The impact of trench defects in InGaN/GaN light emitting diodes and implications for the "green gap" problem

The impact of trench defects in blue InGaN/GaN light emitting diodes (LEDs) has been investigated. Two mechanisms responsible for the structural degradation of the multiple quantum well (MQW) active region were identified. It was found that during the growth of the p-type GaN capping layer, loss of part of the active region enclosed within a trench defect occurred, affecting the top-most QWs in the MQW stack. Indium platelets and voids were also found to form preferentially at the bottom of the MQW stack. The presence of high densities of trench defects in the LEDs was found to relate to a significant reduction in photoluminescence and electroluminescence emission efficiency, for a range of excitation power densities and drive currents. This reduction in emission efficiency was attributed to an increase in the density of non-radiative recombination centres within the MQW stack, believed to be associated with the stacking mismatch boundaries which form part of the sub-surface structure of the trench defects. Investigation of the surface of green-emitting QW structures found a two decade increase in the density of trench defects, compared to its blue-emitting counterpart, suggesting that the efficiency of green-emitting LEDs may be strongly affected by the presence of these defects. Our results are therefore consistent with a model that the “green gap” problem might relate to localized strain relaxation occurring through defects.This is the accepted manuscript version. The final version is available from AIP at http://scitation.aip.org/content/aip/journal/apl/105/11/10.1063/1.4896279?showFTTab=true&containerItemId=content/aip/journal/apl

Optimisation of the Schizosaccharomyces pombe urg1 expression system

The ability to study protein function in vivo often relies on systems that regulate the presence and absence of the protein of interest. Two limitations for previously described transcriptional control systems that are used to regulate protein expression in fission yeast are: the time taken for inducing conditions to initiate transcription and the ability to achieve very low basal transcription in the "OFF-state". In previous work, we described a Cre recombination-mediated system that allows the rapid and efficient regulation of any gene of interest by the urg1 promoter, which has a dynamic range of approximately 75-fold and which is induced within 30-60 minutes of uracil addition. In this report we describe easy-to-use and versatile modules that can be exploited to significantly tune down P urg1 "OFF-levels" while maintaining an equivalent dynamic range. We also provide plasmids and tools for combining P urg1 transcriptional control with the auxin degron tag to help maintain a null-like phenotype. We demonstrate the utility of this system by improved regulation of HO-dependent site-specific DSB formation, by the regulation Rtf1-dependent replication fork arrest and by controlling Rhp18(Rad18)-dependent post replication repair

Enhancing European capabilities for application of multi-omics studies in biology and biomedicine space research

Following on from the NASA twins’ study, there has been a tremendous interest in the use of omics techniques in spaceflight. Individual space agencies, NASA's GeneLab, JAXA's ibSLS, and the ESA-funded Space Omics Topical Team and the International Standards for Space Omics Processing (ISSOP) groups have established several initiatives to support this growth. Here, we present recommendations from the Space Omics Topical Team to promote standard application of space omics in Europe. We focus on four main themes: i) continued participation in and coordination with international omics endeavors, ii) strengthening of the European space omics infrastructure including workforce and facilities, iii) capitalizing on the emerging opportunities in the commercial space sector, and iv) capitalizing on the emerging opportunities in human subjects research

Three Toxoplasma gondii dense granule proteins are required for induction of Lewis rat macrophage pyroptosis

Upon invasion of Lewis rat macrophages, Toxoplasma rapidly induces programmed cell death (pyroptosis), which prevents Toxoplasma replication, possibly explaining the resistance of the Lewis rat to Toxoplasma Using a chemical mutagenesis screen, we identified Toxoplasma mutants that no longer induced pyroptosis. Whole-genome sequencing led to the identification of three Toxoplasma parasitophorous vacuole-localized dense granule proteins, GRA35, GRA42, and GRA43, that are individually required for induction of Lewis rat macrophage pyroptosis. Macrophage infection with Δgra35, Δgra42, and Δgra43 parasites led to greatly reduced cell death rates and enhanced parasite replication. Lewis rat macrophages infected with parasites containing a single, double, or triple deletion of these GRAs showed similar levels of cell viability, suggesting that the three GRAs function in the same pathway. Deletion of GRA42 or GRA43 resulted in GRA35 (and other GRAs) being retained inside the parasitophorous vacuole instead of being localized to the parasitophorous vacuole membrane. Despite having greatly enhanced replication in Lewis rat macrophages in vitro, Δgra35, Δgra42, and Δgra43 parasites did not establish a chronic infection in Lewis rats. Toxoplasma did not induce F344 rat macrophage pyroptosis, but F344 rats infected with Δgra35, Δgra42, and Δgra43 parasites had reduced cyst numbers. Thus, these GRAs determined parasite in vivo fitness in F344 rats. Overall, our data suggest that these three Toxoplasma dense granule proteins play a critical role in establishing a chronic infection in vivo, independently of their role in mediating macrophage pyroptosis, likely due to their importance in regulating protein localization to the parasitophorous vacuole membrane.IMPORTANCE Inflammasomes are major components of the innate immune system and are responsible for detecting various microbial and environmental danger signals. Upon invasion of Lewis rat macrophages, the parasite rapidly activates the NLRP1 inflammasome, resulting in pyroptosis and elimination of the parasite's replication niche. The work reported here revealed that Toxoplasma GRA35, GRA42, and GRA43 are required for induction of Lewis rat macrophage pyroptosis. GRA42 and GRA43 mediate the correct localization of other GRAs, including GRA35, to the parasitophorous vacuole membrane. These three GRAs were also found to be important for parasite in vivo fitness in a Toxoplasma-susceptible rat strain, independently of their role in NLRP1 inflammasome activation, suggesting that they perform other important functions. Thus, this study identified three GRAs that mediate the induction of Lewis rat macrophage pyroptosis and are required for pathogenesis of the parasite

Spectroscopic studies as a toolbox for biophysical and chemical characterization of lipid-based nanotherapeutics

The goal of this study is to provide tools to minimize trial-and-error in the development of novel lipid-based nanotherapeutics, in favor of a rational design process. For this purpose, we present case-study examples of biophysical assays that help addressing issues of lipid-based nanotherapeutics' profiling and assist in the design of lipid nanocarriers for therapeutic usage. The assays presented are rooted in spectroscopic methods (steady-state and time-resolved fluorescence; UV-Vis derivative spectroscopy; fluorescence anisotropy and fluorescence lifetime image microscopy) and allow accessing physical-chemical interactions between drugs and lipid nanocarriers, as well as studying interactions between lipid-based nanotherapeutics and membranes and/or proteins, as this is a key factor in predicting their therapeutic and off target effects. Derivative spectroscopy revealed Naproxen's high distribution (LogD ≈ 3) in different lipid-based nanocarriers (micelles and unilamellar or multilamellar vesicles) confirming the adequacy of such systems for encapsulating this anti-inflammatory drug. Fluorescence quenching studies revealed that the anti-inflammatory drugs Acemetacin and Indomethacin can reach an inner location at the lipid nanocarrier while being anchored with its carboxylic moiety at the polar headgroup. The least observed quenching effect suggested that Tolmetin is probably located at the polar headgroup region of the lipid nanocarriers and this superficial location may translate in a fast drug release from the nanocarriers. Fluorescent anisotropy measurements indicated that the drugs deeply buried within the lipid nanocarrier where the ones that had a greater fluidizing effect which can also translate in a faster drug release. The drug binding strength to serum albumin was also compared for a free drug (Clonixin) or for the same drug after encapsulation in a lipid nanocarrier DSPC:DODAP (2:1). Under both conditions there is a strong binding to serum albumin, at one binding site, suggesting the need to produce a stealth nanosystem. Finally the cellular uptake of lipid nanocarriers loaded with Daunorubicin was investigated in cancer cells using fluorescence lifetime imaging microscopy. From the images obtained it was possible to conclude that even at short incubation times (15 min) there was a distribution of the drug in the cytoplasm, whereas for longer incubation periods (4 h) the drug has reached the nucleus.This work was supported by the Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Funding UID/FIS/04650/2013 and in the ambit of the project IF/00498/2012

PCNA ubiquitylation ensures timely completion of unperturbed DNA replication in fission yeast

PCNA ubiquitylation on lysine 164 is required for DNA damage tolerance. In many organisms PCNA is also ubiquitylated in unchallenged S phase but the significance of this has not been established. Using Schizosaccharomyces pombe, we demonstrate that lysine 164 ubiquitylation of PCNA contributes to efficient DNA replication in the absence of DNA damage. Loss of PCNA ubiquitylation manifests most strongly at late replicating regions and increases the frequency of replication gaps. We show that PCNA ubiquitylation increases the proportion of chromatin associated PCNA and the co-immunoprecipitation of Polymerase δ with PCNA during unperturbed replication and propose that ubiquitylation acts to prolong the chromatin association of these replication proteins to allow the efficient completion of Okazaki fragment synthesis by mediating gap filling

Evidence of phytotoxicity and genotoxicity in Hordeum vulgare L. exposed to CeO2 and TiO2 nanoparticles.

Engineered nanoscale materials (ENMs) are considered emerging contaminants since they are perceived as a potential threat to the environment and the human health. The reactions of living organisms when exposed to metal nanoparticles (NPs) or NPs of different size are not well known. Very few studies on NPs–plant interactions have been published, so far. For this reason there is also great concern regarding the potential NPs impact to food safety. Early genotoxic and phytotoxic effects of cerium oxide NPs (nCeO(2)) and titanium dioxide NPs (nTiO(2)) were investigated in seedlings of Hordeum vulgare L. Caryopses were exposed to an aqueous dispersion of nCeO(2) and nTiO(2) at, respectively 0, 500, 1000, and 2000 mg l(-1) for 7 days. Genotoxicity was studied by Randomly Amplified Polymorphism DNA (RAPDs) and mitotic index on root tip cells. Differences between treated and control plants were observed in RAPD banding patterns as well as at the chromosomal level with a reduction of cell divisions. At cellular level we monitored the oxidative stress of treated plants in terms of reactive oxygen species (ROS) generation and ATP content. Again nCeO(2) influenced clearly these two physiological parameters, while nTiO(2) were ineffective. In particular, the dose 500 mg l(-1) showed the highest increase regarding both ROS generation and ATP content; the phenomenon were detectable, at different extent, both at root and shoot level. Total Ce and Ti concentration in seedlings was detected by ICP-OES. TEM EDSX microanalysis demonstrated the presence of aggregates of nCeO(2) and nTiO(2) within root cells of barley. nCeO(2) induced modifications in the chromatin aggregation mode in the nuclei of both root and shoot cells

Switchgrass

Switchgrass (Panicum virgatum L.) is a perennialwarm-season grass native to the grasslands of North America, is a model perennial grass for bioenergy, and is the most advanced herbaceous perennial bioenergy feedstock. Best management practices have been developed for switchgrass bioenergy production for the agroecoregions to which it is adapted. Field production of switchgrass likely will occur on cropland that is marginally productive for row crops, similar to land that was enrolled in the Conservation Reserve Program. Long-term, field-scale research demonstrates that switchgrass for bioenergy is productive, profitable for the farmer, and protective of the environment. Switchgrass was selected by the Bioenergy Feedstock Development Program (BFDP) at the U.S. Department of Energy (DoE) as a model herbaceous species because of its potential to simultaneously meet energy demands and address global climate change [1]. It is a perennial, warm-season (C4) grass native to North America that is broadly adapted throughout the United States and is found in every state east of the Rocky Mountains [2]. Like many perennial C4 grasses, switchgrass is highly tolerant to abiotic stresses such as drought, temperature extremes, and salinity. For that reason, it is being recommended for biomass production on marginally productive cropland where it would have minimal land use competition with commercial food crops

Tumor surveillance by circulating microRNAs: a hypothesis

A growing body of experimental evidence supports the diagnostic relevance of circulating microRNAs in various diseases including cancer. The biological relevance of circulating microRNAs is, however, largely unknown, particularly in healthy individuals. Here, we propose a hypothesis based on the relative abundance of microRNAs with predominant tumor suppressor activity in the blood of healthy individuals. According to our hypothesis, certain sets of circulating microRNAs might function as a tumor surveillance mechanism exerting continuous inhibition on tumor formation. The microRNA-mediated tumor surveillance might complement cancer immune surveillance