenogenic Genotype of the Mediterranean arundo wasp, Tetramesa romana1, In the Variable Climate of Texas

As part of a biological control program for the invasive weed, Arundo donax L., several genotypically unique populations of the parthenogenetic stemgalling wasp, Tetramesa romana Walker (Hymenoptera: Eurytomidae), from Spain and France were released in an infested riparian zone along the Rio Grande from Brownsville to Del Rio, TX. An adventive population of the wasp of unknown origin with limited distribution in Texas was also discovered, evaluated, and released as part of the program. More than 1.2 million wasps representing the mixture of genotypes were aerially released from 2009 to 2011. Wasps dispersed from their original release locations and now have a continuous distribution along the Rio Grande from Brownsville to Del Rio, and have dispersed throughout most of Central Texas with satellite populations as far west as San Angelo (Tom Green County), north as far as Kaufman (Kaufman County), and east to Navasota (Grimes County). The most successful genotype (#4) represented 390 of the 409 wasps recovered and matched both an imported population from the Mediterranean coast of Spain and an adventive population established in Texas before the start of the biological control program. Several other European genotypes of the wasp released in the program apparently failed to establish. This result demonstrated the benefits of evaluating and releasing the maximum genetic diversity of the biological control agent in the introduced range. Abundance of T. romana on the Rio Grande from Laredo to Del Rio averaged 190% more in 2013-2014 compared to a similar study in 2008-2009 before release of the European wasps. A favorability index was developed that showed that conditions from 1969 to 1977 would have been adverse to the wasp; conditions after 2009 were more favorable. Climate matching predicts the wasp will disperse throughout the southern U.S. and Mexico

Extreme debris disk variability : exploring the diverse outcomes of large asteroid impacts during the era of terrestrial planet formation

The most dramatic phases of terrestrial planet formation are thought to be oligarchic and chaotic growth, on timescales of up to 100─200 Myr, when violent impacts occur between large planetesimals of sizes up to protoplanets. Such events are marked by the production of large amounts of debris, as has been observed in some exceptionally bright and young debris disks (termed extreme debris disks). Here we report five years of Spitzer measurements of such systems around two young solar-type stars: ID8 and P1121. The short-term (weekly to monthly) and long-term (yearly) disk variability is consistent with the aftermaths of large impacts involving large asteroid-sized bodies. We demonstrate that an impact-produced clump of optically thick dust, under the influence of the dynamical and viewing geometry effects, can produce short-term modulation in the disk light curves. The long-term disk flux variation is related to the collisional evolution within the impact-produced fragments once released into a circumstellar orbit. The time-variable behavior observed in the P1121 system is consistent with a hypervelocity impact prior to 2012 that produced vapor condensates as the dominant impact product. Two distinct short-term modulations in the ID8 system suggest two violent impacts at different times and locations. Its long-term variation is consistent with the collisional evolution of two different populations of impact-produced debris dominated by either vapor condensates or escaping boulders. The bright, variable emission from the dust produced in large impacts from extreme debris disks provides a unique opportunity to study violent events during the era of terrestrial planet formation

TESS Discovery of a Transiting Super-Earth in the π\pi Mensae System

We report the detection of a transiting planet around $\pi$ Mensae (HD 39091), using data from the Transiting Exoplanet Survey Satellite (TESS). The solar-type host star is unusually bright (V=5.7) and was already known to host a Jovian planet on a highly eccentric, 5.7-year orbit. The newly discovered planet has a size of $2.04\pm 0.05$ $R_\oplus$ and an orbital period of 6.27 days. Radial-velocity data from the HARPS and AAT/UCLES archives also displays a 6.27-day periodicity, confirming the existence of the planet and leading to a mass determination of $4.82\pm 0.85$ $M_\oplus$. The star's proximity and brightness will facilitate further investigations, such as atmospheric spectroscopy, asteroseismology, the Rossiter--McLaughlin effect, astrometry, and direct imaging.Comment: Accepted for publication ApJ Letters. This letter makes use of the TESS Alert data, which is currently in a beta test phase. The discovery light curve is included in a table inside the arxiv submissio

Therapeutic hypothermia for neonatal hypoxic ischaemic encephalopathy should not be discontinued in low- and middle-income countries

Perinatal asphyxia is a major cause of death and disability in children. Therapeutic hypothermia (TH) has become a standard of care for newborn infants who have sustained hypoxic ischaemic encephalopathy (HIE) due to perinatal asphyxia. There is compelling evidence to support this approach. A Cochrane systematic review of 11 prospective randomised controlled trials including 1 505 newborns showed that TH started within 6 hours of birth in infants with HIE significantly decreased mortality and neurodevelopmental disability in survivors.http://www.samj.org.zadm2022ImmunologyPaediatrics and Child Healt

The development of computational biology in South Africa: successes achieved and lessons learnt

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo