Analysis of the chlorophyll catabolism pathway in leaves of an introgression senescence mutant of Lolium temulentum

Maria Roca, Caron James, Adriana Pruzinsk?, Stefan H?rtensteiner, Howard Thomas and Helen Ougham. Analysis of the chlorophyll catabolism pathway in leaves of an introgression senescence mutant of Lolium temulentum. Phytochemistry, 65 (9), 1231-1238. Sponsorship: BBSRC RAE2008

Synoptic conditions governing upwelling along the Polish Baltic coast

The study analyses atmospheric feedback to the occurrence of upwelling along the Polish Baltic coast. Upwelling events were identified on the basis of daily mean sea surface temperature (SST) maps from the period 1982–2010 derived from the NOAA OI SST V2 High Resolution Dataset. Synoptic conditions favourable to the occurrence of upwelling were determined on the basis of the NCEP/NCAR reanalysis data. On average, there are approximately 23 days with upwelling each year along the Polish Baltic coast, which account for approximately 13%

Photonic integrated circuit for the manipulation of coherent optical combs

Photonic integration has become an important research topic in research for applications in the telecommunications industry. Current optical internet infrastructure has reached capacity with current generation dense wavelength division multiplexing (DWDM) systems fully occupying the low absorption region of optical fibre from 1530 nm to 1625 nm (the C and L bands). This is both due to an increase in the number of users worldwide and existing users demanding more bandwidth. Therefore, current research is focussed on using the available telecommunication spectrum more efficiently. To this end, coherent communication systems are being developed. Advanced coherent modulation schemes can be quite complex in terms of the number and array of devices required for implementation. In order to make these systems viable both logistically and commercially, photonic integration is required. In traditional DWDM systems, arrayed waveguide gratings (AWG) are used to both multiplex and demultiplex the multi-wavelength signal involved. AWGs are used widely as they allow filtering of the many DWDM wavelengths simultaneously. However, when moving to coherent telecommunication systems such as coherent optical frequency division multiplexing (OFDM) smaller FSR ranges are required from the AWG. This increases the size of the device which is counter to the miniaturisation which integration is trying to achieve. Much work was done with active filters during the 1980s. This involved using a laser device (usually below threshold) to allow selective wavelength filtering of input signals. By using more complicated cavity geometry devices such as distributed feedback (DFB) and sampled grating distributed Bragg gratings (SG-DBR) narrowband filtering is achievable with high suppression (>30 dB) of spurious wavelengths. The active nature of the devices also means that, through carrier injection, the index can be altered resulting in tunability of the filter. Used above threshold, active filters become useful in filtering coherent combs. Through injection locking, the coherence of the filtered wavelengths with the original comb source is retained. This gives active filters potential application in coherent communication system as demultiplexers. This work will focus on the use of slotted Fabry-Pérot (SFP) semiconductor lasers as active filters. Experiments were carried out to ensure that SFP lasers were useful as tunable active filters. In all experiments in this work the SFP lasers were operated above threshold and so injection locking was the mechanic by which the filters operated. Performance of the lasers under injection locking was examined using both single wavelength and coherent comb injection. In another experiment two discrete SFP lasers were used simultaneously to demultiplex a two-line coherent comb. The relative coherence of the comb lines was retained after demultiplexing. After showing that SFP lasers could be used to successfully demultiplex coherent combs a photonic integrated circuit was designed and fabricated. This involved monolithic integration of a MMI power splitter with an array of single facet SFP lasers. This device was tested much in the same way as the discrete devices. The integrated device was used to successfully demultiplex a two line coherent comb signal whilst retaining the relative coherence between the filtered comb lines. A series of modelling systems were then employed in order to understand the resonance characteristics of the fabricated devices, and to understand their performance under injection locking. Using this information, alterations to the SFP laser designs were made which were theoretically shown to provide improved performance and suitability for use in filtering coherent comb signals.

Alternative splicing in multiple sclerosis and other autoimmune diseases.

Alternative splicing is a general mechanism for regulating gene expression that affects the RNA products of more than 90% of human genes. Not surprisingly, alternative splicing is observed among gene products of metazoan immune systems, which have evolved to efficiently recognize pathogens and discriminate between "self" and "non-self", and thus need to be both diverse and flexible. In this review we focus on the specific interface between alternative splicing and autoimmune diseases, which result from a malfunctioning of the immune system and are characterized by the inappropriate reaction to self-antigens. Despite the widespread recognition of alternative splicing as one of the major regulators of gene expression, the connections between alternative splicing and autoimmunity have not been apparent. We summarize recent findings connecting splicing and autoimmune disease, and attempt to find common patterns of splicing regulation that may advance our understanding of autoimmune diseases and open new avenues for therapy.

Magnitude and breadth of a nonprotective neutralizing antibody response in an efficacy trial of a candidate HIV-1 gp120 vaccine.

BACKGROUND: A candidate vaccine consisting of human immunodeficiency virus type 1 (HIV-1) subunit gp120 protein was found previously to be nonprotective in an efficacy trial (Vax004) despite strong antibody responses against the vaccine antigens. Here we assessed the magnitude and breadth of neutralizing antibody responses in Vax004. METHODS: Neutralizing antibodies were measured against highly sensitive (tier 1) and moderately sensitive (tier 2) strains of HIV-1 subtype B in 2 independent assays. Vaccine recipients were stratified by sex, race, and high versus low behavioral risk of HIV-1 acquisition. RESULTS: Most vaccine recipients mounted potent neutralizing antibody responses against HIV-1(MN) and other tier 1 viruses. Occasional weak neutralizing activity was detected against tier 2 viruses. The response against tier 1 and tier 2 viruses was significantly stronger in women than in men. Race and behavioral risk of HIV-1 acquisition had no significant effect on the response. Prior vaccination had little effect on the neutralizing antibody response that arose after infection. CONCLUSIONS: Weak overall neutralizing antibody responses against tier 2 viruses is consistent with a lack of protection in this trial. The magnitude and breadth of neutralization reported here should be useful for identifying improved vaccines.

Intensification of summer rainfall variability in the southeastern United States during recent decades

The variability of summer precipitation in the southeastern United States is examined in this study using 60-yr (1948-2007) rainfall data. The Southeast summer rainfalls exhibited higher interannual variability with more intense summer droughts and anomalous wetness in the recent 30 years (1978-2007) than in the prior 30 years (1948-77). Such intensification of summer rainfall variability was consistent with a decrease of light (0.1-1 mm day-1) and medium (1-10 mm day-1) rainfall events during extremely dry summers and an increase of heavy (.10 mm day-1) rainfall events in extremely wet summers. Changes in rainfall variability were also accompanied by a southward shift of the region of maximum zonal wind variability at the jet stream level in the latter period. The covariability between the Southeast summer precipitation and sea surface temperatures (SSTs) is also analyzed using the singular value decomposition (SVD) method. It is shown that the increase of Southeast summer precipitation variability is primarily associated with a higher SST variability across the equatorial Atlantic and also SST warming in the Atlantic. © 2010 American Meteorological Society.

Reevaluation of mid-Pliocene North Atlantic sea surface temperatures

Multiproxy temperature estimation requires careful attention to biological, chemical, physical, temporal, and calibration differences of each proxy and paleothermometry method. We evaluated mid-Pliocene sea surface temperature (SST) estimates from multiple proxies at Deep Sea Drilling Project Holes 552A, 609B, 607, and 606, transecting the North Atlantic Drift. SST estimates derived from faunal assemblages, foraminifer Mg/Ca, and alkenone unsaturation indices showed strong agreement at Holes 552A, 607, and 606 once differences in calibration, depth, and seasonality were addressed. Abundant extinct species and/or an unrecognized productivity signal in the faunal assemblage at Hole 609B resulted in exaggerated faunal-based SST estimates but did not affect alkenone-derived or Mg/Ca-derived estimates. Multiproxy mid-Pliocene North Atlantic SST estimates corroborate previous studies documenting high-latitude mid-Pliocene warmth and refine previous faunal-based estimates affected by environmental factors other than temperature. Multiproxy investigations will aid SST estimation in high-latitude areas sensitive to climate change and currently underrepresented in SST reconstructions. Copyright 2008 by the American Geophysical Union.

Methane contamination of drinking water accompanying gas-well drilling and hydraulic fracturing.

Directional drilling and hydraulic-fracturing technologies are dramatically increasing natural-gas extraction. In aquifers overlying the Marcellus and Utica shale formations of northeastern Pennsylvania and upstate New York, we document systematic evidence for methane contamination of drinking water associated with shale-gas extraction. In active gas-extraction areas (one or more gas wells within 1 km), average and maximum methane concentrations in drinking-water wells increased with proximity to the nearest gas well and were 19.2 and 64 mg CH(4) L(-1) (n = 26), a potential explosion hazard; in contrast, dissolved methane samples in neighboring nonextraction sites (no gas wells within 1 km) within similar geologic formations and hydrogeologic regimes averaged only 1.1 mg L(-1) (P < 0.05; n = 34). Average δ(13)C-CH(4) values of dissolved methane in shallow groundwater were significantly less negative for active than for nonactive sites (-37 ± 7‰ and -54 ± 11‰, respectively; P < 0.0001). These δ(13)C-CH(4) data, coupled with the ratios of methane-to-higher-chain hydrocarbons, and δ(2)H-CH(4) values, are consistent with deeper thermogenic methane sources such as the Marcellus and Utica shales at the active sites and matched gas geochemistry from gas wells nearby. In contrast, lower-concentration samples from shallow groundwater at nonactive sites had isotopic signatures reflecting a more biogenic or mixed biogenic/thermogenic methane source. We found no evidence for contamination of drinking-water samples with deep saline brines or fracturing fluids. We conclude that greater stewardship, data, and-possibly-regulation are needed to ensure the sustainable future of shale-gas extraction and to improve public confidence in its use.

On the multiple ecological roles of water in river networks

The distribution and movement of water can influence the state and dynamics of terrestrial and aquatic ecosystems through a diversity of mechanisms. These mechanisms can be organized into three general categories wherein water acts as (1) a resource or habitat for biota, (2) a vector for connectivity and exchange of energy, materials, and organisms, and (3) as an agent of geomorphic change and disturbance. These latter two roles are highlighted in current models, which emphasize hydrologic connectivity and geomorphic change as determinants of the spatial and temporal distributions of species and processes in river systems. Water availability, on the other hand, has received less attention as a driver of ecological pattern, despite the prevalence of intermittent streams, and strong potential for environmental change to alter the spatial extent of drying in many regions. Here we summarize long-term research from a Sonoran Desert watershed to illustrate how spatial patterns of ecosystem structure and functioning reflect shifts in the relative importance of different 'roles of water' across scales of drainage size. These roles are distributed and interact hierarchically in the landscape, and for the bulk of the drainage network it is the duration of water availability that represents the primary determinant of ecological processes. Only for the largest catchments, with the most permanent flow regimes, do flood-associated disturbances and hydrologic exchange emerge as important drivers of local dynamics. While desert basins represent an extreme case, the diversity of mechanisms by which the availability and flow of water influence ecosystem structure and functioning are general. Predicting how river ecosystems may respond to future environmental pressures will require clear understanding of how changes in the spatial extent and relative overlap of these different roles of water shape ecological patterns. © 2013 Sponseller et al.

Cryptococcus gattii VGIII isolates causing infections in HIV/AIDS patients in Southern California: identification of the local environmental source as arboreal.

Ongoing Cryptococcus gattii outbreaks in the Western United States and Canada illustrate the impact of environmental reservoirs and both clonal and recombining propagation in driving emergence and expansion of microbial pathogens. C. gattii comprises four distinct molecular types: VGI, VGII, VGIII, and VGIV, with no evidence of nuclear genetic exchange, indicating these represent distinct species. C. gattii VGII isolates are causing the Pacific Northwest outbreak, whereas VGIII isolates frequently infect HIV/AIDS patients in Southern California. VGI, VGII, and VGIII have been isolated from patients and animals in the Western US, suggesting these molecular types occur in the environment. However, only two environmental isolates of C. gattii have ever been reported from California: CBS7750 (VGII) and WM161 (VGIII). The incongruence of frequent clinical presence and uncommon environmental isolation suggests an unknown C. gattii reservoir in California. Here we report frequent isolation of C. gattii VGIII MATα and MATa isolates and infrequent isolation of VGI MATα from environmental sources in Southern California. VGIII isolates were obtained from soil debris associated with tree species not previously reported as hosts from sites near residences of infected patients. These isolates are fertile under laboratory conditions, produce abundant spores, and are part of both locally and more distantly recombining populations. MLST and whole genome sequence analysis provide compelling evidence that these environmental isolates are the source of human infections. Isolates displayed wide-ranging virulence in macrophage and animal models. When clinical and environmental isolates with indistinguishable MLST profiles were compared, environmental isolates were less virulent. Taken together, our studies reveal an environmental source and risk of C. gattii to HIV/AIDS patients with implications for the >1,000,000 cryptococcal infections occurring annually for which the causative isolate is rarely assigned species status. Thus, the C. gattii global health burden could be more substantial than currently appreciated.

Characterization of porous, dexamethasone-releasing polyurethane coatings for glucose sensors.

Commercially available implantable needle-type glucose sensors for diabetes management are robust analytically but can be unreliable clinically primarily due to tissue-sensor interactions. Here, we present the physical, drug release and bioactivity characterization of tubular, porous dexamethasone (Dex)-releasing polyurethane coatings designed to attenuate local inflammation at the tissue-sensor interface. Porous polyurethane coatings were produced by the salt-leaching/gas-foaming method. Scanning electron microscopy and micro-computed tomography (micro-CT) showed controlled porosity and coating thickness. In vitro drug release from coatings monitored over 2 weeks presented an initial fast release followed by a slower release. Total release from coatings was highly dependent on initial drug loading amount. Functional in vitro testing of glucose sensors deployed with porous coatings against glucose standards demonstrated that highly porous coatings minimally affected signal strength and response rate. Bioactivity of the released drug was determined by monitoring Dex-mediated, dose-dependent apoptosis of human peripheral blood derived monocytes in culture. Acute animal studies were used to determine the appropriate Dex payload for the implanted porous coatings. Pilot short-term animal studies showed that Dex released from porous coatings implanted in rat subcutis attenuated the initial inflammatory response to sensor implantation. These results suggest that deploying sensors with the porous, Dex-releasing coatings is a promising strategy to improve glucose sensor performance.

Sound the alarm: fraud in neuroscience.

We expect scientists to follow a code of honor and conduct and to report their research honestly and accurately, but so-called scientific misconduct, which includes plagiarism, faked data, and altered images, has led to a tenfold increase in the number of retractions over the past decade. Among the reasons for this troubling upsurge is increased competition for journal placement, grant money, and prestigious appointments. The solutions are not easy, but reform and greater vigilance is needed.

Characterization of porous, dexamethasone-releasing polyurethane coatings for glucose sensors

© 2014 Acta Materialia Inc.Commercially available implantable needle-type glucose sensors for diabetes management are robust analytically but can be unreliable clinically primarily due to tissue-sensor interactions. Here, we present the physical, drug release and bioactivity characterization of tubular, porous dexamethasone (Dex)-releasing polyurethane coatings designed to attenuate local inflammation at the tissue-sensor interface. Porous polyurethane coatings were produced by the salt-leaching/gas-foaming method. Scanning electron microscopy and micro-computed tomography (micro-CT) showed controlled porosity and coating thickness. In vitro drug release from coatings monitored over 2 weeks presented an initial fast release followed by a slower release. Total release from coatings was highly dependent on initial drug loading amount. Functional in vitro testing of glucose sensors deployed with porous coatings against glucose standards demonstrated that highly porous coatings minimally affected signal strength and response rate. Bioactivity of the released drug was determined by monitoring Dex-mediated, dose-dependent apoptosis of human peripheral blood derived monocytes in culture. Acute animal studies were used to determine the appropriate Dex payload for the implanted porous coatings. Pilot short-term animal studies showed that Dex released from porous coatings implanted in rat subcutis attenuated the initial inflammatory response to sensor implantation. These results suggest that deploying sensors with the porous, Dex-releasing coatings is a promising strategy to improve glucose sensor performance.

Hydraulic redistribution of soil water by roots affects whole-stand evapotranspiration and net ecosystem carbon exchange.

*Hydraulic redistribution (HR) of water via roots from moist to drier portions of the soil occurs in many ecosystems, potentially influencing both water use and carbon assimilation. *By measuring soil water content, sap flow and eddy covariance, we investigated the temporal variability of HR in a loblolly pine (Pinus taeda) plantation during months of normal and below-normal precipitation, and examined its effects on tree transpiration, ecosystem water use and carbon exchange. *The occurrence of HR was explained by courses of reverse flow through roots. As the drought progressed, HR maintained soil moisture above 0.15 cm(3) cm(-3) and increased transpiration by 30-50%. HR accounted for 15-25% of measured total site water depletion seasonally, peaking at 1.05 mm d(-1). The understory species depended on water redistributed by the deep-rooted overstory pine trees for their early summer water supply. Modeling carbon flux showed that in the absence of HR, gross ecosystem productivity and net ecosystem exchange could be reduced by 750 and 400 g C m(-2) yr(-1), respectively. *Hydraulic redistribution mitigated the effects of soil drying on understory and stand evapotranspiration and had important implications for net primary productivity by maintaining this whole ecosystem as a carbon sink.