Search Results - "Michael J. Sweredoski"

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice by Sharon, Gil, Cruz, Nikki Jamie, Kang, Dae-Wook, Gandal, Michael J., Wang, Bo, Kim, Young-Mo, Zink, Erika M., Casey, Cameron P., Taylor, Bryn C., Lane, Christianne J., Bramer, Lisa M., Isern, Nancy G., Hoyt, David W., Noecker, Cecilia, Sweredoski, Michael J., Moradian, Annie, Borenstein, Elhanan, Jansson, Janet K., Knight, Rob, Metz, Thomas O., Lois, Carlos, Geschwind, Daniel H., Krajmalnik-Brown, Rosa, Mazmanian, Sarkis K.

“…Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic…”
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Cand1 Promotes Assembly of New SCF Complexes through Dynamic Exchange of F Box Proteins by Pierce, Nathan W., Lee, J. Eugene, Liu, Xing, Sweredoski, Michael J., Graham, Robert L.J., Larimore, Elizabeth A., Rome, Michael, Zheng, Ning, Clurman, Bruce E., Hess, Sonja, Shan, Shu-ou, Deshaies, Raymond J.

“…The modular SCF (Skp1, cullin, and F box) ubiquitin ligases feature a large family of F box protein substrate receptors that enable recognition of diverse…”
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Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins by Dopie, Joseph, Sweredoski, Michael J, Moradian, Annie, Belmont, Andrew S

“…We present a simple ratio method to infer protein composition within cellular structures using proximity labeling approaches but compensating for the diffusion…”
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PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure by Sweredoski, Michael J., Baldi, Pierre

“…Motivation: Accurate prediction of B-cell epitopes is an important goal of computational immunology. Up to 90% of B-cell epitopes are discontinuous in nature,…”
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Composition and Regulation of the Cellular Repertoire of SCF Ubiquitin Ligases by Reitsma, Justin M., Liu, Xing, Reichermeier, Kurt M., Moradian, Annie, Sweredoski, Michael J., Hess, Sonja, Deshaies, Raymond J.

“…SCF (Skp1-Cullin-F-box) ubiquitin ligases comprise several dozen modular enzymes that have diverse roles in biological regulation. SCF enzymes share a common…”
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Ribosomal proteins produced in excess are degraded by the ubiquitin-proteasome system by Sung, Min-Kyung, Reitsma, Justin M, Sweredoski, Michael J, Hess, Sonja, Deshaies, Raymond J

“…Ribosome assembly is an essential process that consumes prodigious quantities of cellular resources. Ribosomal proteins cannot be overproduced in Saccharomyces…”
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LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding by Shin, Chun-Shik, Meng, Shuxia, Garbis, Spiros D., Moradian, Annie, Taylor, Robert W., Sweredoski, Michael J., Lomenick, Brett, Chan, David C.

“…Most mitochondrial precursor polypeptides are imported from the cytosol into the mitochondrion, where they must efficiently undergo folding. Mitochondrial…”
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Broad activation of the ubiquitin―proteasome system by Parkin is critical for mitophagy by CHAN, Nickie C, SALAZAR, Anna M, PHAM, Anh H, SWEREDOSKI, Michael J, KOLAWA, Natalie J, GRAHAM, Robert L. J, HESS, Sonja, CHAN, David C

“…Parkin, an E3 ubiquitin ligase implicated in Parkinson's disease, promotes degradation of dysfunctional mitochondria by autophagy. Using proteomic and cellular…”
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Evaluation and Optimization of Mass Spectrometric Settings during Data-dependent Acquisition Mode: Focus on LTQ-Orbitrap Mass Analyzers by Kalli, Anastasia, Smith, Geoffrey T, Sweredoski, Michael J, Hess, Sonja

“…Mass-spectrometry-based proteomics has evolved as the preferred method for the analysis of complex proteomes. Undoubtedly, recent advances in mass spectrometry…”
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A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins by Sung, Min-Kyung, Porras-Yakushi, Tanya R, Reitsma, Justin M, Huber, Ferdinand M, Sweredoski, Michael J, Hoelz, André, Hess, Sonja, Deshaies, Raymond J

“…Overproduced yeast ribosomal protein (RP) Rpl26 fails to assemble into ribosomes and is degraded in the nucleus/nucleolus by a ubiquitin-proteasome system…”
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Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon by Van Nguyen, Thang, Lee, J. Eugene, Sweredoski, Michael J., Yang, Seung-Joo, Jeon, Seung-Je, Harrison, Joseph S., Yim, Jung-Hyuk, Lee, Sang Ghil, Handa, Hiroshi, Kuhlman, Brian, Jeong, Ji-Seon, Reitsma, Justin M., Park, Chul-Seung, Hess, Sonja, Deshaies, Raymond J.

“…Cereblon (CRBN), a substrate receptor for the cullin-RING ubiquitin ligase 4 (CRL4) complex, is a direct protein target for thalidomide teratogenicity and…”
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Mitochondrial fusion is required for spermatogonial differentiation and meiosis by Varuzhanyan, Grigor, Rojansky, Rebecca, Sweredoski, Michael J, Graham, Robert L J, Hess, Sonja, Ladinsky, Mark S, Chan, David C

“…Differentiating cells tailor their metabolism to fulfill their specialized functions. We examined whether mitochondrial fusion is important for metabolic…”
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Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes by Renata, Hans, Lewis, Russell D, Sweredoski, Michael J, Moradian, Annie, Hess, Sonja, Wang, Z. Jane, Arnold, Frances H

“…Following the recent discovery that heme proteins can catalyze the cyclopropanation of styrenyl olefins with high efficiency and selectivity, interest in…”
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Stable Isotope Analysis of Intact Oxyanions Using Electrospray Quadrupole-Orbitrap Mass Spectrometry by Neubauer, Cajetan, Crémière, Antoine, Wang, Xingchen T, Thiagarajan, Nivedita, Sessions, Alex L, Adkins, Jess F, Dalleska, Nathan F, Turchyn, Alexandra V, Clegg, Josephine A, Moradian, Annie, Sweredoski, Michael J, Garbis, Spiros D, Eiler, John M

“…The stable isotopes of sulfate, nitrate, and phosphate are frequently used to study geobiological processes of the atmosphere, ocean, as well as land…”
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Phosphorylation of Synaptic GTPase-activating Protein (synGAP) by Ca2+/Calmodulin-dependent Protein Kinase II (CaMKII) and Cyclin-dependent Kinase 5 (CDK5) Alters the Ratio of Its GAP Activity toward Ras and Rap GTPases by Walkup, Ward G., Washburn, Lorraine, Sweredoski, Michael J., Carlisle, Holly J., Graham, Robert L., Hess, Sonja, Kennedy, Mary B.

“…synGAP is a neuron-specific Ras and Rap GTPase-activating protein (GAP) found in high concentrations in the postsynaptic density (PSD) fraction from the…”
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Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) Enables Time-Resolved Analysis of Protein Synthesis in Native Plant Tissue by Glenn, Weslee S., Stone, Shannon E., Ho, Samuel H., Sweredoski, Michael J., Moradian, Annie, Hess, Sonja, Bailey-Serres, Julia, Tirrell, David A.

“…Proteomic plasticity undergirds stress responses in plants, and understanding such responses requires accurate measurement of the extent to which proteins…”
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Cell-specific proteomic analysis in Caenorhabditis elegans by Yuet, Kai P, Doma, Meenakshi K, Ngo, John T, Sweredoski, Michael J, Graham, Robert L J, Moradian, Annie, Hess, Sonja, Schuman, Erin M, Sternberg, Paul W, Tirrell, David A

“…Proteomic analysis of rare cells in heterogeneous environments presents difficult challenges. Systematic methods are needed to enrich, identify, and quantify…”
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SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa by Babin, Brett M., Bergkessel, Megan, Sweredoski, Michael J., Moradian, Annie, Hess, Sonja, Newman, Dianne K., Tirrell, David A.

“…Microbial quiescence and slow growth are ubiquitous physiological states, but their study is complicated by low levels of metabolic activity. To address this…”
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Data-Dependent Middle-Down Nano-Liquid Chromatography–Electron Capture Dissociation-Tandem Mass Spectrometry: An Application for the Analysis of Unfractionated Histones by Kalli, Anastasia, Sweredoski, Michael J, Hess, Sonja

“…Middle-down mass spectrometry (MS) combined with electron capture dissociation (ECD) represents an attractive method for characterization of proteins and their…”
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Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient by Kaplan, Mohammed, Sweredoski, Michael J., Rodrigues, Joa˜o P. G. L. M., Tocheva, Elitza I., Chang, Yi-Wei, Ortega, Davi R., Beeby, Morgan, Jensen, Grant J.

“…The bacterial flagellum is an amazing nanomachine. Understanding how such complex structures arose is crucial to our understanding of cellular evolution. We…”
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