Peter Y. Wong

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Identification of protein–protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization–time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein–protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein–protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

Thermal expansion coefficient of polycrystalline silicon and silicon dioxide thin films at high temperatures

The rapid growth of microelectromechanical systems (MEMS) industry has introduced a need for the characterization of thin film properties at all temperatures encountered during fabrication and application of the devices. A technique was developed to use MEMS test structures for the determination of the difference in thermal expansion coefficients (α) between poly-Si and SiO2 thin films at high temperatures. The test structure consists of multilayered cantilever beams, fabricated using standard photolithography techniques. An apparatus was developed to measure the thermally induced curvature of beams at high temperatures using imaging techniques. The curvatures measured were compared to the numerical model for multilayered beam curvature. The model accounts for the variation in thermomechanical properties with temperature. The beams were designed so that the values of Young’s moduli had negligible effect on beam curvature; therefore, values from literature were used for ESi and ESiO2 without introducing si...

β‐Subunit appendages promote 20S proteasome assembly by overcoming an Ump1‐dependent checkpoint

Proteasomes are responsible for most intracellular protein degradation in eukaryotes. The 20S proteasome comprises a dyad‐symmetric stack of four heptameric rings made from 14 distinct subunits. How it assembles is not understood. Most subunits in the central pair of β‐subunit rings are synthesized in precursor form. Normally, the β5 (Doa3) propeptide is essential for yeast proteasome biogenesis, but overproduction of β7 (Pre4) bypasses this requirement. Bypass depends on a unique β7 extension, which contacts the opposing β ring. The resulting proteasomes appear normal but assemble inefficiently, facilitating identification of assembly intermediates. Assembly occurs stepwise into precursor dimers, and intermediates contain the Ump1 assembly factor and a novel complex, Pba1–Pba2. β7 incorporation occurs late and is closely linked to the association of two half‐proteasomes. We propose that dimerization is normally driven by the β5 propeptide, an intramolecular chaperone, but β7 addition overcomes an Ump1‐dependent assembly checkpoint and stabilizes the precursor dimer.

Difference detection in LC-MS data for protein biomarker discovery

MOTIVATION There is a pressing need for improved proteomic screening methods allowing for earlier diagnosis of disease, systematic monitoring of physiological responses and the uncovering of fundamental mechanisms of drug action. The combined platform of LC-MS (Liquid-Chromatography-Mass-Spectrometry) has shown promise in moving toward a solution in these areas. In this paper we present a technique for discovering differences in protein signal between two classes of samples of LC-MS serum proteomic data without use of tandem mass spectrometry, gels or labeling. This method works on data from a lower-precision MS instrument, the type routinely used by and available to the community at large today. We test our technique on a controlled (spike-in) but realistic (serum biomarker discovery) experiment which is therefore verifiable. We also develop a new method for helping to assess the difficulty of a given spike-in problem. Lastly, we show that the problem of class prediction, sometimes mistaken as a solution to biomarker discovery, is actually a much simpler problem. RESULTS Using precision-recall curves with experimentally extracted ground truth, we show that (1) our technique has good performance using seven replicates from each class, (2) performance degrades with decreasing number of replicates, (3) the signal that we are teasing out is not trivially available (i.e. the differences are not so large that the task is easy). Lastly, we easily obtain perfect classification results for data in which the problem of extracting differences does not produce absolutely perfect results. This emphasizes the different nature of the two problems and also their relative difficulties. AVAILABILITY Our data are publicly available as a benchmark for further studies of this nature at http://www.cs.toronto.edu/~jenn/LCMS

ARGOS: a display system for augmenting reality

This video describes the development of the ARGOS (Augmented Reality through Graphic Overlays on Stereovideo) system, as a tool for enhancing humantelerobot interaction, and as a more general tool with applications in a variety of areas, including image enhancement, simulation, sensor fusion, and virtual reality.

Effects of a butterfly scale microstructure on the iridescent color observed at different angles

Multilayer thin-film structures in butterfly wing scales produce a colorful iridescence from reflected sunlight. Because of optical phenomena, changes in the angle of incidence of light and the viewing angle of an observer result in shifts in the color of butterfly wings. Colors ranging from green to purple, which are due to nonplanar specular reflection, can be observed on Papilio blumei iridescent scales. This refers to a phenomenon in which the curved surface patterns in the thin-film structure cause the specular component of the reflected light to be directed at various angles while affecting the spectral reflectivity at the same time by changing the optical path length through the structure. We determined the spectral reflectivities of P. blumei iridescent scales numerically by using models of a butterfly scale microstructure and experimentally by using a microscale-reflectance spectrometer. The numerical models accurately predict the shifts in spectral reflectivity observed experimentally.

Interactions of the Escherichia coli hydrogenase biosynthetic proteins: HybG complex formation☆

Assembly of the active site of the [NiFe]‐hydrogenase enzymes involves a multi‐step pathway and the coordinated activity of many accessory proteins. To analyze complex formation between these factors in Escherichia coli, they were genomically tagged and native multi‐protein complexes were isolated. This method validated multiple interactions reported in separate studies from several organisms and defined a new complex containing the putative chaperone HybG and the large subunit of hydrogenase 1 or 2. The complex also includes HypE and HypD, which interact with each other before joining the larger complex.

Factors selecting for avoidance of drilled shells by the hermit crab Pagurus longicarpus

Periwinkle shells (Littorina littorea) that have been drilled by moon snails are abundant at Nahant, MA, and yet hermit crabs (Pagurus longicarpus) are rarely found living in them. In the laboratory, hermit crabs will occupy drilled shells only if no other options are provided to them; they will, in fact, choose intact shells that are too small for them over drilled shells of appropriate size. This paper documents the selective forces that might account for this marked avoidance of drilled shells by hermit crabs. We show that drilled shells increase the vulnerability of the hermit crabs to decapod predators (e.g., the green crab, Carcinus maenas), in part by allowing predators to enlarge the drill hole and also by reducing the force needed for predators to crack the shells open. Living in drilled shells also made the hermit crabs in our study more vulnerable to eviction by conspecifics and more vulnerable to low-salinity stress. Thus, moon snail predation on periwinkles, rather than supplying the Nahant hermit crab population with suitable empty snail shells, actually serves to destroy a potential resource for the hermit crabs and apparently to heighten competition among hermit crabs for intact shells.

Thermal radiation modeling in multilayer thin film structures

Abstract A general technique is developed to account for the microscale heat transfer effects involved with the interaction of thermal radiation and multilayer thin films. In particular, the microscale radiation effects involved with both the emission from the multilayer structure and the reflection of incident radiation are described in detail. Considerable optical interference within the structure occurs when the film thicknesses are on the same order of magnitude as the wavelengths of the incident or emitted radiation; therefore, the net surface reflectivity and emission from the film structure are altered by slight changes in film thickness. Consequently, during high temperature thermal processing of micron thickness films, the resultant temperature profiles and the quality of the processed structure will be affected. The reflectivities and emissivities are calculated numerically using the matrix method for several different layering structures subject to thermal radiation. For the special case of equal optical film thicknesses, cross-correlation peaks are identified; these layering schemes are very sensitive to small film thickness changes. Maximum temperatures attained during thermal processing are calculated for several specific film structures to illustrate the significance of these effects.

Thermal modeling of zone‐melting‐recrystallization processing of silicon‐on‐insulator film structures

A numerical simulation model that considers changes in thermal and radiation properties during zone‐melting‐recrystallization processing of silicon‐on‐insulator film structures with a graphite strip heater was developed. A series of numerical experiments were conducted to investigate the conductive, convective, and radiative parameters affecting the process. The variability of the thermal conductivity of silicon as a function of temperature at the premelting stage and the variation in thermal conductivity due to the multilayer nature of the structure were found not to affect of the temperature distribution during processing. The convective heat losses induced by the inert gas in the processing chamber does not affect significantly the temperature profiles in the film structure, but can reduce the melt zone width by 10%–25%. The study of radiative effects focused on the effects of varying the width and height of the graphite strip and the distance between the graphite strip and the film structure. These pa...