Effects of formalin preservation on stable carbon and nitrogen isotope signatures in Calanoid copepods: implications for the use of Continuous Plankton Recorder Survey samples in stable isotope analyses

Preserved and archived organic material offers huge potential for the conduct of retrospective and long-term historical ecosystem reconstructions using stable isotope analyses, but because of isotopic exchange with preservatives the obtained values require validation. The Continuous Plankton Recorder (CPR) Survey is the most extensive long-term monitoring program for plankton communities worldwide and has utilised ships of opportunity to collect samples since 1931. To keep the samples intact for subsequent analysis, they are collected and preserved in formalin; however, previous studies have found that this may alter stable carbon and nitrogen isotope ratios in zooplankton. A maximum ~0.9‰ increase of δ15N and a time dependent maximum ~1.0‰ decrease of δ13C were observed when the copepod, Calanus helgolandicus, was experimentally exposed to two formalin preservatives for 12 months. Applying specific correction factors to δ15N and δ13C values for similarly preserved Calanoid species collected by the CPR Survey within 12 months of analysis may be appropriate to enable their use in stable isotope studies. The isotope values of samples stored frozen did not differ significantly from those of controls. Although the impact of formalin preservation was relatively small in this and other studies of marine zooplankton, changes in isotope signatures are not consistent across taxa, especially for δ15N, indicating that species-specific studies may be required. Copyright © 2011 John Wiley & Sons, Ltd.

Time signatures of impulsively generated coronal fast wave trains

Impulsively generated short-period fast magneto-acoustic wave trains, guided by solar and stellar coronal loops, are numerically modelled. In the developed stage of the evolution, the wave trains have a characteristic quasi-periodic signature. The quasi-periodicity results from the geometrical dispersion of the guided fast modes, determined by the transverse profile of the loop. A typical feature of the signature is a tadpole wavelet Spectrum: a narrow-spectrum tail precedes a broad-band head. The instantaneous period of the oscillations in the wave train decreases gradually with time. The period and the spectral amplitude evolution are shown to be determined by the steepness of the transverse density profile and the density contrast ratio in the loop. The propagating wave trains recently discovered with the Solar Eclipse Coronal Imaging System (SECIS) instrument are noted to have similar wavelet spectral features, which strengthens the interpretation of SECIS results as guided fast wave trains.

The first polarimetric signatures of infrared jets in X-ray binaries

We present near-infrared linear spectropolarimetry of a sample of persistent X-ray binaries, Sco X-1, Cyg X-2, and GRS 1915+105. The slopes of the spectra are shallower than what is expected from a standard steady state accretion disk, and can be explained if the near-infrared flux contains a contribution from an optically thin jet. For the neutron star systems, Sco X-1 and Cyg X-2, the polarization levels at 2.4 mu m are 1.3% +/- 0.10% and 5.4% +/- 0.7%, respectively, which is greater than the polarization level at 1.65 mu m. This cannot be explained by interstellar polarization or electron scattering in the anisotropic environment of the accretion flow. We propose that the most likely explanation is that this is the polarimetric signature of synchrotron emission arising from close to the base of the jets in these systems. In the black hole system GRS 1915+105 the observed polarization, although high (5.0% +/- 1.2% at 2.4 mu m), may be consistent with interstellar polarization. For Sco X-1 the position angle of the radio jet on the sky is approximately perpendicular to the near-infrared position angle (electric vector), suggesting that the magnetic field is aligned with the jet. These observations may be a first step toward probing the ordering, alignment, and variability of the outflow magnetic field in a region closer to the central accreting object than is observed in the radio band.

sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background
Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures.

Results
This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies.

Conclusion
The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Background

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene expression profile. Lamb et al first proposed the Connectivity Map [Lamb et al (2006), Science 313, 1929–1935] to make successful connections among small molecules, genes, and diseases using genomic signatures.

Results

Here we have built on the principles of the Connectivity Map to present a simpler and more robust method for the construction of reference gene-expression profiles and for the connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with two randomly generated gene signatures and three experimentally derived gene signatures (for HDAC inhibitors, estrogens, and immunosuppressive drugs, respectively). Our testing with this method indicates that it achieves a higher level of specificity and sensitivity and so advances the original method.

Conclusion

The method presented here not only offers more principled statistical procedures for testing connections, but more importantly it provides effective safeguard against false connections at the same time achieving increased sensitivity. With its robust performance, the method has potential use in the drug development pipeline for the early recognition of pharmacological and toxicological properties in chemicals and new drug candidates, and also more broadly in other 'omics sciences.

Polarimetric signatures of infrared jets in X-ray binaries

We present near-infrared linear spectropolarimetry of a sample of persistent X-ray binaries, Sco X-1, Cyg X-2 and GRS 1915+105. For Sco X-1 and Cyg X-2, the polarization levels at 2.4 µm are 1.3+/-0.10% and 5.4+/-0.7%, respectively, which is greater than the polarization level at 1.65 µm. This cannot be explained by interstellar polarization or electron scattering in the anisotropic environment of the accretion flow. We propose that the most likely explanation is that this is the polarimetric signature of synchrotron emission arising from close to the base of the jet. For Sco X-1 the position angle of the radio jet on the sky is approximately perpendicular to the near-infrared position angle (electric vector), suggesting that the magnetic field is aligned with the jet. These observations may be a first step towards probing the ordering, alignment, and variability of the outflow magnetic field, in a region closer to the central accreting object than is observed in the radio band.

Spectral induced polarization signatures of abiotic FeS precipitation

In recent years, geophysical methods have been shown to be sensitive to microbial-induced mineralization processes. The spectral induced-polarization (SIP) method appears to be very promising for monitoring mineralization and microbial processes. With this work, we study the links of mineralization and SIP signals, in the absence of microbial activity. We recorded the SIP response during abiotic FeS precipitation. We show that the SIP signals are diagnostic of FeS mineralization and can be differentiated from SIP signals from biomineralization processes. More specifically, the imaginary conductivity shows almost linear dependence on the amount of FeS precipitating out of solution, above the threshold value 0.006 gr under our experimental conditions. This research has direct implications for the use of the SIP method as a monitoring and decision-making tool for sustainable remediation of metals in contaminated soils and groundwater.