A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations.

BackgroundEukaryotic cell proliferation involves DNA replication, a tightly regulated process mediated by a multitude of protein factors. In budding yeast, the initiation of replication is facilitated by the heterohexameric origin recognition complex (ORC). ORC binds to specific origins of replication and then serves as a scaffold for the recruitment of other factors such as Cdt1, Cdc6, the Mcm2-7 complex, Cdc45 and the Dbf4-Cdc7 kinase complex. While many of the mechanisms controlling these associations are well documented, mathematical models are needed to explore the network's dynamic behaviour. We have developed an ordinary differential equation-based model of the protein-protein interaction network describing replication initiation.ResultsThe model was validated against quantified levels of protein factors over a range of cell cycle timepoints. Using chromatin extracts from synchronized Saccharomyces cerevisiae cell cultures, we were able to monitor the in vivo fluctuations of several of the aforementioned proteins, with additional data obtained from the literature. The model behaviour conforms to perturbation trials previously reported in the literature, and accurately predicts the results of our own knockdown experiments. Furthermore, we successfully incorporated our replication initiation model into an established model of the entire yeast cell cycle, thus providing a comprehensive description of these processes.ConclusionsThis study establishes a robust model of the processes driving DNA replication initiation. The model was validated against observed cell concentrations of the driving factors, and characterizes the interactions between factors implicated in eukaryotic DNA replication. Finally, this model can serve as a guide in efforts to generate a comprehensive model of the mammalian cell cycle in order to explore cancer-related phenotypes

The origin recognition complex protein family

The proteins of the origin recognition complex are found throughout all eukaryotes and have roles beyond that of DNA replication

Differential chromatin proteomics of the MMS-induced DNA damage response in yeast

<p>Abstract</p> <p>Background</p> <p>Protein enrichment by sub-cellular fractionation was combined with differential-in-gel-electrophoresis (DIGE) to address the detection of the low abundance chromatin proteins in the budding yeast proteome. Comparisons of whole-cell extracts and chromatin fractions were used to provide a measure of the degree of chromatin association for individual proteins, which could be compared across sample treatments. The method was applied to analyze the effect of the DNA damaging agent methyl methanesulfonate (MMS) on levels of chromatin-associated proteins.</p> <p>Results</p> <p>Up-regulation of several previously characterized DNA damage checkpoint-regulated proteins, such as Rnr4, Rpa1 and Rpa2, was observed. In addition, several novel DNA damage responsive proteins were identified and assessed for genotoxic sensitivity using either DAmP (decreased abundance by mRNA perturbation) or knockout strains, including Acf2, Arp3, Bmh1, Hsp31, Lsp1, Pst2, Rnr4, Rpa1, Rpa2, Ste4, Ycp4 and Yrb1. A strain in which the expression of the Ran-GTPase binding protein Yrb1 was reduced was found to be hypersensitive to genotoxic stress.</p> <p>Conclusion</p> <p>The described method was effective at unveiling chromatin-associated proteins that are less likely to be detected in the absence of fractionation. Several novel proteins with altered chromatin abundance were identified including Yrb1, pointing to a role for this nuclear import associated protein in DNA damage response.</p

Extra-corporeal membrane oxygenation in the management of 2009 influenza A (H1N1) refractory respiratory failure.

Rapidly progressive acute respiratory failure attributed to 2009 H1N1 influenza A infection has been reported worldwide-3. Refractory hypoxaemia despite conventional mechanical ventilation and lung protective strategies has resulted in the use a combination of rescue therapies, such as conservative fluid management, prone positioning, inhaled nitric oxide, high frequency oscillatory ventilation and extracorporeal membrane oxygenation (ECMO)4. ECMO allows for pulmonary or cardiopulmonary support as an adjunct to respiratory and cardiac failure, minimising ventilator-associated lung injury (VALI). This permits treatment of the underlying disease process, while concurrently allowing for recovery of the acute lung injury. This case documents a previously healthy twenty-two year old Asian male patient with confirmed pandemic (H 1N1) 2009 influenza A who was successfully managed with ECMO in the setting of severe refractory hypoxaemia and progressive hypercapnia

The Quantum Socket: Three-Dimensional Wiring for Extensible Quantum Computing

Quantum computing architectures are on the verge of scalability, a key requirement for the implementation of a universal quantum computer. The next stage in this quest is the realization of quantum error correction codes, which will mitigate the impact of faulty quantum information on a quantum computer. Architectures with ten or more quantum bits (qubits) have been realized using trapped ions and superconducting circuits. While these implementations are potentially scalable, true scalability will require systems engineering to combine quantum and classical hardware. One technology demanding imminent efforts is the realization of a suitable wiring method for the control and measurement of a large number of qubits. In this work, we introduce an interconnect solution for solid-state qubits: The quantum socket. The quantum socket fully exploits the third dimension to connect classical electronics to qubits with higher density and better performance than two-dimensional methods based on wire bonding. The quantum socket is based on spring-mounted micro wires the three-dimensional wires that push directly on a micro-fabricated chip, making electrical contact. A small wire cross section (~1 mmm), nearly non-magnetic components, and functionality at low temperatures make the quantum socket ideal to operate solid-state qubits. The wires have a coaxial geometry and operate over a frequency range from DC to 8 GHz, with a contact resistance of ~150 mohm, an impedance mismatch of ~10 ohm, and minimal crosstalk. As a proof of principle, we fabricated and used a quantum socket to measure superconducting resonators at a temperature of ~10 mK.Comment: Main: 31 pages, 19 figs., 8 tables, 8 apps.; suppl.: 4 pages, 5 figs. (HiRes figs. and movies on request). Submitte

The art of being human : a project for general philosophy of science

Throughout the medieval and modern periods, in various sacred and secular guises, the unification of all forms of knowledge under the rubric of ‘science’ has been taken as the prerogative of humanity as a species. However, as our sense of species privilege has been called increasingly into question, so too has the very salience of ‘humanity’ and ‘science’ as general categories, let alone ones that might bear some essential relationship to each other. After showing how the ascendant Stanford School in the philosophy of science has contributed to this joint demystification of ‘humanity’ and ‘science’, I proceed on a more positive note to a conceptual framework for making sense of science as the art of being human. My understanding of ‘science’ is indebted to the red thread that runs from Christian theology through the Scientific Revolution and Enlightenment to the Humboldtian revival of the university as the site for the synthesis of knowledge as the culmination of self-development. Especially salient to this idea is science‘s epistemic capacity to manage modality (i.e. to determine the conditions under which possibilities can be actualised) and its political capacity to organize humanity into projects of universal concern. However, the challenge facing such an ideal in the twentyfirst century is that the predicate ‘human’ may be projected in three quite distinct ways, governed by what I call ‘ecological’, ‘biomedical’ and ‘cybernetic’ interests. Which one of these future humanities would claim today’s humans as proper ancestors and could these futures co-habit the same world thus become two important questions that general philosophy of science will need to address in the coming years

Modular Evolution and the Origins of Symmetry: Reconstruction of a Three-Fold Symmetric Globular Protein

SummaryThe high frequency of internal structural symmetry in common protein folds is presumed to reflect their evolutionary origins from the repetition and fusion of ancient peptide modules, but little is known about the primary sequence and physical determinants of this process. Unexpectedly, a sequence and structural analysis of symmetric subdomain modules within an abundant and ancient globular fold, the β-trefoil, reveals that modular evolution is not simply a relic of the ancient past, but is an ongoing and recurring mechanism for regenerating symmetry, having occurred independently in numerous existing β-trefoil proteins. We performed a computational reconstruction of a β-trefoil subdomain module and repeated it to form a newly three-fold symmetric globular protein, ThreeFoil. In addition to its near perfect structural identity between symmetric modules, ThreeFoil is highly soluble, performs multivalent carbohydrate binding, and has remarkably high thermal stability. These findings have far-reaching implications for understanding the evolution and design of proteins via subdomain modules