The cold‐water climate shield: delineating refugia for preserving salmonid fishes through the 21st century

The distribution and future fate of ectothermic organisms in a warming world will be dictated by thermalscapes across landscapes. That is particularly true for stream fishes and cold‐water species like trout, salmon, and char that are already constrained to high elevations and latitudes. The extreme climates in those environments also preclude invasions by most non‐native species, so identifying especially cold habitats capable of absorbing future climate change while still supporting native populations would highlight important refugia. By coupling crowd‐sourced biological datasets with high‐resolution stream temperature scenarios, we delineate network refugia across >250 000 stream km in the Northern Rocky Mountains for two native salmonids—bull trout (BT) and cutthroat trout (CT). Under both moderate and extreme climate change scenarios, refugia with high probabilities of trout population occupancy (>0.9) were predicted to exist (33–68 BT refugia; 917–1425 CT refugia). Most refugia are on public lands (>90%) where few currently have protected status in National Parks or Wilderness Areas (<15%). Forecasts of refuge locations could enable protection of key watersheds and provide a foundation for climate smart planning of conservation networks. Using cold water as a ‘climate shield’ is generalizable to other species and geographic areas because it has a strong physiological basis, relies on nationally available geospatial data, and mines existing biological datasets. Importantly, the approach creates a framework to integrate data contributed by many individuals and resource agencies, and a process that strengthens the collaborative and social networks needed to preserve many cold‐water fish populations through the 21st century.     

Aromatic ring cleavage by homoprotocatechuate 2,3-dioxygenase: role of His200 in the kinetics of interconversion of reaction cycle intermediates

Homoprotocatechuate 2,3-dioxygenase (WT 2,3-HPCD) isolated from Brevibacterium fuscum utilizes an active site Fe(II) and O(2) to catalyze proximal extradiol cleavage of the aromatic ring of the substrate (HPCA). Here, the conserved active site residue His200 is changed to Gln, Glu, Ala, Asn, and Phe, and the reactions of the mutant enzymes are probed using steady-state and transient kinetic techniques. Each mutant catalyzes ring cleavage of HPCA to yield the normal product. H200Q and H200N retain 30-40% of the WT 2,3-HPCD activity at 24 degrees C, but the other mutants reduce the k(cat) to less than 9% of normal. The origin of the reduced activity is unlikely to be the substrate binding phase of the catalytic cycle, because the multistep anaerobic binding reaction of the chromophoric substrate 4-nitrocatechol (4NC) is shown to proceed with rate constants similar to those observed for WT 2,3-HPCD. In contrast, the rate constants of several steps in the multistep O(2) binding/insertion and product release half of the reaction cycle are substantially slowed, in particular the steps in which activated oxygen attacks the organic substrate and in which product is released. In the case of the H200N mutant, the product of 4NC oxidation is not the usual ring cleavage product, but rather the 4NC quinone. These results suggest that the main role of His200 is in facilitating the steps in the second half of the reaction cycle. The decreased rate constants for the O(2) insertion steps in the catalytic cycles of the mutant enzymes allow the oxygen adduct of an extradiol dioxygenase to be detected for the first time.     

Predicting patch occupancy in fragmented landscapes at the rangewide scale for an endangered species: an example of an American warbler

AIM: Our objective was to identify the distribution of the endangered golden-cheeked warbler (Setophaga chrysoparia) in fragmented oak-juniper woodlands by applying a geoadditive semiparametric occupancy model to better assist decision-makers in identifying suitable habitat across the species breeding range on which conservation or mitigation activities can be focused and thus prioritize management and conservation planning. LOCATION: Texas, USA. METHODS: We used repeated double-observer detection/non-detection surveys of randomly selected (n = 287) patches of potential habitat to evaluate warbler patch-scale presence across the species breeding range. We used a geoadditive semiparametric occupancy model with remotely sensed habitat metrics (patch size and landscape composition) to predict patch-scale occupancy of golden-cheeked warblers in the fragmented oak-juniper woodlands of central Texas, USA. RESULTS: Our spatially explicit model indicated that golden-cheeked warbler patch occupancy declined from south to north within the breeding range concomitant with reductions in the availability of large habitat patches. We found that 59% of woodland patches, primarily in the northern and central portions of the warbler's range, were predicted to have occupancy probabilities ≤0.10 with only 3% of patches predicted to have occupancy probabilities >0.90. Our model exhibited high prediction accuracy (area under curve = 0.91) when validated using independently collected warbler occurrence data. MAIN CONCLUSIONS: We have identified a distinct spatial occurrence gradient for golden-cheeked warblers as well as a relationship between two measurable landscape characteristics. Because habitat-occupancy relationships were key drivers of our model, our results can be used to identify potential areas where conservation actions supporting habitat mitigation can occur and identify areas where conservation of future potential habitat is possible. Additionally, our results can be used to focus resources on maintenance and creation of patches that are more likely to harbour viable local warbler populations.     

Lipid composition of deep-sea hydrothermal vent tubeworm Riftia pachyptila, crabs Munidopsis subsquamosa and Bythograea thermydron, mussels Bathymodiolus sp. and limpets Lepetodrilus spp

Lipid composition was determined for hydrothermal vent species collected by the Deep Submergence Vehicle ALVIN from chimneys at 2,500 m depth on the East Pacific Rise. These are the first lipid biomarker studies for most of these species. Lipid content was low and dominated by polar lipid in the vestimentiferan tubeworm Riftia pachyptila, mussels Bathymodiolus sp. and limpets Lepetodrilus spp. The galatheid (Munidopsis subsquamosa) and most brachyuran adult (Bythograea thermydron) crabs were characterized by higher storage lipid (triacylglycerol). Total polyunsaturated fatty acids were similar in R. pachyptila plume and body, but higher in the posterior part of the soft body, which had more docosahexaenoic acid (2-5% of total FA) compared to the anterior and plume (< or =0.3%). Two sulphur-oxidizing bacterial markers, 16:1(n-7)c and 18:1(n-7)c, were high in R. pachyptila and mussel (up to 23%), but lower in both crab species (4-17%). R. pachyptila had greater nonmethylene interrupted diunsaturated fatty acids (8-13%) than all other species (2-8%). R. pachyptila may desaturate and elongate 18:1(n-7)c to obtain essential polyunsaturated fatty acids 20:5(n-3) and 20:4(n-6). The sterol composition of R. pachyptila included similar amounts of cholesterol and desmosterol, whereas the other species had a more diverse sterol composition. These differences in lipids, fatty acids and sterols reflect diverse nutritional strategies and possibly temperature regimes in these species.     

Single-turnover kinetics of homoprotocatechuate 2,3-dioxygenase

Homoprotocatechuate 2,3-dioxygenase isolated from Brevibacterium fuscum utilizes an active site Fe(II) and O(2) to catalyze proximal extradiol cleavage of the substrate aromatic ring. In contrast to other members of the ring cleaving dioxygenase family, the transient kinetics of the extradiol dioxygenase catalytic cycle have been difficult to study because the iron is nearly colorless and EPR silent. Here, it is shown that the reaction cycle kinetics can be monitored by utilizing the alternative substrate 4-nitrocatechol (4NC), which is also cleaved in the proximal extradiol position. Changes in the optical spectrum of 4NC occurring as a result of ionization, environmental changes, and ring cleavage allow both the substrate binding and product formation phases of the reaction to be studied. It is shown that substrate binding occurs in a four-step process probably involving binding to two ionization states of the enzyme at different rates. Following an initial rapid binding of the monoanionic 4NC in the active site, slower binding to the Fe(II) and conversion to the dianionic form occur. The bound dianionic 4NC reacts rapidly with O(2) in four additional steps, apparently occurring in sequence. On the basis of the optical properties of the intermediates, these steps are hypothesized to be O(2) binding to the iron, isomerization of the resulting complex, ring opening, and product release. The natural substrate appears to form the same intermediates but with much larger rate constants. These are the first transient intermediates to be reported for an extradiol dioxygenase reaction.     

Hydrogen Peroxide Sensitivity of Catechol-2,3-Dioxygenase: a Cautionary Note on Use of xylE Reporter Fusions under Aerobic Conditions

Catechol-2,3-dioxygenase (C23O) of Pseudomonas putida, encoded by the xylE gene, was found to be sensitive to hydrogen peroxide (H₂O₂) when used as a reporter in gene fusion constructs. Exposure of Pseudomonas aeruginosa katA or katA katB mutants harboring katA- or katB-lacZ (encoding β-galactosidase) or -xylE fusion plasmids to H₂O₂ stimulated β-galactosidase activity, while there was little or no detectable C23O activity in these strains. More than 95% of C23O activity was lost after a 5-min exposure to equimolar H₂O₂, while a 10,000-fold excess was required for similar inhibition of β-galactosidase. Electron paramagnetic resonance spectra of the nitrosyl complexes of C23O showed that H₂O₂ nearly stoichiometrically oxidized the essential active-site ferrous ion, thus accounting for the loss of activity. Our results suggest using caution in interpreting data derived from xylE reporter fusions under aerobic conditions, especially where oxidative stress is present or when catalase-deficient strains are used.     

Estimating breeding season abundance of golden-cheeked warblers in Texas,USA

Population abundance estimates using predictive models are important for describing habitat use and responses to population-level impacts, evaluating conservation status of a species, and for establishing monitoring programs. The golden-cheeked warbler (Setophaga chrysoparia) is a neotropical migratory bird that was listed as federally endangered in 1990 because of threats related to loss and fragmentation of its woodland habitat. Since listing, abundance estimates for the species have mainly relied on localized population studies on public lands and qualitative-based methods. Our goal was to estimate breeding population size of male warblers using a predictive model based on metrics for patches of woodland habitat throughout the species' breeding range. We first conducted occupancy surveys to determine range-wide distribution. We then conducted standard point-count surveys on a subset of the initial sampling locations to estimate density of males. Mean observed patch-specific density was 0.23 males/ha (95% CI = 0.197–0.252, n = 301). We modeled the relationship between patch-specific density of males and woodland patch characteristics (size and landscape composition) and predicted patch occupancy. The probability of patch occupancy, derived from a model that used patch size and landscape composition as predictor variables while addressing effects of spatial relatedness, best predicted patch-specific density. We predicted patch-specific densities as a function of occupancy probability and estimated abundance of male warblers across 63,616 woodland patches accounting for 1.678 million ha of potential warbler habitat. Using a Monte Carlo simulation, our approach yielded a range-wide male warbler population estimate of 263,339 (95% CI: 223,927–302,620). Our results provide the first abundance estimate using habitat and count data from a sampling design focused on range-wide inference. Managers can use the resulting model as a tool to support conservation planning and guide recovery efforts. © 2012 The Wildlife Society.     

Is Qualitative Research Second Class Science? A Quantitative Longitudinal Examination of Qualitative Research in Medical Journals

Background

Qualitative research appears to be gaining acceptability in medical journals. Yet, little is actually known about the proportion of qualitative research and factors affecting its publication. This study describes the proportion of qualitative research over a 10 year period and correlates associated with its publication.

Design

A quantitative longitudinal examination of the proportion of original qualitative research in 67 journals of general medicine during a 10 year period (1998–2007). The proportion of qualitative research was determined by dividing original qualitative studies published (numerator) by all original research articles published (denominator). We used a generalized estimating equations approach to assess the longitudinal association between the proportion of qualitative studies and independent variables (i.e. journals'' country of publication and impact factor; editorial/methodological papers discussing qualitative research; and specific journal guidelines pertaining to qualitative research).

Findings

A 2.9% absolute increase and 3.4-fold relative increase in qualitative research publications occurred over a 10 year period (1.2% in 1998 vs. 4.1% in 2007). The proportion of original qualitative research was independently and significantly associated with the publication of editorial/methodological papers in the journal (b = 3.688, P = 0.012); and with qualitative research specifically mentioned in guidelines for authors (b = 6.847, P<0.001). Additionally, a higher proportion of qualitative research was associated only with journals published in the UK in comparison to other countries, yet with borderline statistical significance (b = 1.776, P = 0.075). The journals'' impact factor was not associated with the publication of qualitative research.

Conclusions

Despite an increase in the proportion of qualitative research in medical journals over a 10 year period, the proportion remains low. Journals'' policies pertaining to qualitative research, as expressed by the appearance of specific guidelines and editorials/methodological papers on the subject, are independently associated with the publication of original qualitative research; irrespective of the journals'' impact factor.