Ecological Aspects of a Wood Turtle, Glyptemys insculpta, Population at the Northern Limit of its Range in Québec

As part of a conservation research initiative, a population of Wood Turtles (Glyptemys insculpta) at the northern limit of its range was studied to ascertain characteristics of its demographics, morphometrics, density, mortality, feeding, and mating activities. Turtles were captured and marked during the activity period in 1996 and 1997. In addition, 20 individuals were radio-tracked weekly. A total of 188 turtles was captured and the size of the population in the study area was estimated at 238 turtles. The estimated population density based on this calculation is 0.44 turtles/ha. This is less than other studies indicating that population densities are greater in southern populations. Turtles from this population were large (carapace length of males=214.5 ± 4.21 mm, females=201.1 ± 10.88 mm) which supports the hypothesis that turtle size is negatively correlated with number of frost free days. The sex ratio was not significantly different from 1:1. Juvenile turtles accounted for 31.4% of the population. Observations of feeding habits support the claim that Wood Turtles are opportunistic omnivores. Of the 35 mating or courtship events observed, 77 % occurred in the fall and half of them between 11:00 and 13:00. Although limb and tail injuries and parasites were observed on many turtles, no dead turtles were observed. This last result, combined with the high rate of recruitment and even sex ratio suggests that this population is stable, making it an ideal population with which to make comparisons with other studies in areas where the species could be in decline

The Brazilian Tunable Filter Imager for the SOAR telescope

This paper presents a new Tunable Filter Instrument for the SOAR telescope. The Brazilian Tunable Filter Imager (BTFI) is a versatile, new technology, tunable optical imager to be used in seeing-limited mode and at higher spatial fidelity using the SAM Ground-Layer Adaptive Optics facility at the SOAR telescope. The instrument opens important new science capabilities for the SOAR community, from studies of the centers of nearby galaxies and the insterstellar medium to statistical cosmological investigations. The BTFI takes advantage of three new technologies. The imaging Bragg Tunable Filter concept utilizes Volume Phase Holographic Gratings in a double-pass configuration, as a tunable filter, while a new Fabry-Perot (FP) concept involves technologies which allow a single FP etalon to act over a large range of interference orders and spectral resolutions. Both technologies will be in the same instrument. Spectral resolutions spanning the range between 25 and 30,000 can be achieved through the use of iBTF at low resolution and scanning FPs beyond R ~2,000. The third new technologies in BTFI is the use of EMCCDs for rapid and cyclically wavelength scanning thus mitigating the damaging effect of atmospheric variability through data acquisition. An additional important feature of the instrument is that it has two optical channels which allow for the simultaneous recording of the narrow-band, filtered image with the remaining (complementary) broad-band light. This avoids the uncertainties inherent in tunable filter imaging using a single detector. The system was designed to supply tunable filter imaging with a field-of-view of 3 arcmin on a side, sampled at 0.12" for direct Nasmyth seeing-limited area spectroscopy and for SAM's visitor instrument port for GLAO-fed area spectroscopy. The instrument has seen first light, as a SOAR visitor instrument. It is now in comissioning phase.Comment: accepted in PAS

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The mexEF-oprN multidrug efflux operon of P. aeruginosa: regulation by the MexT activator in response to nitrosative stress and chloramphenicol

A null mutation in the mexS gene of P. aeruginosa yielded increased expression of a 3-gene operon containing a gene, xenB, whose product is highly homologous to a xenobiotic reductase in Pseudomonas fluorescens shown to remove nitro groups from trinitrotouleune and nitroglycerin (Blehert, D.S. et al. 1999. J. Bacteriol. 181:6254). This expression, which paralleled an increase in mexEF-oprN expression in the same mutant, was, like mexEF-oprN, dependent on the MexT LysR-family positive regulator previously implicated in mexEF-oprN expression. As nitrosation is a well-known product of nitrosative stress, a role of xenB (and the co-regulated mexEF-oprN) in a nitrosative stress response was hypothesized and tested. Using s-nitrosoglutathione (GSNO) as a source of nitrosative stress, expression of xenB and mexEF-oprN was shown to be GSNO-inducible, though in the case of xenB this was only seen in a mutant lacking MexEF-OprN. In both instances this GSNO-inducible expression was dependent upon MexT. The mexS gene encoding a probable oxidoreductase was also inducible by GSNO though, again, only in the absence of MexEF-OprN. Expression of the OprD outer membrane amino acid/peptide porin gene that is characteristically inversely regulated with mexEF-oprN in nfxC and mexS mutants was reduced in the presence of GSNO, though this was independent of MexT. Chloramphenicol, a nitroaromatic antimicrobial that is a substrate for MexEF-OprN was shown to induce mexEF-oprN, but not xenB or mexS, possibly because it resembles a nitrosated nitrosative stress product accommodated by MexEF-OprN. Again, this was dependent upon the MexT regulator

Continuous porosity characterization : metric-scale intervals in heterogeneous sedimentary rocks using medical CT-scanner

Although computed tomography (CT-Scanning) has been regularly applied to core analyses in petroleum geology, there is still a need to improve our ways to document porosity and porosity distribution in the entire pore scale spectrum, from the tens of nanometer to the meter-scale. Porosity imaging is particularly crucial for complex and heterogeneous rocks such as hydrothermally altered and fractured carbonates. The present work proposes an improved method using medical-CT to reliably estimate reservoir porosity. An in-house core-flooding setup allowed to analyse several individual core samples, scanned simultaneously (dry and saturated), as well as continuous core sections up to 1.5 m long. Without any prior knowledge of samples, three-dimensional alignment and subtraction of the two data sets (dry and saturated states) results in the generation of 3D porosity matrices. The methodology tested on a large set of reference core material shows a strong correlation between conventional gas porosimetry techniques and porosity from CT-scan. The added value of the porosity measurements by CT-scan is, first of all, the generation of 3D images of pore network, allowing to assess spatial attributes of macropores, their distribution and connectivity. Secondly, the CT-scan method also provides continuous porosity profile at the millimetric scale. Both developments are crucial for the understanding of reservoir rock properties

Protein Modulator of Multidrug Efflux Gene Expression in Pseudomonas aeruginosa▿

nalC multidrug-resistant mutants of Pseudomonas aeruginosa show enhanced expression of the mexAB-oprM multidrug efflux system as a direct result of the production of a ca. 6,100-Da protein, PA3719, in these mutants. Using a bacterial two-hybrid system, PA3719 was shown to interact in vivo with MexR, a repressor of mexAB-oprM expression. Isothermal titration calorimetry (ITC) studies confirmed a high-affinity interaction (equilibrium dissociation constant [KD], 158.0 ± 18.1 nM) of PA3719 with MexR in vitro. PA3719 binding to and formation of a complex with MexR obviated repressor binding to its operator, which overlaps the efflux operon promoter, suggesting that mexAB-oprM hyperexpression in nalC mutants results from PA3719 modulation of MexR repressor activity. Consistent with this, MexR repression of mexA transcription in an in vitro transcription assay was alleviated by PA3719. Mutations in MexR compromising its interaction with PA3719 in vivo were isolated and shown to be located internally and distributed throughout the protein, suggesting that they impacted PA3719 binding by altering MexR structure or conformation rather than by having residues interacting specifically with PA3719. Four of six mutant MexR proteins studied retained repressor activity even in a nalC strain producing PA3719. Again, this is consistent with a PA3719 interaction with MexR being necessary to obviate MexR repressor activity. The gene encoding PA3719 has thus been renamed armR (antirepressor for MexR). A representative “noninteracting” mutant MexR protein, MexRI104F, was purified, and ITC confirmed that it bound PA3719 with reduced affinity (5.4-fold reduced; KD, 853.2 ± 151.1 nM). Consistent with this, MexRI104F repressor activity, as assessed using the in vitro transcription assay, was only weakly compromised by PA3719. Finally, two mutations (L36P and W45A) in ArmR compromising its interaction with MexR have been isolated and mapped to a putative C-terminal α-helix of the protein that alone is sufficient for interaction with MexR

Role of the AcrAB-TolC efflux pump in determining susceptibility of Haemophilus influenzae to the novel peptide deformylase inhibitor LBM415.

Haemophilus influenzae isolates vary widely in their susceptibilities to the peptide deformylase inhibitor LBM415 (MIC range, 0.06 to 32 microg/ml); however, on average, they are less susceptible than gram-positive organisms, such as Staphylococcus aureus and Streptococcus pneumoniae. Insertional inactivation of the H. influenzae acrB or tolC gene in strain NB65044 (Rd strain KW20) increased susceptibility to LBM415, confirming a role for the AcrAB-TolC pump in determining resistance. Consistent with this, sequencing of a PCR fragment generated with primers flanking the acrRA region from an LBM415-hypersusceptible H. influenzae clinical isolate revealed a genetic deletion of acrA. Inactivation of acrB or tolC in several clinical isolates with atypically reduced susceptibility to LBM415 (MIC of 16 microg/ml or greater) significantly increased susceptibility, confirming that the pump is also a determinant of decreased susceptibility in these clinical isolates. Examination of acrR, encoding the putative repressor of pump gene expression, from several of these strains revealed mutations introducing frameshifts, stop codons, and amino acid changes relative to the published sequence, suggesting that loss of pump repression leads to decreased susceptibility. Supporting this, NB65044 acrR mutants selected by exposure to LBM415 at 8 microg/ml had susceptibilities to LBM415 and other pump substrates comparable to the least sensitive clinical isolates and showed increased expression of pump genes