System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

Yeast remains an important model for systems biology and for evaluating proteomics strategies. In-depth shotgun proteomics studies have reached nearly comprehensive coverage, and rapid, targeted approaches have been developed for this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns and gradients coupled to a linear ion trap Orbitrap instrument had an unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell Proteomics 10, 10.1074/mcp.M110.003699). Here we couple an ultra high pressure liquid chromatography system to a novel bench top Orbitrap mass spectrometer (Q Exactive) with the goal of nearly complete, rapid, and robust analysis of the yeast proteome. Single runs of filter-aided sample preparation (FASP)-prepared and LysC-digested yeast cell lysates identified an average of 3923 proteins. Combined analysis of six single runs improved these values to more than 4000 identified proteins/run, close to the total number of proteins expressed under standard conditions, with median sequence coverage of 23%. Because of the absence of fractionation steps, only minuscule amounts of sample are required. Thus the yeast model proteome can now largely be covered within a few hours of measurement time and at high sensitivity. Median coverage of proteins in Kyoto Encyclopedia of Genes and Genomes pathways with at least 10 members was 88%, and pathways not covered were not expected to be active under the conditions used. To study perturbations of the yeast proteome, we developed an external, heavy lysine-labeled SILAC yeast standard representing different proteome states. This spike-in standard was employed to measure the heat shock response of the yeast proteome. Bioinformatic analysis of the heat shock response revealed that translation-related functions were down-regulated prominently, including nucleolar processes. Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities

Ptychographic X-ray tomography reveals additive zoning in nanocomposite single crystals

Single crystals containing nanoparticles represent a unique class of nanocomposites whose properties are defined by both their compositions and the structural organization of the dispersed phase in the crystalline host. Yet, there is still a poor understanding of the relationship between the synthesis conditions and the structures of these materials. Here ptychographic X-ray computed tomography is used to visualize the three-dimensional structures of two nanocomposite crystals – single crystals of calcite occluding diblock copolymer worms and vesicles. This provides unique information about the distribution of the copolymer nano-objects within entire, micron-sized crystals with nanometer spatial resolution and reveals how occlusion is governed by factors including the supersaturation and calcium concentration. Both nanocomposite crystals are seen to exhibit zoning effects that are governed by the solution composition and interactions of the additives with specific steps on the crystal surface. Additionally, the size and shape of the occluded vesicles varies according to their location within the crystal, and therefore the solution composition at the time of occlusion. This work contributes to our understanding of the factors that govern nanoparticle occlusion within crystalline materials, where this will ultimately inform the design of next generation nanocomposite materials with specific structure/property relationships

Development of an approximate method for quantum optical models and their pseudo-Hermicity

An approximate method is suggested to obtain analytical expressions for the eigenvalues and eigenfunctions of the some quantum optical models. The method is based on the Lie-type transformation of the Hamiltonians. In a particular case it is demonstrated that $E\times \epsilon$ Jahn-Teller Hamiltonian can easily be solved within the framework of the suggested approximation. The method presented here is conceptually simple and can easily be extended to the other quantum optical models. We also show that for a purely imaginary coupling the $E\times \epsilon$ Hamiltonian becomes non-Hermitian but $P\sigma _{0}$-symmetric. Possible generalization of this approach is outlined.Comment: Paper prepared fo the "3rd International Workshop on Pseudo-Hermitian Hamiltonians in Quantum Physics" June 2005 Istanbul. To be published in Czechoslovak Journal of Physic

In search of the origins and enduring impact of agile software development

The Agile Manifesto is a philosophical touchpoint for all agile software development (ASD) methods. We examine the manifesto and some of its associated agile methods in an effort to identify the major impacts of ASD. We have encountered some difficulty in delineating agile and non-agile software processes, which is partially the result of terminological confusion. It is clear from the volume of published research that ASD has made a significant contribution, and we have identified two lasting and important impacts. Firstly, the reduction in iteration durations and secondly, the push for reduced levels of documentation (especially in relation to software requirements). Other aspects of the Agile Manifesto may not have exerted a significant impact; for example, the use of tooling to automate processes has become central to continuous software engineering (CSE) and may not be wholly congruent with the manifesto. Furthermore, many organisations may still rely on business contracts despite calls in the manifesto for greater levels of informal customer collaboration