Negative regulation of Ire1 during the unfolded protein response

When cells undergo endoplasmic reticulum stress due to a build-up of unfolded or misfolded proteins, the cell must adapt to this stress and does so through the unfolded protein response (UPR). Ire1, a protein kinase endoribonuclease, is a protein found in the endoplasmic reticulum (ER) of Saccharomyces cerevisiae and plays a major role in the cell’s adaptive response to ER stress. Upon accumulation of unfolded proteins in the ER, Ire1 becomes active and splices HAC1 mRNA. After splicing the HAC1 mRNA is translated to produce the Hac1i protein, the Hac1i protein contains a bZIP transcription factor which leads to alleviation of ER stress by promoting inducing expression of UPR-associated genes. Previous work has shown that although phosphorylation is not essential to RNase activation, it still plays a critical role. Therefore, this study investigates previously identified phosphatases, Dcr2 and Ptc2, which were proposed to be negative regulators of Ire1. This study shows that out of the two investigated phosphatases, only Ptc2 was observed to negatively regulate the UPR. The mechanism of activation for the way in which the UPR was inactivated determined that interference of IRE1 clustering was affected by overexpression of either phosphatase, which suggests an alternative mechanism

Cumulative weighing of time in intertemporal tradeoffs

We examine preferences for sequences of delayed monetary gains. In the experimental literature, two prominent models have been advanced as psychological descriptions of preferences for sequences. In one model, the instantaneous utilities of the outcomes in a sequence are discounted as a function of their delays, and assembled into a discounted utility of the sequence. In the other model, the ccumulated utility of the outcomes in a sequence is considered along with utility or disutility from improvement in outcome utilities and utility or disutility from the spreading of outcome utilities. Drawing on three threads of evidence concerning preferences for sequences of monetary gains, we propose that the accumulated utility of the outcomes in a sequence is traded off against the duration of utility accumulation. In our first experiment, aggregate choice behavior provides qualitative support for the tradeoff model. In three subsequent experiments, one of which incentivized, disaggregate choice behavior provides quantitative support for the tradeoff model in Bayesian model contests. The third experiment addresses one thread of evidence that motivated the tradeoff model: When, in the choice between two single dated outcomes, it is conveyed that receiving less sooner means receiving nothing later, preference for receiving more later increases, but when it is conveyed that receiving more later means receiving nothing sooner, preference is left unchanged. Our results show that this asymmetric hidden-zero effect is indeed driven by those supporting the tradeoff model. The tradeoff model also accommodates all remaining evidence on preferences for sequences of monetary gains

An evaluation of the largest resource efficiency club programme in England (2005-2008) to underpin future design and delivery of a cost effective policy instrument.

In England, the Department of Environment, Food and Rural Affairs (Defra) allocated £5 million over three years from 2005 to 2008 to support the establishment of a wide range of innovative Resource Efficiency Clubs (RECs). During the funding period (2005 – 2008) the programme funded 70 RECs with 45 remaining active at the end of the three years (2008). Some 1,330 businesses were active in the 70 RECs with 1,014 providing data including potential and actual savings. In excess of £50 million of potential savings were identified and by the end of 2008 some £25 million were achieved. The total savings to total grant ratio for all RECs was, by 2008, some 5.8; this was in excess of the original ratio set by Defra. The Programme made clear to key decision makers that well designed RECs are a key policy instrument. The research showed that the future for RECs in England is uncertain and strategists should consider innovative ways to fund their continued contribution to national, regional and local practice

Promoting environmental management in very small businesses through “Green Angels” in a local collaborative partnership: a case study from Brighton, England

This paper describes the results of the East Brighton Employment and Environment Centre (EBEEC), a 15 month URBAN project, promoting environmental management to very small businesses in east Brighton, England. Some 31 volunteers, termed `Green Angels`, were trained in waste minimisation at the University of Brighton, and provided practical support to local firms through site reviews and research. The EBEEC project provided information and support to some 600 SMEs in east Brighton, via newsletters, email, telephone helpline, seminars and other projects. The Project was managed by a collaborative partnership formed from regional as well as local organisations. The involvement of a University to train potential `Green Angels`, so as to support SMEs in an area designated for economic regeneration, was an innovative and successful method of providing environmental management support to small firms. To stimulate the uptake of environmental management, case study material based on Best Practice was produced and disseminated to local companies via an Internet Site. A CD-Rom containing the Green Angel training package has been produced to help other projects like this. The outcomes from this Project will inform the regional and potentially the national approach to providing environmental business support and advice via local collaborative partnerships containing Universities

Radiation-Induced Magnetoresistance Oscillations in a 2D Electron Gas

Recent measurements of a 2D electron gas subjected to microwave radiation reveal a magnetoresistance with an oscillatory dependence on the ratio of radiation frequency to cyclotron frequency. We perform a diagrammatic calculation and find radiation-induced resistivity oscillations with the correct period and phase. Results are explained via a simple picture of current induced by photo-excited disorder-scattered electrons. The oscillations increase with radiation intensity, easily exceeding the dark resistivity and resulting in negative-resistivity minima. At high intensity, we identify additional features, likely due to multi-photon processes, which have yet to be observed experimentally.Comment: 5 pages, 3 figures; final version as published in Phys Rev Let

Evolutionary History and Attenuation of Myxoma Virus on Two Continents

The attenuation of myxoma virus (MYXV) following its introduction as a biological control into the European rabbit populations of Australia and Europe is the canonical study of the evolution of virulence. However, the evolutionary genetics of this profound change in host-pathogen relationship is unknown. We describe the genome-scale evolution of MYXV covering a range of virulence grades sampled over 49 years from the parallel Australian and European epidemics, including the high-virulence progenitor strains released in the early 1950s. MYXV evolved rapidly over the sampling period, exhibiting one of the highest nucleotide substitution rates ever reported for a double-stranded DNA virus, and indicative of a relatively high mutation rate and/or a continually changing selective environment. Our comparative sequence data reveal that changes in virulence involved multiple genes, likely losses of gene function due to insertion-deletion events, and no mutations common to specific virulence grades. Hence, despite the similarity in selection pressures there are multiple genetic routes to attain either highly virulent or attenuated phenotypes in MYXV, resulting in convergence for phenotype but not genotype. © 2012 Kerr et al

Cloning of the rice Xo1 resistance gene and interaction of the Xo1 protein with the defense-suppressing Xanthomonas effector Tal2h

The Xo1 locus in the heirloom rice variety Carolina Gold Select confers resistance to bacterial leaf streak and bacterial blight, caused by Xanthomonas oryzae pv. oryzicola and X. oryzae pv. oryzae, respectively. Resistance is triggered by pathogen-delivered transcription activator-like effectors (TALEs) independent of their ability to activate transcription and is suppressed by truncated variants called truncTALEs, common among Asian strains. By transformation of the susceptible variety Nipponbare, we show that one of 14 nucleotide-binding, leucine-rich repeat (NLR) protein genes at the locus, with a zinc finger BED domain, is the Xo1 gene. Analyses of published transcriptomes revealed that the Xo1-mediated response is more similar to those mediated by two other NLR resistance genes than it is to the response associated with TALE-specific transcriptional activation of the executor resistance gene Xa23 and that a truncTALE dampens or abolishes activation of defense-associated genes by Xo1. In Nicotiana benthamiana leaves, fluorescently tagged Xo1 protein, like TALEs and truncTALEs, localized to the nucleus. And endogenous Xo1 specifically coimmunoprecipitated from rice leaves with a pathogen-delivered, epitope-tagged truncTALE. These observations suggest that suppression of Xo1-function by truncTALEs occurs through direct or indirect physical interaction. They further suggest that effector coimmunoprecipitation may be effective for identifying or characterizing other resistance genes

Activation of bicyclic nitro-drugs by a novel nitroreductase (NTR2) in <i>Leishmania</i>

Drug discovery pipelines for the "neglected diseases" are now heavily populated with nitroheterocyclic compounds. Recently, the bicyclic nitro-compounds (R)-PA-824, DNDI-VL-2098 and delamanid have been identified as potential candidates for the treatment of visceral leishmaniasis. Using a combination of quantitative proteomics and whole genome sequencing of susceptible and drug-resistant parasites we identified a putative NAD(P)H oxidase as the activating nitroreductase (NTR2). Whole genome sequencing revealed that deletion of a single cytosine in the gene for NTR2 that is likely to result in the expression of a non-functional truncated protein. Susceptibility of leishmania was restored by reintroduction of the wild-type gene into the resistant line, which was accompanied by the ability to metabolise these compounds. Overexpression of NTR2 in wild-type parasites rendered cells hyper-sensitive to bicyclic nitro-compounds, but only marginally to the monocyclic nitro-drugs, nifurtimox and fexinidazole sulfone, known to be activated by a mitochondrial oxygen-insensitive nitroreductase (NTR1). Conversely, a double knockout NTR2 null cell line was completely resistant to bicyclic nitro-compounds and only marginally resistant to nifurtimox. Sensitivity was fully restored on expression of NTR2 in the null background. Thus, NTR2 is necessary and sufficient for activation of these bicyclic nitro-drugs. Recombinant NTR2 was capable of reducing bicyclic nitro-compounds in the same rank order as drug sensitivity in vitro. These findings may aid the future development of better, novel anti-leishmanial drugs. Moreover, the discovery of anti-leishmanial nitro-drugs with independent modes of activation and independent mechanisms of resistance alleviates many of the concerns over the continued development of these compound series

Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

Long-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes constitute one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice variety Carolina Gold Select, to a region that in the Nipponbare reference genome is NLR gene-rich. Here, toward identification of the Xo1 gene, we combined Nanopore and Illumina reads and generated a high-quality Carolina Gold Select genome assembly. We identified 529 complete or partial NLR genes and discovered, relative to Nipponbare, an expansion of NLR genes at the Xo1 locus. One of these has high sequence similarity to the cloned, functionally similar Xa1 gene. Both harbor an integrated zfBED domain, and the repeats within each protein are nearly perfect. Across diverse Oryzeae, we identified two sub-clades of NLR genes with these features, varying in the presence of the zfBED domain and the number of repeats. The Carolina Gold Select genome assembly also uncovered at the Xo1 locus a rice blast resistance gene and a gene encoding a polyphenol oxidase (PPO). PPO activity has been used as a marker for blast resistance at the locus in some varieties; however, the Carolina Gold Select sequence revealed a loss-of-function mutation in the PPO gene that breaks this association. Our results demonstrate that whole genome sequencing combining Nanopore and Illumina reads effectively resolves NLR gene loci. Our identification of an Xo1 candidate is an important step toward mechanistic characterization, including the role(s) of the zfBED domain. Finally, the Carolina Gold Select genome assembly will facilitate identification of other useful traits in this historically important variety. Author summary Plants lack adaptive immunity, and instead contain repeat-rich, disease resistance genes that evolve rapidly through duplication, recombination, and transposition. The number, variation, and often clustered arrangement of these genes make them challenging to sequence and catalog. The US heirloom rice variety Carolina Gold Select has resistance to two important bacterial diseases. Toward identifying the responsible gene(s), we combined long- and short-read sequencing technologies to assemble the whole genome and identify the resistance gene repertoire. We previously narrowed the location of the gene(s) to a region on chromosome four. The region in Carolina Gold Select is larger than in the rice reference genome (Nipponbare) and contains twice as many resistance genes. One shares unusual features with a known bacterial disease resistance gene, suggesting that it confers the resistance. Across diverse varieties and related species, we identified two widely-distributed groups of such genes. The results are an important step toward mechanistic characterization and deployment of the bacterial disease resistance. The genome assembly also identified a resistance gene for a fungal disease and predicted a marker phenotype used in breeding for resistance. Thus, the Carolina Gold Select genome assembly can be expected to aid in the identification and deployment of other valuable traits