Mapping the secondary star in QQ Vulpeculae

We present high- and medium-resolution phase-resolved far-red spectra of the magnetic cataclysmic variable QQ Vul. The spectra show the Na i doublet absorption features near λ 8190 Å from the cool secondary star, and the lines of He ii, O i, Mg ii, C i, N i, Ca ii and Paschen in emission. Using a Doppler imaging technique, we find that the H i, He ii, C i and O i lines have a narrow component originating near the L1 point and a strong component from the stream, while the Mg ii and Ca ii emission arises solely from the illuminated hemisphere of the red dwarf. We carry out an exhaustive analysis of the emission- and absorption-line velocities and fluxes seen in the QQ Vul spectrum. By simultaneously fitting the radial velocity and flux information we are able to produce surface maps of each line on the secondary star using a technique analogous to the one employed by Davey. The Na i and Mg ii maps show an asymmetric distribution akin to that seen in AM Her. Although the observed velocity semi-amplitudes (K2) of the lines can potentially be corrected for the effects of irradiation, we find that time-dependent changes in the degree of heating on the secondary can lead to large discrepancies in the results, significant enough to give inconsistent values from data taken at different epochs. We discuss the limitations of the surface mapping method as a means of correcting the observed K2. Our results also suggest that the emission features from the red dwarf are likely to be formed at quite high levels of the stellar chromosphere, in some cases probably even beyond the L1 point and inside the Roche lobe of the white dwarf, with the different lines possibly forming at different depths. Using the Na i absorption doublet, we find a velocity semi-amplitude for the secondary star of K2=219±6 km s−1 and a projected rotational velocity of vrot sin i=110±15 km s−1. Thus we estimate the mass ratio to be q=0.54±0.14. Based on the results of the best-fitting surface maps on all the lines, and the nature of the phase-dependent variations of the continuum and lines, we infer a binary inclination of i=65°±7°, and obtain a complete set of binary parameters for QQ Vul. We classify the secondary star as M4V from the TiO band ratios

A spectroscopic search for faint secondaries in cataclysmic variables

The secondary in cataclysmic variables (CV's) is usually detected by cross-correlation of the CV spectrum with that of a K or M dwarf template, to produce a radial velocity curve. Although this method has demonstrated its power, it has its limits in the case of noisy spectra, such as are found when the secondary is faint. A method of co-adding spectra, called skew mapping, has been proposed in the past. Gradually, examples of its application are being published. Nonetheless, so far no journal article has described the technique in detail. To answer this need, this paper explores in detail the capabilities of skew mapping when determining the amplitude of the radial velocity for faint secondaries. It demonstrates the method's power over techniques that are more conventional, when the signal-to-noise (s/n) ratio is poor. The paper suggests an approach to assessing the quality of results. This leads in the case of the investigated objects to a first tier of results, where we find K2=127+-23 km/s for SY Cnc, K2=144+-18 km/s for RW Sex, and K2=262+-14 km/s for UX UMa. These we believe to be the first direct determinations of K2 for these objects. Furthermore, we also obtain K2=263+-30 km/s for RW Tri, close to a skew mapping result obtained elsewhere. In the first three cases, we use these results to derive the mass of the white dwarf companion. A second tier of results includes UU Aqr, EX Hya, and LX Ser, for which we propose more tentative values of K2. Clear failures of the method are also discussed (EF Eri, VV Pup, SW Sex).Comment: 23 pages, 22 figures, 10 tables; translated to pdf from a Word file - no TeX version available. Accepted for publication in MNRA

Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy

Archaeal anaerobic methanotrophs (“ANME”) and sulfate-reducing Deltaproteobacteria (“SRB”) form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b—SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b—SEEP-SRB1g consortia incubated with a headspace containing CH₄ and ¹⁵N₂ revealed differences in cellular ¹⁵N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in ¹⁵N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph

Expression of target and reference genes in Daphnia magna exposed to ibuprofen

Background: Transcriptomic techniques are now being applied in ecotoxicology and toxicology to measure the impact of stressors and develop understanding of mechanisms of toxicity. Microarray technology in particular offers the potential to measure thousands of gene responses simultaneously. However, it is important that microarrays responses should be validated, at least initially, using real-time quantitative polymerase chain reaction (QPCR). The accurate measurement of target gene expression requires normalisation to an invariant internal control e. g., total RNA or reference genes. Reference genes are preferable, as they control for variation inherent in the cDNA synthesis and PCR. However, reference gene expression can vary between tissues and experimental conditions, which makes it crucial to validate them prior to application. Results: We evaluated 10 candidate reference genes for QPCR in Daphnia magna following a 24 h exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen (IB) at 0, 20, 40 and 80 mg IB l(-1). Six of the 10 candidates appeared suitable for use as reference genes. As a robust approach, we used a combination normalisation factor (NF), calculated using the geNorm application, based on the geometric mean of three selected reference genes: glyceraldehyde-3-phosphate dehydrogenase, ubiquitin conjugating enzyme and actin. The effects of normalisation are illustrated using as target gene leukotriene B4 12-hydroxydehydrogenase (Ltb4dh), which was upregulated following 24 h exposure to 63-81 mg IB l(-1). Conclusions: As anticipated, use of the NF clarified the response of Ltb4dh in daphnids exposed to sublethal levels of ibuprofen. Our findings emphasise the importance in toxicogenomics of finding and applying invariant internal QPCR control(s) relevant to the study conditions

The biomechanics of amnion rupture: an X-ray diffraction study

Pre-term birth is the leading cause of perinatal and neonatal mortality, 40% of which are attributed to the pre-term premature rupture of amnion. Rupture of amnion is thought to be associated with a corresponding decrease in the extracellular collagen content and/or increase in collagenase activity. However, there is very little information concerning the detailed organisation of fibrillar collagen in amnion and how this might influence rupture. Here we identify a loss of lattice like arrangement in collagen organisation from areas near to the rupture site, and present a 9% increase in fibril spacing and a 50% decrease in fibrillar organisation using quantitative measurements gained by transmission electron microscopy and the novel application of synchrotron X-ray diffraction. These data provide an accurate insight into the biomechanical process of amnion rupture and highlight X-ray diffraction as a new and powerful tool in our understanding of this process

Linking mechanistic and behavioral responses to sublethal esfenvalerate exposure in the endangered delta smelt; Hypomesus transpacificus (Fam. Osmeridae)

<p>Abstract</p> <p>Background</p> <p>The delta smelt (<it>Hypomesus transpacificus</it>) is a pelagic fish species listed as endangered under both the USA Federal and Californian State Endangered Species Acts and considered an indicator of ecosystem health in its habitat range, which is limited to the Sacramento-San Joaquin estuary in California, USA. Anthropogenic contaminants are one of multiple stressors affecting this system, and among them, current-use insecticides are of major concern. Interrogative tools are required to successfully monitor effects of contaminants on the delta smelt, and to research potential causes of population decline in this species. We have created a microarray to investigate genome-wide effects of potentially causative stressors, and applied this tool to assess effects of the pyrethroid insecticide esfenvalerate on larval delta smelt. Selected genes were further investigated as molecular biomarkers using quantitative PCR analyses.</p> <p>Results</p> <p>Exposure to esfenvalerate affected swimming behavior of larval delta smelt at concentrations as low as 0.0625 μg.L^-1, and significant differences in expression were measured in genes involved in neuromuscular activity. Alterations in the expression of genes associated with immune responses, along with apoptosis, redox, osmotic stress, detoxification, and growth and development appear to have been invoked by esfenvalerate exposure. Swimming impairment correlated significantly with expression of aspartoacylase (ASPA), an enzyme involved in brain cell function and associated with numerous human diseases. Selected genes were investigated for their use as molecular biomarkers, and strong links were determined between measured downregulation in ASPA and observed behavioral responses in fish exposed to environmentally relevant pyrethroid concentrations.</p> <p>Conclusions</p> <p>The results of this study show that microarray technology is a useful approach in screening for, and generation of molecular biomarkers in endangered, non-model organisms, identifying specific genes that can be directly linked with sublethal toxicological endpoints; such as changes in expression levels of neuromuscular genes resulting in measurable swimming impairments. The developed microarrays were successfully applied on larval fish exposed to esfenvalerate, a known contaminant of the Sacramento-San Joaquin estuary, and has permitted the identification of specific biomarkers which could provide insight into the factors contributing to delta smelt population decline.</p

Astrocyte-derived vascular endothelial growth factor stabilizes vessels in the developing retinal vasculature.

Vascular endothelial growth factor (VEGF) plays a critical role in normal development as well as retinal vasculature disease. During retinal vascularization, VEGF is most strongly expressed by not yet vascularized retinal astrocytes, but also by retinal astrocytes within the developing vascular plexus, suggesting a role for retinal astrocyte-derived VEGF in angiogenesis and vessel network maturation. To test the role of astrocyte-derived VEGF, we used Cre-lox technology in mice to delete VEGF in retinal astrocytes during development. Surprisingly, this only had a minor impact on retinal vasculature development, with only small decreases in plexus spreading, endothelial cell proliferation and survival observed. In contrast, astrocyte VEGF deletion had more pronounced effects on hyperoxia-induced vaso-obliteration and led to the regression of smooth muscle cell-coated radial arteries and veins, which are usually resistant to the vessel-collapsing effects of hyperoxia. These results suggest that VEGF production from retinal astrocytes is relatively dispensable during development, but performs vessel stabilizing functions in the retinal vasculature and might be relevant for retinopathy of prematurity in humans

Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna

Background: Ibuprofen and other nonsteroidal anti-inflammatory drugs have been designed to interrupt eicosanoid metabolism in mammals, but little is known of how they affect nontarget organisms. Here we report a systems biology study that simultaneously describes the transcriptomic and phenotypic stress responses of the model crustacean Daphnia magna after exposure to ibuprofen. Results: Our findings reveal intriguing similarities in the mode of action of ibuprofen between vertebrates and invertebrates, and they suggest that ibuprofen has a targeted impact on reproduction at the molecular, organismal, and population level in daphnids. Microarray expression and temporal real-time quantitative PCR profiles of key genes suggest early ibuprofen interruption of crustacean eicosanoid metabolism, which appears to disrupt signal transduction affecting juvenile hormone metabolism and oogenesis. Conclusion: Combining molecular and organismal stress responses provides a guide to possible chronic consequences of environmental stress for population health. This could improve current environmental risk assessment by providing an early indication of the need for higher tier testing. Our study demonstrates the advantages of a systems approach to stress ecology, in which Daphnia will probably play a major role

High-dispersion absorption-line spectroscopy of AE Aqr

High-dispersion time-resolved spectroscopy of the unique magnetic cataclysmic variable AE Aqr is presented. A radial velocity analysis of the absorption lines yields K2= 168.7 ± 1 km s−1. Substantial deviations of the radial velocity curve from a sinusoid are interpreted in terms of intensity variations over the secondary star's surface. A complex rotational velocity curve as a function of orbital phase is detected which has a modulation frequency of twice the orbital frequency, leading to an estimate of the binary inclination angle that is close to 70°. The minimum and maximum rotational velocities are used to indirectly derive a mass ratio of q= 0.6 and a radial velocity semi-amplitude of the white dwarf of K1= 101 ± 3 km s−1. We present an atmospheric temperature indicator, based on the absorption-line ratio of Fe I and Cr I lines, whose variation indicates that the secondary star varies from K0 to K4 as a function of orbital phase. The ephemeris of the system has been revised, using more than 1000 radial velocity measurements, published over nearly five decades. From the derived radial velocity semi-amplitudes and the estimated inclination angle, we calculate that the masses of the stars are M1= 0.63 ± 0.05 M⊙; M2= 0.37 ± 0.04 M⊙, and their separation is a= 2.33 ± 0.02 R⊙. Our analysis indicates the presence of a late-type star whose radius is larger, by a factor of nearly 2, than the radius of a normal main-sequence star of the same mass. Finally, we discuss the possibility that the measured variations in the rotational velocity, temperature and spectral type of the secondary star as functions of orbital phase may, like the radial velocity variations, be attributable to regions of enhanced absorption on the star's surface