Large-scale variations in ozone and polar stratospheric clouds measured with airborne lidar during formation of the 1987 ozone hole over Antarctica

A joint field experiment between NASA and NOAA was conducted during August to September 1987 to obtain in situ and remote measurements of key gases and aerosols from aircraft platforms during the formation of the ozone (O3) hole over Antarctica. The ER-2 (advanced U-2) and DC-8 aircraft from the NASA Ames Research Center were used in this field experiment. The NASA Langley Research Center's airborne differential absorption lidar (DIAL) system was operated from the DC-8 to obtain profiles of O3 and polar stratospheric clouds in the lower stratosphere during long-range flights over Antarctica from August 28 to September 29, 1987. The airborne DIAL system was configured to transmit simultaneously four laser wavelengths (301, 311, 622, and 1064 nm) above the DC-8 for DIAL measurements of O3 profiles between 11 to 20 km ASL (geometric altitude above sea level) and multiple wavelength aerosol backscatter measurements between 11 to 24 km ASL. A total of 13 DC-8 flights were made over Antarctica with 2 flights reaching the South Pole. Polar stratospheric clouds (PSC's) were detected in multiple thin layers in the 11 to 21 km ASL altitude range with each layer having a typical thickness of less than 1 km. Two types of PSC's were found based on aerosol backscattering ratios: predominantly water ice clouds (type 2) and clouds with scattering characteristics consistent with binary solid nitric acid/water clouds (type 1). Large-scale cross sections of O3 distributions were obtained. The data provides additional information about a potentially important transport mechanism that may influence the O3 budget inside the vortex. There is also some evidence that strong low pressure systems in the troposphere are associated with regions of lower stratospheric O3. This paper discusses the spatial and temporal variations of O3 inside and outside the polar vortex region during the development of the O3 hole and relates these data to other measurements obtained during this field experiment

Use of short-tandem repeat (STR) fingerprinting to validate sample origins in hepatitis C virus molecular epidemiology studies

Sequence analysis is used to define the molecular epidemiology and evolution of the hepatitis C virus. Whilst most studies have shown that individual patients harbour viruses that are derived from a limited number of highly related strains, some recent reports have shown that some patients can be co-infected with very distinct variants whose frequency can fluctuate greatly. Whilst co-infection with highly divergent strains is possible, an alternative explanation is that such data represent contamination or sample mix-up. In this study, we have shown that DNA fingerprinting techniques can accurately assess sample provenance and differentiate between samples that are truly exhibiting mixed infection from those that harbour distinct virus populations due to sample mix-up. We have argued that this approach should be adopted routinely in virus sequence analyses to validate sample provenance

Maximum Running Speed of Captive Bar-Headed Geese Is Unaffected by Severe Hypoxia

While bar-headed geese are renowned for migration at high altitude over the Himalayas, previous work on captive birds suggested that these geese are unable to maintain rates of oxygen consumption while running in severely hypoxic conditions. To investigate this paradox, we re-examined the running performance and heart rates of bar-headed geese and barnacle geese (a low altitude species) during exercise in hypoxia. Bar-headed geese (n = 7) were able to run at maximum speeds (determined in normoxia) for 15 minutes in severe hypoxia (7% O2; simulating the hypoxia at 8500 m) with mean heart rates of 466±8 beats min−1. Barnacle geese (n = 10), on the other hand, were unable to complete similar trials in severe hypoxia and their mean heart rate (316 beats.min−1) was significantly lower than bar-headed geese. In bar-headed geese, partial pressures of oxygen and carbon dioxide in both arterial and mixed venous blood were significantly lower during hypoxia than normoxia, both at rest and while running. However, measurements of blood lactate in bar-headed geese suggested that anaerobic metabolism was not a major energy source during running in hypoxia. We combined these data with values taken from the literature to estimate (i) oxygen supply, using the Fick equation and (ii) oxygen demand using aerodynamic theory for bar-headed geese flying aerobically, and under their own power, at altitude. This analysis predicts that the maximum altitude at which geese can transport enough oxygen to fly without environmental assistance ranges from 6,800 m to 8,900 m altitude, depending on the parameters used in the model but that such flights should be rare

Sources of Nonnative Centrarchids in the Upper Colorado River Revealed by Stable Isotope and Microchemical Analyses of Otoliths

Nonnative fishes represent a significant impediment to the recovery of imperiled fishes, including those endemic to the Colorado River in the southwestern United States. Efforts to control nonindigenous fish abundance in the upper Colorado River basin have been unsuccessful owing in part to lack of knowledge regarding nonnative fish recruitment sources. We determined the source habitat (floodplain pond versus riverine habitats) for nonnative centrarchid fishes (largemouth bass Micropterus salmoides, green sunfish Lepomis cyanellus, bluegill L. macrochirus, and black crappie Pomoxis nigromaculatus) in the upper Colorado River using stable hydrogen isotopic composition (δD) and strontium:calcium (Sr:Ca) ratios in fish otoliths as natural markers of environmental history. Stable hydrogen isotope analysis revealed that 59% of centrarchids exhibited the otolith core signatures expected for riverine-origin fish, while 22% had emigrated from floodplain ponds and 19% were of uncertain origin. Strontium:calcium ratio data were consistent with the δD assays and indicated that relatively few fish immigrated to the river from high-salinity habitats. Black crappie was the only species that originated primarily from floodplain ponds. Efforts to control the abundance of most of the fishes included in this study should be concentrated in riverine habitats given the hydrologic conditions (below-average river discharge) present during our study. However, the proportion of pond-origin fish increased with fish age, which, coupled with historical river discharge data, suggested that floodplain pond contributions to riverine nonnative fish populations fluctuate with the interannual variations in flow regime and river–pond connectivity. Our results are the first to demonstrate the utility of δD as a natural marker of fish environmental history that will probably provide valuable insights into the management of fish in other environments

The driver landscape of sporadic chordoma.

Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases. Intriguingly, one of the most frequently altered genes, mutated exclusively by inactivating mutation, was LYST (10%), which may represent a novel cancer gene in chordoma.Chordoma is a rare often incurable malignant bone tumour. Here, the authors investigate driver mutations of sporadic chordoma in 104 cases, revealing duplications in notochordal transcription factor brachyury (T), PI3K signalling mutations, and mutations in LYST, a potential novel cancer gene in chordoma

In-flight calibration and verification of the Planck-LFI instrument

In this paper we discuss the Planck-LFI in-flight calibration campaign. After a brief overview of the ground test campaigns, we describe in detail the calibration and performance verification (CPV) phase, carried out in space during and just after the cool-down of LFI. We discuss in detail the functionality verification, the tuning of the front-end and warm electronics, the preliminary performance assessment and the thermal susceptibility tests. The logic, sequence, goals and results of the in-flight tests are discussed. All the calibration activities were successfully carried out and the instrument response was comparable to the one observed on ground. For some channels the in-flight tuning activity allowed us to improve significantly the noise performance.Comment: Long technical paper on Planck LFI in flight calibration campaign: 109 pages in this (not final) version, 100 page in the final JINST versio

Vision and Foraging in Cormorants: More like Herons than Hawks?

Background Great cormorants (Phalacrocorax carbo L.) show the highest known foraging yield for a marine predator and they are often perceived to be in conflict with human economic interests. They are generally regarded as visually-guided, pursuit-dive foragers, so it would be expected that cormorants have excellent vision much like aerial predators, such as hawks which detect and pursue prey from a distance. Indeed cormorant eyes appear to show some specific adaptations to the amphibious life style. They are reported to have a highly pliable lens and powerful intraocular muscles which are thought to accommodate for the loss of corneal refractive power that accompanies immersion and ensures a well focussed image on the retina. However, nothing is known of the visual performance of these birds and how this might influence their prey capture technique. Methodology/Principal Findings We measured the aquatic visual acuity of great cormorants under a range of viewing conditions (illuminance, target contrast, viewing distance) and found it to be unexpectedly poor. Cormorant visual acuity under a range of viewing conditions is in fact comparable to unaided humans under water, and very inferior to that of aerial predators. We present a prey detectability model based upon the known acuity of cormorants at different illuminances, target contrasts and viewing distances. This shows that cormorants are able to detect individual prey only at close range (less than 1 m). Conclusions/Significance We conclude that cormorants are not the aquatic equivalent of hawks. Their efficient hunting involves the use of specialised foraging techniques which employ brief short-distance pursuit and/or rapid neck extension to capture prey that is visually detected or flushed only at short range. This technique appears to be driven proximately by the cormorant's limited visual capacities, and is analogous to the foraging techniques employed by herons

Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao. Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species. Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories. A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database. To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection. A large collection of new genetic markers was provided by this ESTs collection. This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high density gene map of T. cacao. This EST collection represents a unique and important molecular resource for T. cacao study and improvement, facilitating the discovery of candidate genes for important T. cacao trait variation. (Résumé d'auteur