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

VUV Study of Electron Impact Dissociative Excitation of Thymine

Dissociative excitation of thymine following electron impact was studied in the energy range up to 430 eV. Emissions in the vacuum ultra-violet spectral region below 150 nm were studied and found to be dominated by the hydrogen Lyman series. Emission cross section data reveal that Lyman-α excitation displays a broad maximum at an electron impact energy of 160 eV. The probability of extracting other excited atoms from the parent molecule is found to be insignificant. Possible excitation and dissociation mechanisms in the parent molecule are discussed

Production of O(1D) following electron impact on CO2

We have studied the excitation of metastable O(1D) following dissociative excitation of CO2 in the electron impact energy range from threshold to 400 eV. A solid Ne matrix at ∼20 K forms the heart of the detector. This is sensitive to the metastable species through the formation of excited excimers (NeO*), The resultant excimer radiation is readily detected, providing a means of measuring the production of the metastables. Using a pulsed electron beam and time-of-flight techniques, we have measured the O(1D) kinetic energy spectrum and its relative production cross sections as a function of electron impact energy. Threshold energy data are used to gain information about the excitation channels involved. In addition, an emission excitation function for the red photons, emitted in coincidence with the exciting electron pulse, has been measured in the 0–400 eV energy range

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

Flying Solo

This article is designed to assist solo librarians in thinking through their libraries, responsibilities,clientele, support personnel, and work habits in order to determine best practices to maximize their professional and personal effectiveness

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

Response of cereals to fertilizer N on pulse and other stubbles

Non-Peer ReviewedTo optimize cropping systems requires knowledge of effects of the preceding crop on the grain yield and protein and the response to N of a following cereal crop. To gain this knowledge, we grew hard red spring (HRS) wheat, durum wheat, Canadian Prairie Spring (CPS)-class wheat, Canadian Western Extra Strong (CWES)-class wheat, and barley on barley, bean, coriander, fenugreek, kabuli chickpea, lentil, mustard, and pea stubble at different N fertilizer rates over 9 site-yr: Swift Current (1998-2002), Redvers (2001-02), and Canora (1999 and 2002). N rates were medium (recommended rate based on fall soil nitrate in cereal stubble), low (15-30 kg ha-1 less than medium) and high (15-30 kg ha-1). There was a significant effect of stubble on subsequent cereal grain yield. Cereal on cereal stubble was consistently lowest or second lowest yielding (typically 100 – 800 kg ha-1 lower than other stubbles) with the exception of 2001 at Swift Current when it was the highest yielding. This latter effect was attributed to the superior moisture conserving benefits of cereal stubble during this year with extreme early drought. No single cereal crop was consistently highest or lowest yielding. The trend was for greatest grain protein on pulse stubbles although stubble effects on protein were not as great as on yield owing to confounding yield dilution effects. Within this narrow range of fertilizer N rates, yield or protein response to N was weak. Generally, there were no significant interactions between stubble and cereal crop or stubble and fertilizer indicating the effect of stubble was consistent across cereal type and N rates. The cereal yield and protein response to N on the non-cereal stubbles was not significantly different than that on cereal stubble with the exception that barley protein responded more positively to N on lentil stubble than on cereal stubble. Cereals grown on pulse stubbles tended to have higher yields and protein than on other stubbles. For HRS wheat and durum, the chance of achieving high protein grain was greatest with high fertilizer N on pea stubble (>75% of years). Applying a high fertilizer N rate on cereal stubbles did not markedly increase the chance of attaining high protein wheat or durum. For barley, where low protein is desired for malting, the best chance for low protein barley was on cereal and mustard stubble although barley protein appeared less affected by stubble and fertilizer N than wheat or durum

Atomic, Molecular, and Optical Physics: Optical Excitation Function of H(1s-2p) Produced by electron Impact from Threshold to 1.8 keV

The optical excitation function of prompt Lyman-Alpha radiation, produced by electron impact on atomic hydrogen, has been measured over the extended energy range from threshold to 1.8 keV. Measurements were obtained in a crossed-beams experiment using both magnetically confined and electrostatically focused electrons in collision with atomic hydrogen produced by an intense discharge source. A vacuum-ultraviolet mono- chromator system was used to measure the emitted Lyman-Alpha radiation. The absolute H(1s-2p) electron impact excitation cross section was obtained from the experimental optical excitation function by normalizing to the accepted optical oscillator strength, with corrections for polarization and cascade. Statistical and known systematic uncertainties in our data range from +/- 4% near threshold to +/- 2% at 1.8 keV. Multistate coupling affecting the shape of the excitation function up to 1 keV impact energy is apparent in both the present experimental data and present theoretical results obtained with convergent close- coupling (CCC) theory. This shape function effect leads to an uncertainty in absolute cross sections at the 10% level in the analysis of the experimental data. The derived optimized absolute cross sections are within 7% of the CCC calculations over the 14 eV-1.8 keV range. The present CCC calculations converge on the Bethe- Fano profile for H(1s-2p) excitation at high energy. For this reason agreement with the CCC values to within 3% is achieved in a nonoptimal normalization of the experimental data to the Bethe-Fano profile. The fundamental H(1s-2p) electron impact cross section is thereby determined to an unprecedented accuracy over the 14 eV - 1.8 keV energy range