Search Results - "Sweredoski, Michael"

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…”
Get full text

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…”
Get full text

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…”
Get full text

The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications by Moradian, Annie, Kalli, Anastasia, Sweredoski, Michael J., Hess, Sonja

“…Epigenetic regulation of gene expression is, at least in part, mediated by histone modifications. PTMs of histones change chromatin structure and regulate gene…”
Get full text

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,…”
Get full text

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3 by McHugh, Colleen A., Chen, Chun-Kan, Chow, Amy, Surka, Christine F., Tran, Christina, McDonel, Patrick, Pandya-Jones, Amy, Blanco, Mario, Burghard, Christina, Moradian, Annie, Sweredoski, Michael J., Shishkin, Alexander A., Su, Julia, Lander, Eric S., Hess, Sonja, Plath, Kathrin, Guttman, Mitchell

“…The mechanisms by which Xist , a long non-coding RNA, silences one X chromosome in female mammals are unknown; here a mass spectrometry-based approach is…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

Data-Independent Acquisition for the Orbitrap Q Exactive HF: A Tutorial by Reubsaet, Léon, Sweredoski, Michael J, Moradian, Annie

“…Data-independent acquisition (DIA) is a powerful mass spectrometric technique to perform both protein identification and quantification of complex protein…”
Get full text

Identification of new OPA1 cleavage site reveals that short isoforms regulate mitochondrial fusion by Wang, Ruohan, Mishra, Prashant, Garbis, Spiros D, Moradian, Annie, Sweredoski, Michael J, Chan, David C

“…OPA1, a large GTPase of the dynamin superfamily, mediates fusion of the mitochondrial inner membranes, regulates cristae morphology, and maintains respiratory…”
Get full text

COBEpro: a novel system for predicting continuous B-cell epitopes by Sweredoski, Michael J., Baldi, Pierre

“…Accurate prediction of B-cell epitopes has remained a challenging task in computational immunology despite several decades of research. Only 10% of the known…”
Get full text

BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7 by Frankiw, Luke, Majumdar, Devdoot, Burns, Christian, Vlach, Logan, Moradian, Annie, Sweredoski, Michael J., Baltimore, David

“…Intron retention (IR) has emerged as an important mechanism of gene expression control, but the factors controlling IR events remain poorly understood. We…”
Get full text

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…”
Get full text

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…”
Get full text

WNK1 is an assembly factor for the human ER membrane protein complex by Pleiner, Tino, Hazu, Masami, Tomaleri, Giovani Pinton, Januszyk, Kurt, Oania, Robert S., Sweredoski, Michael J., Moradian, Annie, Guna, Alina, Voorhees, Rebecca M.

“…The assembly of nascent proteins into multi-subunit complexes is a tightly regulated process that must occur at high fidelity to maintain cellular homeostasis…”
Get full text

A Trichomonas vaginalis Rhomboid Protease and Its Substrate Modulate Parasite Attachment and Cytolysis of Host Cells by Riestra, Angelica M, Gandhi, Shiv, Sweredoski, Michael J, Moradian, Annie, Hess, Sonja, Urban, Sinisa, Johnson, Patricia J

“…Trichomonas vaginalis is an extracellular eukaryotic parasite that causes the most common, non-viral sexually transmitted infection worldwide. Although disease…”
Get full text

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…”
Get full text