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Bauer, S. E.,Wright, D. L.,Koch, D.,Lewis, E. R.,McGraw, R.,Chang, L.-S.,Schwartz, S. E.,Ruedy, R. Copernicus GmbH 2008 Atmospheric Chemistry and Physics Vol.8 No.20
<P>Abstract. A new aerosol microphysical module MATRIX, the Multiconfiguration Aerosol TRacker of mIXing state, and its application in the Goddard Institute for Space Studies (GISS) climate model (ModelE) are described. This module, which is based on the quadrature method of moments (QMOM), represents nucleation, condensation, coagulation, internal and external mixing, and cloud-drop activation and provides aerosol particle mass and number concentration and particle size information for up to 16 mixed-mode aerosol populations. Internal and external mixing among aerosol components sulfate, nitrate, ammonium, carbonaceous aerosols, dust and sea-salt particles are represented. The solubility of each aerosol population, which is explicitly calculated based on its soluble and insoluble components, enables calculation of the dependence of cloud drop activation on the microphysical characterization of multiple soluble aerosol populations. A detailed model description and results of box-model simulations of various aerosol population configurations are presented. The box model experiments demonstrate the dependence of cloud activating aerosol number concentration on the aerosol population configuration; comparisons to sectional models are quite favorable. MATRIX is incorporated into the GISS climate model and simulations are carried out primarily to assess its performance/efficiency for global-scale atmospheric model application. Simulation results were compared with aircraft and station measurements of aerosol mass and number concentration and particle size to assess the ability of the new method to yield data suitable for such comparison. The model accurately captures the observed size distributions in the Aitken and accumulation modes up to particle diameter 1 μm, in which sulfate, nitrate, black and organic carbon are predominantly located; however the model underestimates coarse-mode number concentration and size, especially in the marine environment. This is more likely due to oversimplifications of the representation of sea salt emissions - sea salt emissions are only calculated for two size classes - than to inherent limitations of MATRIX. </P>
Omenn, Gilbert S.,Aebersold, Ruedi,Paik, Young-Ki WILEY-VCH Verlag 2009 Proteomics Vol.9 No.1
<P>The HUPO Plasma Proteome Project new phase, PPP-2, held its initial workshop on 17 August, 2008, at the 7<SUP>th</SUP> World Congress of Proteomics in Amsterdam. Technology platforms, data repositories, informatics, and engagement of research groups for the submission of major datasets were key topics. Plasma is expected to be the common pathway for biomarker development and application through collaboration and integration with other HUPO initiatives.</P>
Gehlenborg, Nils,Yan, Wei,Lee, Inyoul Y,Yoo, Hyuntae,Nieselt, Kay,Hwang, Daehee,Aebersold, Ruedi,Hood, Leroy Oxford University Press 2009 Bioinformatics Vol.25 No.5
<P>SUMMARY: We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies. AVAILABILITY: http://prequips.sourceforge.net</P>
Yoon, Jungmin,Kim, Seung Joong,An, Sojin,Cho, Saehyun,Leitner, Alexander,Jung, Taeyang,Aebersold, Ruedi,Hebert, Hans,Cho, Uhn-Soo,Song, Ji-Joon Elsevier 2018 Journal of molecular biology Vol.430 No.6
<P><B>Abstract</B></P> <P>Importin4 transports histone H3/H4 in complex with Asf1a to the nucleus for chromatin assembly. Importin4 recognizes the nuclear localization sequence located at the N-terminal tail of histones. Here, we analyzed the structures and interactions of human Importin4, histones and Asf1a by cross-linking mass spectrometry, X-ray crystallography, negative-stain electron microscopy, small-angle X-ray scattering and integrative modeling. The cross-linking mass spectrometry data showed that the C-terminal region of Importin4 was extensively cross-linked with the histone H3 tail. We determined the crystal structure of the C-terminal region of Importin4 bound to the histone H3 peptide, thus revealing that the acidic patch in Importin4 accommodates the histone H3 tail, and that histone H3 Lys14 contributes to the interaction with Importin4. In addition, we show that Asf1a modulates the binding of histone H3/H4 to Importin4. Furthermore, the molecular architecture of the Importin4_histone H3/H4_Asf1a complex was produced through an integrative modeling approach. Overall, this work provides structural insights into how Importin4 recognizes histones and their chaperone complex.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The C-terminal region of Importin4 extensively interacts with the N-terminal tail of histone H3. </LI> <LI> The crystal structure of the C-terminal region of Importin4 with a histone H3 peptide shows that histone H3 binds to the acidic patch in Importin4. </LI> <LI> Histone H3 K14 is the primary residue interacting with Importin4. </LI> <LI> Asf1a modulates the binding of histone H3/H4 to Importin4. </LI> <LI> The molecular architecture of the Importin4_Histone H3/H4_Asf1a complex was produced through an integrative modeling approach that combined X-ray crystallography, cross-linking mass-spectrometry and negative-stain electron microscopy data. </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>
Hyung, Seok-Won,Lee, Min Young,Yu, Jong-Han,Shin, Byunghee,Jung, Hee-Jung,Park, Jong-Moon,Han, Wonshik,Lee, Kyung-Min,Moon, Hyeong-Gon,Zhang, Hui,Aebersold, Ruedi,Hwang, Daehee,Lee, Sang-Won,Yu, Myeon American Society for Biochemistry and Molecular Bi 2011 Molecular & cellular proteomics Vol.10 No.10
Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population
Williams, Evan G.,Wu, Yibo,Wolski, Witold,Kim, Jun Yong,Lan, Jiayi,Hasan, Moaraj,Halter, Christian,Jha, Pooja,Ryu, Dongryeol,Auwerx, Johan,Aebersold, Ruedi American Society for Biochemistry and Molecular Bi 2018 Molecular and Cellular Proteomics Vol.17 No.9
<P>We have used SWATH mass spectrometry to quantify 3648 proteins across 76 proteomes collected from genetically diverse BXD mouse strains in two fractions (mitochondria and total cell) from five tissues: liver, quadriceps, heart, brain, and brown adipose (BAT). Across tissues, expression covariation between genes' proteins and transcripts-measured in the same individuals-broadly aligned. Covariation was however far stronger in certain subsets than others: only 8% of transcripts in the lowest expression and variance quintile covaried with their protein, in contrast to 65% of transcripts in the highest quintiles. Key functional differences among the 3648 genes were also observed across tissues, with electron transport chain (ETC) genes particularly investigated. ETC complex proteins covary and form strong gene networks according to tissue, but their equivalent transcripts do not. Certain physiological consequences, such as the depletion of ATP synthase in BAT, are thus obscured in transcript data. Lastly, we compared the quantitative proteomic measurements between the total cell and mitochondrial fractions for the five tissues. The resulting enrichment score highlighted several hundred proteins which were strongly enriched in mitochondria, which included several dozen proteins were not reported in literature to be mitochondrially localized. Four of these candidates were selected for biochemical validation, where we found MTAP, SOAT2, and IMPDH2 to be localized inside the mitochondria, whereas ABCC6 was in the mitochondria-associated membrane. These findings demonstrate the synergies of a multi-omics approach to study complex metabolic processes, and this provides a resource for further discovery and analysis of proteoforms, modified proteins, and protein localization.</P>