Structural Analysis of the CDK-Cyclin Complex of Pho85-Pho80 and Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe

Inorganic phosphate is an essential nutrient required by all organisms for optimal growth. During phosphate starvation, Saccharomyces cerevisiae induces a set of genes responsible for the regulation of inorganic phosphate acquisition. The phosphate-responsive signaling (PHO) pathway controls this response, with the CDK-cyclin complex Pho85-Pho80 playing a prominent role. Here we report the X-ray structure of the Pho85-Pho80 complex, identifying the unique structural features that distinguish it from other cell cycle associated CDK-cyclin complexes. The structure reveals a specific salt bridge between a Pho85 arginine and a Pho80 aspartate that maintains a Pho80 loop confirmation important for substrate recognition and makes phosphorylation of the Pho85 activation loop dispensible. We show that a cluster of residues distal to the kinase active site are involved in a high affinity interaction between the Pho80 cyclin and the transcription factor substrate (Pho4). The structure also reveals a separate high affinity binding site for the CDK inhibitor (Pho81). The fission yeast, Schizosaccharomyces pombe, regulates expression of the secreted acid phosphatase $(pho1^+)$ via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive $(pho7^+)$ and negative $(csk1^+)$ regulators function are not known. Here we use a combination of molecular biology, expression microarrays, chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq), and global transcriptome sequencing (RNA-Seq) to characterize the role of $pho7^+$ and $csk1^+$ in the PHO response. We show that there is a fast and slow response to phosphate starvation, each with defined regulatory roles. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding dynamics in response to phosphate-limitation and Csk1 activity. We identify a conserved PHO response for the PHO5 $(pho1^+)$, PHO84 $(spbc8e4.01c^+)$, and GIT1 $(spbc1271.09^+)$ orthologs. We show that activation of $pho1^+$ requires Pho7 binding to a UAS in the $pho1^+$ promoter and that a URS is necessary for Csk1 repression. We find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require $pho7^+$ for maximal induction. Using RNA-Seq we show that Pho7 is also involved in regulating non-coding transcription and is a bi-functional transcription factor

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe

Background: Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway, leading to expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway involving genetically identified positive (pho7+) and negative (csk1+) regulators. The genes induced by phosphate limitation and the molecular mechanism by which pho7+ and csk1+ function are unknown. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. Results: We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response that contains the ScPHO5 (pho1+), ScPHO84 (SPBC8E4.01c), and ScGIT1 (SPBC1271.09) orthologs. We identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. Conclusions: We provide a global analysis of the transcriptional response to phosphate limitation in S. pombe. Our results elucidate the conserved core regulon induced in response to phosphate starvation in this ascomycete distantly related to S. cerevisiae and provide a better understanding of flexibility in environmental stress response networks.Chemistry and Chemical BiologyMolecular and Cellular Biolog

An electrophysiological signal that precisely tracks the emergence of error awareness

Recent electrophysiological research has sought to elucidate the neural mechanisms necessary for the conscious awareness of action errors. Much of this work has focused on the error positivity (Pe), a neural signal that is specifically elicited by errors that have been consciously perceived. While awareness appears to be an essential prerequisite for eliciting the Pe, the precise functional role of this component has not been identified. Twenty-nine participants performed a novel variant of the Go/No-go Error Awareness Task (EAT) in which awareness of commission errors was indicated via a separate speeded manual response. Independent component analysis (ICA) was used to isolate the Pe from other stimulus- and response-evoked signals. Single-trial analysis revealed that Pe peak latency was highly correlated with the latency at which awareness was indicated. Furthermore, the Pe was more closely related to the timing of awareness than it was to the initial erroneous response. This finding was confirmed in a separate study which derived IC weights from a control condition in which no indication of awareness was required, thus ruling out motor confounds. A receiver-operating-characteristic (ROC) curve analysis showed that the Pe could reliably predict whether an error would be consciously perceived up to 400 ms before the average awareness response. Finally, Pe latency and amplitude were found to be significantly correlated with overall error awareness levels between subjects. Our data show for the first time that the temporal dynamics of the Pe trace the emergence of error awareness. These findings have important implications for interpreting the results of clinical EEG studies of error processing

Uncovering the Neural Signature of Lapsing Attention: Electrophysiological Signals Predict Errors up to 20 s before They Occur

The extent to which changes in brain activity can foreshadow human error is uncertain yet has important theoretical and practical implications. The present study examined the temporal dynamics of electrocortical signals preceding a lapse of sustained attention. Twenty-one participants performed a continuous temporal expectancy task, which involved continuously monitoring a stream of regularly alternating patterned stimuli to detect a rarely occurring target stimulus whose duration was 40% longer. The stimulus stream flickered at a rate of 25 Hz to elicit a steady-state visual-evoked potential (SSVEP), which served as a continuous measure of basic visual processing. Increasing activity in the band (8 –14 Hz) was found beginning20 s before a missed target. This was followed by decreases in the amplitude of two event-related components over a short pretarget time frame: the frontal P3 (3– 4 s) and contingent-negative variation (during the target interval). In contrast, SSVEP amplitude before hits and misses was closely matched, suggesting that the efficacy of ongoing basic visual processing was unaffected. Our results show that the specific neural signatures of attentional lapses are registered in the EEG up to 20 s before an error

Observation of peripheral charge induced low frequency capacitance-voltage behaviour in metal-oxide-semiconductor capacitors on Si and GaAs substrates

We report on experimental observations of room temperature low frequency capacitance-voltage (CV) behaviour in metal oxide semiconductor (MOS) capacitors incorporating high dielectric constant (high-k) gate oxides, measured at ac signal frequencies (2 kHz to 1 MHz), where a low frequency response is not typically expected for Si or GaAs MOS devices. An analysis of the inversion regions of the CV characteristics as a function of area and ac signal frequency for both n and p doped Si and GaAs substrates indicates that the source of the low frequency CV response is an inversion of the semiconductor/high-k interface in the peripheral regions outside the area defined by the metal gate electrode, which is caused by charge in the high-k oxide and/or residual charge on the high-k oxide surface. This effect is reported for MOS capacitors incorporating either MgO or GdSiOx as the high-k layers on Si and also for Al2O3 layers on GaAs(111B). In the case of NiSi/MgO/Si structures, a low frequency CV response is observed on the p-type devices, but is absent in the n-type devices, consistent with positive charge (>8 x 10(10) cm(-2)) on the MgO oxide surface. In the case of the TiN/GdSiOx/Si structures, the peripheral inversion effect is observed for n-type devices, in this case confirmed by the absence of such effects on the p-type devices. Finally, for the case of Au/Ni/Al2O3/GaAs(111B) structures, a low-frequency CV response is observed for n-type devices only, indicating that negative charge (> 3 x 10(12) cm(-2)) on the surface or in the bulk of the oxide is responsible for the peripheral inversion effect. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4729331

Strain-induced phonon shifts in tungsten disulfide nanoplatelets and nanotubes

The relationship between structure and properties has been followed for different nanoscale forms of tungsten disulfide (2H-WS2) namely exfoliated monolayer and few-layer nanoplatelets, and nanotubes. The similarities and differences between these nanostructured materials have been examined using a combination of optical microscopy, scanning and high-resolution transmissionelectron microscopy (SEM and HRTEM) and atomic force microscopy (AFM). Photoluminescence (PL) and Raman spectroscopy have also been used to distinguish between monolayer and few-layer material. Strain induced phonon shifts have been followed from the changes in the positions of the A1g and E2g1 Raman bands during uniaxial deformation. This has been modelled for monolayer using density functional theory (DFT) with excellent agreement between the measured and predicted behaviour. It has been found that as the number of WS2 layers increases for few-layer crystals or nanotubes, the A1g mode hardens whereas the E2g1 mode softens. This is believed to be due to theA1g mode, which involves out of plane atomic movements, being constrained by the increasing number of WS2 layers whereas easy sliding reduces stress transfer to the individual layers for the E2g1mode, involving only in-plane vibrations. This finding has enabled the anomalous phonon shift behaviour in earlier pressure measurements on WS2 to be resolved, as well as similar effects in othertransition metal dichalcogenides, such as molybdenum disulfide (MoS2), to be explained. <br/

A restatement of the natural science evidence concerning catchment-based "natural” flood management in the United Kingdom

Flooding is a very costly natural hazard in Great Britain and is expected to increase further under future climate change scenarios. Flood defences are commonly deployed to protect communities and property from flooding, but in recent years flood management policy has looked towards solutions that seek to mitigate flood risk at flood-prone sites through targeted interventions throughout the catchment, sometimes using techniques which involve working with natural processes. This paper describes a project to provide a succinct summary of the natural science evidence base concerning the effectiveness of catchment-based “natural” flood management in the United Kingdom. The evidence summary is designed to be read by an informed but not technically-specialist audience. Each evidence statement is placed into one of four categories describing the nature of the underlying information. The evidence summary forms the appendix to this paper and an annotated bibliography is provided in the electronic supplementary material