Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene

Background: Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicator species for soil toxicity. Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida. Results: Microarrays wereused to examine two different exposure concentrations of phenanthrene, namely the EC10 (24.95 mg kg-1 soil) and EC50 (45.80 mg kg-1 soil) on reproduction of this springtail, which evoked 405 and 251 differentially expressed transcripts, respectively. Fifty transcripts were differential in response to either concentration. Many transcripts encoding xenobiotic detoxification and biotransformation enzymes (phases I, II, and III) were upregulated in response to either concentration. Furthermore, indications of general and oxidative stress were found in response to phenanthrene. Chitin metabolism appeared to be disrupted particularly at the low concentration, and protein translation appeared suppressed at the high concentration of phenanthrene; most likely in order to reallocate energy budgets for the detoxification process. Finally, an immune response was evoked especially in response to the high effect concentration, which was also described in a previous transcriptomic study using the same effect concentration (EC50) of cadmium. Conclusion: Our study provides new insights in the molecular mode of action of the important polluting class of polycyclic aromatic hydrocarbons in soil animals. Furthermore, we present a fast, sensitive, and specific soil toxicity test which enhances traditional tests and may help to improve current environmental risk assessments and monitoring of potentially polluted sites. © 2009 Nota et al; licensee BioMed Central Ltd

Reference genes for QRT-PCR tested under various stress conditions in Folsomia candida and Orchesella cincta (Insecta, Collembola)

<p>Abstract</p> <p>Background</p> <p>Genomic studies measuring transcriptional responses to changing environments and stress currently make their way into the field of evolutionary ecology and ecotoxicology. To investigate a small to medium number of genes or to confirm large scale microarray studies, Quantitative Reverse Transcriptase PCR (QRT-PCR) can achieve high accuracy of quantification when key standards, such as normalization, are carefully set. In this study, we validated potential reference genes for their use as endogenous controls under different chemical and physical stresses in two species of soil-living Collembola, <it>Folsomia candida </it>and <it>Orchesella cincta</it>. Treatments for <it>F. candida </it>were cadmium exposure, phenanthrene exposure, desiccation, heat shock and pH stress, and for <it>O. cincta </it>cadmium, desiccation, heat shock and starvation.</p> <p>Results</p> <p>Eight potential reference genes for <it>F. candida </it>and seven for <it>O. cincta </it>were ranked by their stability per stress factor using the programs geNorm and Normfinder. For <it>F. candida </it>the succinate dehydrogenase (<it>SDHA</it>) and eukaryotic transcription initiation factor 1A (<it>ETIF</it>) genes were found the most stable over the different treatments, while for <it>O. cincta</it>, the beta actin (<it>ACTb</it>) and tyrosine 3-monooxygenase (<it>YWHAZ</it>) genes were the most stable.</p> <p>Conclusion</p> <p>We present a panel of reference genes for two emerging ecological genomic model species tested under a variety of treatments. Within each species, different treatments resulted in differences in the top stable reference genes. Moreover, the two species differed in suitable reference genes even when exposed to similar stresses. This might be attributed to dissimilarity of physiology. It is vital to rigorously test a panel of reference genes for each species and treatment, in advance of relative quantification of QRT-PCR gene expression measurements.</p

Collembase: a repository for springtail genomics and soil quality assessment

<p>Abstract</p> <p>Background</p> <p>Environmental quality assessment is traditionally based on responses of reproduction and survival of indicator organisms. For soil assessment the springtail <it>Folsomia candida </it>(Collembola) is an accepted standard test organism. We argue that environmental quality assessment using gene expression profiles of indicator organisms exposed to test substrates is more sensitive, more toxicant specific and significantly faster than current risk assessment methods. To apply this species as a genomic model for soil quality testing we conducted an EST sequencing project and developed an online database.</p> <p>Description</p> <p>Collembase is a web-accessible database comprising springtail (<it>F. candida</it>) genomic data. Presently, the database contains information on 8686 ESTs that are assembled into 5952 unique gene objects. Of those gene objects ~40% showed homology to other protein sequences available in GenBank (blastx analysis; non-redundant (nr) database; expect-value < 10^-5). Software was applied to infer protein sequences. The putative peptides, which had an average length of 115 amino-acids (ranging between 23 and 440) were annotated with Gene Ontology (GO) terms. In total 1025 peptides (~17% of the gene objects) were assigned at least one GO term (expect-value < 10^-25). Within Collembase searches can be conducted based on BLAST and GO annotation, cluster name or using a BLAST server. The system furthermore enables easy sequence retrieval for functional genomic and Quantitative-PCR experiments. Sequences are submitted to GenBank (Accession numbers: <ext-link ext-link-type="gen" ext-link-id="EV473060">EV473060</ext-link> – <ext-link ext-link-type="gen" ext-link-id="EV481745">EV481745</ext-link>).</p> <p>Conclusion</p> <p>Collembase <url>http://www.collembase.org</url> is a resource of sequence data on the springtail <it>F. candida</it>. The information within the database will be linked to a custom made microarray, based on the Agilent platform, which can be applied for soil quality testing. In addition, Collembase supplies information that is valuable for related scientific disciplines such as molecular ecology, ecogenomics, molecular evolution and phylogenetics.</p

Investigating the Cosmic-Ray Ionization Rate in the Galactic Diffuse Interstellar Medium through Observations of H3+

Observations of H3+ in the Galactic diffuse interstellar medium (ISM) have led to various surprising results, including the conclusion that the cosmic-ray ionization rate (zeta_2) is about 1 order of magnitude larger than previously thought. The present survey expands the sample of diffuse cloud sight lines with H3+ observations to 50, with detections in 21 of those. Ionization rates inferred from these observations are in the range (1.7+-1.3)x10^-16 s^-1<zeta_2<(10.6+-8.2)x10^-16 s^-1 with a mean value of zeta_2=(3.5^+5.3_-3.0)x10^-16 s^-1. Upper limits (3 sigma) derived from non-detections of H3+ are as low as zeta_2<0.4x10^-16 s^-1. These low upper-limits, in combination with the wide range of inferred cosmic-ray ionization rates, indicate variations in zeta_2 between different diffuse cloud sight lines. A study of zeta_2 versus N_H (total hydrogen column density) shows that the two parameters are not correlated for diffuse molecular cloud sight lines, but that the ionization rate decreases when N_H increases to values typical of dense molecular clouds. Both the difference in ionization rates between diffuse and dense clouds and the variation of zeta_2 among diffuse cloud sight lines are likely the result of particle propagation effects. The lower ionization rate in dense clouds is due to the inability of low-energy (few MeV) protons to penetrate such regions, while the ionization rate in diffuse clouds is controlled by the proximity of the observed cloud to a site of particle acceleration.Comment: 48 pages, 19 figures, 4 tables, accepted for publication in Ap

MN112: a new Galactic candidate Luminous Blue Variable

We report the discovery of a new Galactic candidate Luminous Blue Variable (cLBV) via detection of an infrared circular nebula and follow-up spectroscopy of its central star. The nebula, MN112, is one of many dozens of circular nebulae detected at $24 \mu$m in the {\it Spitzer Space Telescope} archival data, whose morphology is similar to that of nebulae associated with known (c)LBVs and related evolved massive stars. Specifically, the core-halo morphology of MN112 bears a striking resemblance to the circumstellar nebula associated with the Galactic cLBV GAL 079.29+00.46, which suggests that both nebulae might have a similar origin and that the central star of MN112 is a LBV. The spectroscopy of the central star showed that its spectrum is almost identical to that of the bona fide LBV P Cygni, which also supports the LBV classification of the object. To further constrain the nature of MN112, we searched for signatures of possible high-amplitude (\ga 1 mag) photometric variability of the central star using archival and newly obtained photometric data covering a 45 year period. We found that the B magnitude of the star was constant ($\simeq$ 17.1$\pm$0.3 mag) over this period, while in the I band the star brightened by $\simeq 0.4$ mag during the last 17 years. Although the non-detection of large photometric variability leads us to use the prefix `candidate' in the classification of MN112, we remind that the long-term photometric stability is not unusual for genuine LBVs and that the brightness of P Cygni remains relatively stable during the last three centuries.Comment: 6 pages, 3 figures, accepted to MNRA

Revealing evolved massive stars with Spitzer

Massive evolved stars loss a large fraction of their mass via copious stellar wind or instant outbursts and during certain evolutionary phases they can be identified via the presence of their circumstellar nebulae. In this paper, we present the results of search for compact nebulae (reminiscent of circumstellar nebulae around evolved massive stars) using archival 24 $\mu$m data obtained with the Multiband Imaging Photometer for Spitzer. We discovered 115 nebulae, most of which bear a striking resemblance to the circumstellar nebulae associated with Luminous Blue Variables (LBVs) and late WN-type (WNL) Wolf-Rayet (WR) stars in the Milky Way and the Large Magellanic Cloud (LMC). We interpret this similarity as an indication that the central stars of detected nebulae are either LBVs or related evolved massive stars. Our interpretation is supported by follow-up spectroscopy of two dozens of these central stars, most of which turns out to be either candidate LBVs (cLBVs), blue supergiants or WNL stars. We expect that the forthcoming spectroscopy of the remaining objects from our list, accompanied by the spectrophotometric monitoring of the already discovered cLBVs, will further increase the known population of Galactic LBVs, which in turn would have profound consequences for better understanding the LBV phenomenon and its role in the transition between hydrogen burning O stars and helium burning WR stars. We also report the detection of an arc-like structure attached to the cLBV HD326823 and an arc associated with the LBV R99 (HD269445) in the LMC.Comment: 9 pages, 10 figures, accepted to MNRA

First two unrelated cases of isolated sedoheptulokinase deficiency: A benign disorder?

We present the first two reported unrelated patients with an isolated sedoheptulokinase (SHPK) deficiency. The first patient presented with neonatal cholestasis, hypoglycemia, and anemia, while the second patient presented with congenital arthrogryposis multiplex, multiple contractures, and dysmorphisms. Both patients had elevated excretion of erythritol and sedoheptulose, and each had a homozygous nonsense mutation in SHPK. SHPK is an enzyme that phosphorylates sedoheptulose to sedoheptulose-7-phosphate, which is an important intermediate of the pentose phosphate pathway. It is questionable whether SHPK deficiency is a causal factor for the clinical phenotypes of our patients. This study illustrates the necessity of extensive functional and clinical workup for interpreting a novel variant, including nonsense variants

M1-78: a nitrogen-rich Galactic compact HII region beyond the Perseus arm

There is considerable controversy surrounding the nature of M1-78, a compact nebula located beyond the Perseus arm. It was first classified as a planetary nebula and is nowadays generally considered to be a compact HII region. To investigate the nature M1-78 further, we present a detailed spectroscopic study of M1-78 in the optical and near-infrared. M1-78 is a high-density nebula with substantial physical differences between its two main morphological zones: a bright arc to the SW and a blob of emission in the NE. Specifically, the blob in the NE has a higher electron temperature and visual extinction than the SW arc. The most important result, however, is the confirmation of a nitrogen enrichment in M1-78. This enrichment is stronger at the location of the NE blob and is correlated with a defficiency in the O abundance and a (dubious) He enrichment. Such an abundance pattern is typical of ejecta nebulae around evolved massive stars such as Wolf-Rayet and Luminous Blue Variable stars. The spatial variations in the physical conditions and chemical abundances and the presence of more than one possible ionizing source indicates, however, that M1-78 is better described as a combination of a compact HII region + ejecta. Finally, we detect H2 emission that extends over a large (~30 arcsec) area around the ionized nebula. Analysis of the near-infrared H2 lines indicates that the excitation mechanism is UV fluorescence.Comment: 14 pages, 8 figures. Accepted for publication in A&

Blimp-1 Rather Than Hobit Drives the Formation of Tissue-Resident Memory CD8+ T Cells in the Lungs

Tissue-resident memory CD8+ T (TRM) cells that develop in the epithelia at portals of pathogen entry are important for improved protection against re-infection. CD8+ TRM cells within the skin and the small intestine are long-lived and maintained independently of circulating memory CD8+ T cells. In contrast to CD8+ TRM cells at these sites, CD8+ TRM cells that arise after influenza virus infection within the lungs display high turnover and require constant recruitment from the circulating memory pool for long-term persistence. The distinct characteristics of CD8+ TRM cell maintenance within the lungs may suggest a unique program of transcriptional regulation of influenza-specific CD8+ TRM cells. We have previously demonstrated that the transcription factors Hobit and Blimp-1 are essential for the formation of CD8+ TRM cells across several tissues, including skin, liver, kidneys, and the small intestine. Here, we addressed the roles of Hobit and Blimp-1 in CD8+ TRM cell differentiation in the lungs after influenza infection using mice deficient for these transcription factors. Hobit was not required for the formation of influenza-specific CD8+ TRM cells in the lungs. In contrast, Blimp-1 was essential for the differentiation of lung CD8+ TRM cells and inhibited the differentiation of central memory CD8+ T (TCM) cells. We conclude that Blimp-1 rather than Hobit mediates the formation of CD8+ TRM cells in the lungs, potentially through control of the lineage choice between TCM and TRM cells during the differentiation of influenza-specific CD8+ T cells

Girls and Boys Born before 28 Weeks Gestation: Risks of Cognitive, Behavioral, and Neurologic Outcomes at Age 10 Years

To compare the prevalence of cognitive, neurological, and behavioral outcomes at 10 years of age in 428 girls and 446 boys who were born extremely preterm (EP)