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Article ; Online: There is no human interactome.

Washburn, Michael P

2016 Volume 17, Page(s) 48

Abstract: Protein complexes are dynamic. A new analysis of two quantitative proteomic datasets reveals cell type-specific changes in the stoichiometry of complexes, which often involve paralog switching. ...

Abstract	Protein complexes are dynamic. A new analysis of two quantitative proteomic datasets reveals cell type-specific changes in the stoichiometry of complexes, which often involve paralog switching.
MeSH term(s)	Humans ; Protein Interaction Mapping ; Proteomics
Language	English
Publishing date	2016-03-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/s13059-016-0913-4
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Article: Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex.

Goswami, Pratik / Banks, Charles A S / Thornton, Janet / Bengs, Bethany / Sardiu, Mihaela E / Florens, Laurence / Washburn, Michael P

bioRxiv : the preprint server for biology

2024

Abstract: Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC ... ...

Abstract	Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.
Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.05.583553
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Article ; Online: Complications of Percutaneous Tendo-Achilles Lengthening for Treatment and Prevention of Diabetic Foot Ulcers: A Systematic Review.

Dierksheide, Alec J / Liette, Michael D / Washburn, Zachary J / Crisologo, Peter A / Haberer, Benjamin P / Henning, Jordan A

The Journal of foot and ankle surgery : official publication of the American College of Foot and Ankle Surgeons

2024 Volume 63, Issue 3, Page(s) 392–397

Abstract: Percutaneous Achilles tendon lengthening is an effective surgical procedure to treat and prevent forefoot and midfoot ulcerations in patients with diabetes. Patients with diabetes are prone to plantar ulcerations due to a combination of factors, such as ... ...

Abstract	Percutaneous Achilles tendon lengthening is an effective surgical procedure to treat and prevent forefoot and midfoot ulcerations in patients with diabetes. Patients with diabetes are prone to plantar ulcerations due to a combination of factors, such as peripheral neuropathy, decreased tendon elasticity, peripheral vascular disease, and hyperglycemia. Complications such as re-ulceration and transfer lesion to the heel, associated with a calcaneal gait secondary to over-lengthening, are possible with percutaneous Achilles tendon lengthening. Although percutaneous Achilles tendon lengthening is well accepted, the overall incidence of complication has not been well described. A systematic review of the reported data was performed to determine the incidence of complication for percutaneous tendo-Achilles lengthening when used for the treatment and prevention of diabetic plantar ulcerations. Nine studies involving 490 percutaneous lengthening procedures met the inclusion criteria. The overall complication rate was 27.8% (8% with transfer heel ulcerations). Given the high rate of complications associated with a percutaneous Achilles tendon lengthening, careful patient selection and consideration of these risks should be considered prior to proceeding with this procedure. Additional prospective comparative analyses with standardization of surgical technique, degrees of lengthening achieved, and post-operative weightbearing and immobilization modalities are needed to decrease incidence of complication and achieve higher healing rates.
MeSH term(s)	Humans ; Diabetic Foot/surgery ; Diabetic Foot/prevention & control ; Achilles Tendon/surgery ; Tenotomy/methods ; Tenotomy/adverse effects ; Postoperative Complications/prevention & control
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Systematic Review ; Journal Article ; Review
ZDB-ID	1146972-9
ISSN	1542-2224 ; 1067-2516
ISSN (online)	1542-2224
ISSN	1067-2516
DOI	10.1053/j.jfas.2024.01.013
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Zs.A 1468: Show issues

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Article ; Online: The H-index of 'an approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database'.

Washburn, Michael P

Journal of the American Society for Mass Spectrometry

2015 Volume 26, Issue 11, Page(s) 1799–1803

Abstract: Over 20 years ago a remarkable paper was published in the Journal of American Society for Mass Spectrometry. This paper from Jimmy Eng, Ashley McCormack, and John Yates described the use of protein databases to drive the interpretation of tandem mass ... ...

Abstract	Over 20 years ago a remarkable paper was published in the Journal of American Society for Mass Spectrometry. This paper from Jimmy Eng, Ashley McCormack, and John Yates described the use of protein databases to drive the interpretation of tandem mass spectra of peptides. This paper now has over 3660 citations and continues to average more than 260 per year over the last decade. This is an amazing scientific achievement. The reason for this is the paper was a cutting edge development at the moment in time when genomes of organisms were being sequenced, protein and peptide mass spectrometry was growing into the field of proteomics, and the power of computing was growing quickly in accordance with Moore's law. This work by the Yates lab grew in importance as genomics, proteomics, and computation all advanced and eventually resulted in the widely used SEQUEST algorithm and platform for the analysis of tandem mass spectrometry data. This commentary provides an analysis of the impact of this paper by analyzing the citations it has generated and the impact of these citing papers. Graphical Abstract ᅟ.
MeSH term(s)	Algorithms ; Databases, Protein ; Peptides/analysis ; Peptides/chemistry ; Proteins/analysis ; Proteins/chemistry ; Proteomics/methods ; Sequence Analysis, Protein/methods ; Software ; Tandem Mass Spectrometry/methods
Chemical Substances	Peptides ; Proteins
Language	English
Publishing date	2015-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1007/s13361-015-1181-3
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Zs.A 4618: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 241: Show issues

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Article: DCLK1-Mediated Regulation of Invadopodia Dynamics and Matrix Metalloproteinase Trafficking Drives Invasive Progression in Head and Neck Squamous Cell Carcinoma.

Arnold, Levi / Yap, Marion / Jackson, Laura / Barry, Michael / Ly, Thuc / Morrison, Austin / Gomez, Juan P / Washburn, Michael P / Standing, David / Yellapu, Nanda Kumar / Li, Linheng / Umar, Shahid / Anant, Shrikant / Thomas, Sufi Mary

bioRxiv : the preprint server for biology

2024

Abstract: Head and neck squamous cell carcinoma (HNSCC) is a major health concern due to its high mortality from poor treatment responses and locoregional tumor invasion into life sustaining structures in the head and neck. A deeper comprehension of HNSCC invasion ...

Abstract	Head and neck squamous cell carcinoma (HNSCC) is a major health concern due to its high mortality from poor treatment responses and locoregional tumor invasion into life sustaining structures in the head and neck. A deeper comprehension of HNSCC invasion mechanisms holds the potential to inform targeted therapies that may enhance patient survival. We previously reported that doublecortin like kinase 1 (DCLK1) regulates invasion of HNSCC cells. Here, we tested the hypothesis that DCLK1 regulates proteins within invadopodia to facilitate HNSCC invasion. Invadopodia are specialized subcellular protrusions secreting matrix metalloproteinases that degrade the extracellular matrix (ECM). Through a comprehensive proteome analysis comparing DCLK1 control and shDCLK1 conditions, our findings reveal that DCLK1 plays a pivotal role in regulating proteins that orchestrate cytoskeletal and ECM remodeling, contributing to cell invasion. Further, we demonstrate in TCGA datasets that DCLK1 levels correlate with increasing histological grade and lymph node metastasis. We identified higher expression of DCLK1 in the leading edge of HNSCC tissue. Knockdown of DCLK1 in HNSCC reduced the number of invadopodia, cell adhesion and colony formation. Using super resolution microscopy, we demonstrate localization of DCLK1 in invadopodia and colocalization with mature invadopodia markers TKS4, TKS5, cortactin and MT1-MMP. We carried out phosphoproteomics and validated using immunofluorescence and proximity ligation assays, the interaction between DCLK1 and motor protein KIF16B. Pharmacological inhibition or knockdown of DCLK1 reduced interaction with KIF16B, secretion of MMPs, and cell invasion. This research unveils a novel function of DCLK1 within invadopodia to regulate the trafficking of matrix degrading cargo. The work highlights the impact of targeting DCLK1 to inhibit locoregional invasion, a life-threatening attribute of HNSCC.
Language	English
Publishing date	2024-04-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.06.588339
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Article ; Online: Acute exercise dynamically modulates the hepatic mitochondrial proteome.

McCoin, Colin S / Franczak, Edziu / Washburn, Michael P / Sardiu, Mihaela E / Thyfault, John P

Molecular omics

2022 Volume 18, Issue 9, Page(s) 840–852

Abstract: Exercise powerfully increases energy metabolism and substrate flux in tissues, a process reliant on dramatic changes in mitochondrial energetics. Liver mitochondria play a multi-factorial role during exercise to fuel hepatic glucose output. We previously ...

Abstract	Exercise powerfully increases energy metabolism and substrate flux in tissues, a process reliant on dramatic changes in mitochondrial energetics. Liver mitochondria play a multi-factorial role during exercise to fuel hepatic glucose output. We previously showed acute exercise activates hepatic mitophagy, a pathway to recycle low-functioning/damaged mitochondria, however little is known how individual bouts of exercise alters the hepatic mitochondrial proteome. Here we leveraged proteomics to examine changes in isolated hepatic mitochondria both immediately after and 2 hours post an acute, 1 hour bout of treadmill exercise in female mice. Further, we utilized leupeptin, a lysosomal inhibitor, to capture and measure exercise-induced changes in mitochondrial proteins that would have been unmeasured due to their targeting for lysosomal degradation. Proteomic analysis of enriched hepatic mitochondria identified 3241 total proteins. Functional enrichment analysis revealed robust enrichment for proteins critical to the mitochondria including metabolic pathways, tricarboxylic acid cycle, and electron transport system. Compared to the sedentary condition, exercise elevated processes regulating lipid localization, Il-5 signaling, and protein phosphorylation in isolated mitochondria. t-SNE analysis identified 4 unique expressional clusters driven by time-dependent changes in protein expression. Isolation of proteins significantly altered with exercise from each cluster revealed influences of leupeptin and exercise both independently and cooperatively modulating mitochondrial protein expressional profiles. Overall, we provide evidence that acute exercise rapidly modulates changes in the proteins/pathways of isolated hepatic mitochondria that include fatty acid metabolism/storage, post-translational protein modification, inflammation, and oxidative stress. In conclusion, the hepatic mitochondrial proteome undergoes extensive remodeling with a bout of exercise.
MeSH term(s)	Female ; Animals ; Mice ; Proteome/metabolism ; Proteomics ; Leupeptins/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism
Chemical Substances	Proteome ; Leupeptins ; Mitochondrial Proteins
Language	English
Publishing date	2022-10-31
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	2515-4184
ISSN (online)	2515-4184
DOI	10.1039/d2mo00143h
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Article: A rare case of atypical chronic myeloid leukemia associated with t(8;22)(p11.2;q11.2)/ BCR-FGFR1 rearrangement: A case report and literature review.

Washburn, Erik / Bayerl, Michael G / Ketterling, Rhett P / Malysz, Jozef

Cancer genetics

2021 Volume 258-259, Page(s) 69–73

Abstract: Myeloid/lymphoid neoplasm with t(8;22)(p11.2;q11.2)/BCR-FGFR1 is an extremely rare diagnosis, with few reported cases to date. In contrast to other FGFR1-partner rearrangements that are associated with chronic eosinophilic leukemia, acute myeloid ... ...

Abstract	Myeloid/lymphoid neoplasm with t(8;22)(p11.2;q11.2)/BCR-FGFR1 is an extremely rare diagnosis, with few reported cases to date. In contrast to other FGFR1-partner rearrangements that are associated with chronic eosinophilic leukemia, acute myeloid leukemia, and/or lymphoblastic lymphoma, patients with BCR-FGFR1 have a myeloproliferative disorder that closely resembles chronic myeloid leukemia (CML). The current report describes a rare case of a 61 year old man with an atypical CML phenotype associated with t(8;22)(p11.2;q11.2)/BCR-FGFR1. A literature review is presented to enhance the awareness of this rare diagnostic entity.
MeSH term(s)	Chromosomes, Human, Pair 22/genetics ; Chromosomes, Human, Pair 8/genetics ; Gene Rearrangement ; Humans ; Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics ; Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/pathology ; Male ; Middle Aged ; Prognosis ; Proto-Oncogene Proteins c-bcr/genetics ; Receptor, Fibroblast Growth Factor, Type 1/genetics ; Translocation, Genetic
Chemical Substances	FGFR1 protein, human (EC 2.7.10.1) ; Receptor, Fibroblast Growth Factor, Type 1 (EC 2.7.10.1) ; BCR protein, human (EC 2.7.11.1) ; Proto-Oncogene Proteins c-bcr (EC 2.7.11.1)
Language	English
Publishing date	2021-09-13
Publishing country	United States
Document type	Case Reports ; Journal Article ; Review
ZDB-ID	2599227-2
ISSN	2210-7762
ISSN	2210-7762
DOI	10.1016/j.cancergen.2021.09.001
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Zs.A 1521: Show issues

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Article: There is no human interactome

Washburn, Michael P

Genome biology. 2016 Dec., v. 17, no. 1

2016

Abstract	Protein complexes are dynamic. A new analysis of two quantitative proteomic datasets reveals cell type-specific changes in the stoichiometry of complexes, which often involve paralog switching.Please see related Research article: www.dx.doi.org/10.1186/s13059-016-0912-5
Keywords	data collection ; humans ; proteomics ; stoichiometry
Language	English
Dates of publication	2016-12
Size	p. 48.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-016-0913-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Generating topological protein interaction scores and data visualization with TopS.

Sardiu, Mihaela E / Florens, Laurence / Washburn, Michael P

Methods (San Diego, Calif.)

2019 Volume 184, Page(s) 13–18

Abstract: Detecting subnetworks in large networks is of great interest. Recently, we developed a topological score framework for the analysis of protein interaction networks and implemented it as a web application, called TopS. Given a multivariate data presented ... ...

Abstract	Detecting subnetworks in large networks is of great interest. Recently, we developed a topological score framework for the analysis of protein interaction networks and implemented it as a web application, called TopS. Given a multivariate data presented as a matrix, TopS generates topological scores between any column and row in the matrix aiming to identify overwhelming preference interactions. This information can be further used into visualization tools such as clusters and networks to investigate how networks benefit from these interactions. We present a web tool called TopS that aims to have an intuitive user interface. Users can upload data from a simple delimited CSV file that can be created in a spreadsheet program. As an output, user is provided with a scoring matrix as tab-delimited file that can be interchanged with other software, heatmap and clustering figures in pdf format. Here we demonstrate the current capabilities of TopS using an existing dataset generated for the study of the human Sin3 chromatin remodeling complex.
MeSH term(s)	Cluster Analysis ; Computational Biology/methods ; Data Visualization ; Datasets as Topic ; Humans ; Protein Interaction Mapping/methods ; Protein Interaction Maps ; Software ; User-Computer Interface
Language	English
Publishing date	2019-08-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2019.08.010
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Zs.A 3239: Show issues

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Article ; Online: Identification of stem cells from large cell populations with topological scoring.

Sardiu, Mihaela E / Box, Andrew C / Haug, Jeffrey S / Washburn, Michael P

Molecular omics

2020 Volume 17, Issue 1, Page(s) 59–65

Abstract: Machine learning and topological analysis methods are becoming increasingly used on various large-scale omics datasets. Modern high dimensional flow cytometry data sets share many features with other omics datasets like genomics and proteomics. For ... ...

Abstract	Machine learning and topological analysis methods are becoming increasingly used on various large-scale omics datasets. Modern high dimensional flow cytometry data sets share many features with other omics datasets like genomics and proteomics. For example, genomics or proteomics datasets can be sparse and have high dimensionality, and flow cytometry datasets can also share these features. This makes flow cytometry data potentially a suitable candidate for employing machine learning and topological scoring strategies, for example, to gain novel insights into patterns within the data. We have previously developed a Topological Score (TopS) and implemented it for the analysis of quantitative protein interaction network datasets. Here we show that TopS approach for large scale data analysis is applicable to the analysis of a previously described flow cytometry sorted human hematopoietic stem cell dataset. We demonstrate that TopS is capable of effectively sorting this dataset into cell populations and identify rare cell populations. We demonstrate the utility of TopS when coupled with multiple approaches including topological data analysis, X-shift clustering, and t-Distributed Stochastic Neighbor Embedding (t-SNE). Our results suggest that TopS could be effectively used to analyze large scale flow cytometry datasets to find rare cell populations.
MeSH term(s)	Algorithms ; Flow Cytometry/methods ; Hematopoietic Stem Cells ; Humans ; Machine Learning ; Single-Cell Analysis/methods ; Stem Cells/cytology ; Stem Cells/metabolism
Language	English
Publishing date	2020-09-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2515-4184
ISSN (online)	2515-4184
DOI	10.1039/d0mo00039f
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