Two Distinct Cdc2 Pools Regulate Cell Cycle Progression and the DNA Damage Response in the Fission Yeast S.pombe

The activity of Cdc2 (CDK1) kinase, which coordinates cell cycle progression and DNA break repair, is blocked upon its phosphorylation at tyrosine 15 (Y15) by Wee1 kinase in the presence of DNA damage. How Cdc2 can support DNA repair whilst being inactivated by the DNA damage checkpoint remains to be explained. Human CDK1 is phosphorylated by Myt1 kinase at threonine 14 (T14) close to its ATP binding site before being modified at threonine 161 (T167Sp) in its T-loop by the CDK-activating kinase (CAK). While modification of T161 promotes association with the cyclin partner, phosphorylation of T14 inhibits the CDK1-cyclin complex. This inhibition is further enforced by the modification of Y15 by Wee1 in the presence of DNA lesions. In S.pombe, the dominant inhibition of Cdc2 is provided by the phosphorylation of Y15 and only a small amount of Cdc2 is modified at T14 when cells are in S phase. Unlike human cells, both inhibitory modifications are executed by Wee1. Using the novel IEFPT technology, which combines isoelectric focusing (IEF) with Phos-tag SDS electrophoresis (PT), we report here that S.pombe Cdc2 kinase exists in seven forms. While five forms are phosphorylated, two species are not. Four phospho-forms associate with cyclin B (Cdc13) of which only two are modified at Y15 by Wee1. Interestingly, only one Y15-modified species carries also the T14 modification. The fifth phospho-form has a low affinity for cyclin B and is neither Y15 nor T14 modified. The two unphosphorylated forms may contribute directly to the DNA damage response as only they associate with the DNA damage checkpoint kinase Chk1. Interestingly, cyclin B is also present in the unphosphorylated pool. We also show that the G146D mutation in Cdc2.1w, which renders Cdc2 insensitive to Wee1 inhibition, is aberrantly modified in a Wee1-dependent manner. In conclusion, our work adds support to the idea that two distinct Cdc2 pools regulate cell cycle progression and the response to DNA damage

Feasibility of time-lapse seismic methodology for monitoring the injection of small quantities of CO2 into a saline formation, CO2CRC Otway Project

A key objective of Stage 2 of the CO2CRC Otway Project is to explore the ability of geophysical methods to detect and monitor injection of greenhouse gas into a saline formation. For this purpose, injection of some 10,000 30,000 tonnes of CO2-rich mixture into the Paaratte formation, a saline aquifer located at a depth of about 1,400 m, is planned. Before such an injection experiment is undertaken, we assess the feasibility of geophysical monitoring using computer modelling. To examine the detectability of the plume we need to estimate the time-lapse signal and time- lapse noise. The time lapse signal is modelled using flow simulations, fluid substitution and seismic forward modelling. In order to assess the applicability of time-lapse seismic to monitor the injection, the predicted signal is compared to the time-lapse noise level from the recent 4D seismic survey acquired at the Otway site in 2009-2010. The methodology is applied to two alternative reservoir intervals located at a depth of 1392-1399 m and 1445-1465 m below the sea level, respectively. These intervals are considered to be the two possible options for the injection. The results show that injection into the lower interval will produce a plume of a larger thickness and smaller lateral extent, and a seismic response that is more likely to be detectable. The developed feasibility assessment workflow, and the results of its application to the Otway site, can be used to assess the ability of seismic methods to detect and monitor greenhouse gas leakage in other CCS projects

Time-lapse sonic logs reveal patchy CO2 saturation in-situ

Based on time-lapse sonic and neutron porosity logs from the Nagaoka CO2 sequestration experiment, a P-wave velocity-saturation relation at reservoir depth is retrieved. It does not coincide with either of the end-member models of uniform and patchy saturation but falls in between even if realistic error estimates for the host rock properties are considered. Assuming a random distribution of CO2 patches it is shown that the mechanism of wave-induced flow can be evoked to explain this velocity-saturation relation. Characteristic CO2 patch size estimates range from 1 to 5 mm. Such mesoscopic heterogeneity can be responsible for attenuation and dispersion in the well logging frequency band

Checkpoints are blind to replication restart and recombination intermediates that result in gross chromosomal rearrangements

Replication fork inactivation can be overcome by homologous recombination, but this can cause gross chromosomal rearrangements that subsequently missegregate at mitosis, driving further chromosome instability. It is unclear when the chromosome rearrangements are generated and whether individual replication problems or the resulting recombination intermediates delay the cell cycle. Here we have investigated checkpoint activation during HR-dependent replication restart using a site-specific replication fork-arrest system. Analysis during a single cell cycle shows that HR-dependent replication intermediates arise in S phase, shortly after replication arrest, and are resolved into acentric and dicentric chromosomes in G2. Despite this, cells progress into mitosis without delay. Neither the DNA damage nor the intra-S phase checkpoints are activated in the first cell cycle, demonstrating that these checkpoints are blind to replication and recombination intermediates as well as to rearranged chromosomes. The dicentrics form anaphase bridges that subsequently break, inducing checkpoint activation in the second cell cycle

Pyrenoid loss in Chlamydomonas reinhardtii causes limitations in CO2 supply, but not thylakoid operating efficiency

The pyrenoid of the unicellular green alga Chlamydomonas reinhardtii is a microcompartment situated in the centre of the cup-shaped chloroplast, containing up to 90% of cellular Rubisco. Traversed by a network of dense, knotted thylakoid tubules, the pyrenoid has been proposed to influence thylakoid biogenesis and ultrastructure. Mutants that are unable to assemble a pyrenoid matrix, due to expressing a vascular plant version of the Rubisco small subunit, exhibit severe growth and photosynthetic defects and have an ineffective carbon-concentrating mechanism (CCM). The present study set out to determine the cause of photosynthetic limitation in these pyrenoid-less lines. We tested whether electron transport and light use were compromised as a direct structural consequence of pyrenoid loss or as a metabolic effect downstream of lower CCM activity and resulting CO₂ limitation. Thylakoid organization was unchanged in the mutants, including the retention of intrapyrenoid-type thylakoid tubules, and photosynthetic limitations associated with the absence of the pyrenoid were rescued by exposing cells to elevated CO₂ levels. These results demonstrate that Rubisco aggregation in the pyrenoid functions as an essential element for CO₂ delivery as part of the CCM, and does not play other roles in maintenance of photosynthetic membrane energetics.We wish to gratefully acknowledge financial support to ODC by Wolfson College, the Cambridge Philosophical Society and the TH Middleton Fund (Department of Plant Sciences) toward research-related travel, which was crucial to enable this collaborative study. This work was supported by the Biotechnology and Biological Sciences Research Council (PhD studentship 1090746 to ODC and BB/M007693/1 to MTM and HG). The work was also supported by NSF grant MCB 0951094 and US Department of Energy Grants DE-FG02-07ER64427, DE- FG02-12ER16338 awarded to ARG

SUMO chain formation is required for response to replication arrest in S. pombe

SUMO is a ubiquitin-like protein that is post-translationally attached to one or more lysine residues on target proteins. Despite having only 18% sequence identity with ubiquitin, SUMO contains the conserved betabetaalphabetabetaalphabeta fold present in ubiquitin. However, SUMO differs from ubiquitin in having an extended N-terminus. In S. pombe the N-terminus of SUMO/Pmt3 is significantly longer than those of SUMO in S. cerevisiae, human and Drosophila. Here we investigate the role of this N-terminal region. We have used two dimensional gel electrophoresis to demonstrate that S. pombe SUMO/Pmt3 is phosphorylated, and that this occurs on serine residues at the extreme N-terminus of the protein. Mutation of these residues (in pmt3-1) results in a dramatic reduction in both the levels of high Mr SUMO-containing species and of total SUMO/Pmt3, indicating that phosphorylation of SUMO/Pmt3 is required for its stability. Despite the significant reduction in high Mr SUMO-containing species, pmt3-1 cells do not display an aberrant cell morphology or sensitivity to genotoxins or stress. Additionally, we demonstrate that two lysine residues in the N-terminus of S. pombe SUMO/Pmt3 (K14 and K30) can act as acceptor sites for SUMO chain formation in vitro. Inability to form SUMO chains results in aberrant cell and nuclear morphologies, including stretched and fragmented chromatin. SUMO chain mutants are sensitive to the DNA synthesis inhibitor, hydroxyurea (HU), but not to other genotoxins, such as UV, MMS or CPT. This implies a role for SUMO chains in the response to replication arrest in S. pomb

Consensus over Random Graph Processes: Network Borel-Cantelli Lemmas for Almost Sure Convergence

Distributed consensus computation over random graph processes is considered. The random graph process is defined as a sequence of random variables which take values from the set of all possible digraphs over the node set. At each time step, every node updates its state based on a Bernoulli trial, independent in time and among different nodes: either averaging among the neighbor set generated by the random graph, or sticking with its current state. Connectivity-independence and arc-independence are introduced to capture the fundamental influence of the random graphs on the consensus convergence. Necessary and/or sufficient conditions are presented on the success probabilities of the Bernoulli trials for the network to reach a global almost sure consensus, with some sharp threshold established revealing a consensus zero-one law. Convergence rates are established by lower and upper bounds of the $\epsilon$-computation time. We also generalize the concepts of connectivity/arc independence to their analogues from the $*$-mixing point of view, so that our results apply to a very wide class of graphical models, including the majority of random graph models in the literature, e.g., Erd\H{o}s-R\'{e}nyi, gossiping, and Markovian random graphs. We show that under $*$-mixing, our convergence analysis continues to hold and the corresponding almost sure consensus conditions are established. Finally, we further investigate almost sure finite-time convergence of random gossiping algorithms, and prove that the Bernoulli trials play a key role in ensuring finite-time convergence. These results add to the understanding of the interplay between random graphs, random computations, and convergence probability for distributed information processing.Comment: IEEE Transactions on Information Theory, In Pres

Contextual factors in shared decision making: a randomised controlled trial in women with a strong suspicion of breast cancer

Decision aids in North American breast cancer outpatients have been shown to assist with treatment decision making and reduce decisional conflict. To date, appropriate delivery formats to effectively increase patient participation in newly diagnosed breast cancer inpatients have not been investigated in the context of German health care provision. The impact of a decision aid intervention was studied in patients (n=111) with a strong suspicion of breast cancer in a randomised controlled trial. The primary outcome variable was decisional conflict. Participants were followed up 1 week post-intervention with a retention rate of 92%. Analyses revealed that the intervention group felt better informed (ηp2=0.06) but did not experience an overall reduction in decisional conflict as compared with the control group. The intervention had no effect on uptake rates of treatment options, length of consultation with the surgeon, time point of treatment decision making, perceived involvement in decision making, neither decision related nor general patient satisfaction. Patients who received the decision aid intervention experienced a small benefit with regards to how informed they felt about advantages and disadvantages of relevant treatment options. Results are discussed in terms of contextual factors and individual differences as moderators of treatment decision aid effectiveness