LIVIVO - Search results -

Search results

Result 1 - 10 of total 1036

Search options

Article ; Online: DIGE Analysis Software and Protein Identification Approaches.

Dowling, Paul

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2596, Page(s) 39–50

Abstract: Two-dimensional difference gel electrophoresis (2D-DIGE) is a high-resolution protein separation technique, with the excellent dynamic range obtained by fluorescent tag labeling of protein samples. Scanned images of 2D-DIGE gels show thousands of protein ...

Abstract	Two-dimensional difference gel electrophoresis (2D-DIGE) is a high-resolution protein separation technique, with the excellent dynamic range obtained by fluorescent tag labeling of protein samples. Scanned images of 2D-DIGE gels show thousands of protein spots, each spot representing a single or a group of protein isoforms. By using commercially available software, each protein spot is defined by an outline, which is digitized and correlated with the quantity of proteins present in each spot. Software packages include DeCyder, SameSpots, and Dymension 3. In addition, proteins of interest can be excised from post-stained gels and identified with conventional mass spectrometric techniques. High-throughput mass spectrometry is performed using sophisticated instrumentation, including matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF), MALDI-TOF/TOF, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Tandem MS (MALDI-TOF/TOF or LC-MS/MS) analyzes fragmented peptides, resulting in amino acid sequence information, which is especially useful when protein spots are low abundant or where a mixture of proteins is present.
MeSH term(s)	Electrophoresis, Gel, Two-Dimensional/methods ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Software ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Protein Isoforms
Chemical Substances	Protein Isoforms
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2831-7_3
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: DIGE Saturation Labeling for Scarce Amounts of Protein from Formalin-Fixed Paraffin-Embedded (FFPE) Tissue.

Dowling, Paul

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2596, Page(s) 113–118

Abstract: In this chapter, we describe the utility of fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) as a proteomics platform for the global detection of expressed proteins in formalin-fixed paraffin-embedded (FFPE) tissues and its use for ... ...

Abstract	In this chapter, we describe the utility of fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) as a proteomics platform for the global detection of expressed proteins in formalin-fixed paraffin-embedded (FFPE) tissues and its use for biomarker discovery/identification of proteins that may contribute to cancer development and progression. Formalin fixation and paraffin embedding of tissue is the standard processing methodology practiced in pathology laboratories worldwide, resulting in a highly stable form of tissue that is easily stored due to its inherent stability at room temperature. Consequently, FFPE tissues represent an attractive reservoir of clinical material for conducting retrospective protein biomarker analysis. A limitation for proteomics research in this type of clinical sample is the amount of viable protein that can be obtained from fixed tissues. Tissue biopsies are precious samples that can generally be acquired in very small amounts due to the invasive nature of the sample collection, mainly during surgery or biopsy. Subsequently, the amount of extracted protein can be, in many cases, very limited. The saturation 2D-DIGE technology has emerged as a useful method for protein analysis where only scarce amounts of protein are available. This approach can be adapted successfully to label low-level protein isolated from FFPE tissue.
MeSH term(s)	Paraffin Embedding/methods ; Tissue Fixation/methods ; Retrospective Studies ; Proteins/analysis ; Formaldehyde ; Biomarkers
Chemical Substances	Proteins ; Formaldehyde (1HG84L3525) ; Biomarkers
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2831-7_9
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Negative and positive mental health characteristics of affected family members: Findings from a cross-sectional Australian general population gambling study.

Spence, K / Merkouris, S S / Jackson, A C / Wade, A J / Dowling, N A

Addictive behaviors

2024 Volume 155, Page(s) 107998

Abstract: Despite the impact of problem gambling on affected family members (AFMs), there are limited large-scale population level studies identifying the negative mental health (NMH) and positive mental health (PMH) characteristics of AFMs. Furthermore, no study ... ...

Abstract	Despite the impact of problem gambling on affected family members (AFMs), there are limited large-scale population level studies identifying the negative mental health (NMH) and positive mental health (PMH) characteristics of AFMs. Furthermore, no study has explored whether PMH characteristics are protective in the relationships between AFM status and NMH characteristics. This study involved secondary data analysis from the Third Social and Economic Impact Study of Gambling in Tasmania. Using a subsample of 1,869 adults (48.30 % male; mean
Language	English
Publishing date	2024-02-28
Publishing country	England
Document type	Journal Article
ZDB-ID	197618-7
ISSN	1873-6327 ; 0306-4603
ISSN (online)	1873-6327
ISSN	0306-4603
DOI	10.1016/j.addbeh.2024.107998
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1214: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Reverse engineering morphogenesis through Bayesian optimization of physics-based models.

Kumar, Nilay / Dowling, Alexander / Zartman, Jeremiah

bioRxiv : the preprint server for biology

2023

Abstract: Morphogenetic programs direct the cell signaling and nonlinear mechanical interactions between multiple cell types and tissue layers to define organ shape and size. A key challenge for systems and synthetic biology is determining optimal combinations of ... ...

Abstract	Morphogenetic programs direct the cell signaling and nonlinear mechanical interactions between multiple cell types and tissue layers to define organ shape and size. A key challenge for systems and synthetic biology is determining optimal combinations of intra- and inter-cellular interactions to predict an organ's shape, size, and function. Physics-based mechanistic models that define the subcellular force distribution facilitate this, but it is extremely challenging to calibrate parameters in these models from data. To solve this inverse problem, we created a Bayesian optimization framework to determine the optimal cellular force distribution such that the predicted organ shapes match the desired organ shapes observed within the experimental imaging data. This integrative framework employs Gaussian Process Regression (GPR), a non-parametric kernel-based probabilistic machine learning modeling paradigm, to learn the mapping functions relating to the morphogenetic programs that generate and maintain the final organ shape. We calibrated and tested the method on cross-sections of
Language	English
Publishing date	2023-08-22
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.21.553928
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: DIGE Analysis of ProteoMiner™ Fractionated Serum/Plasma Samples.

Murphy, Sandra / Dowling, Paul

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2596, Page(s) 119–125

Abstract: The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins ...

Abstract	The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically fluorescence two-dimensional difference gel electrophoresis (2D-DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins. One of these enrichment technologies, ProteoMiner, is the focus of this chapter. The ProteoMiner technology utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but at the same time suppresses the concentration of high-abundance proteins in subsequent analysis.
MeSH term(s)	Two-Dimensional Difference Gel Electrophoresis/methods ; Proteomics/methods ; Blood Proteins/analysis ; Biomarkers ; Electrophoresis, Gel, Two-Dimensional/methods
Chemical Substances	Blood Proteins ; Biomarkers
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2831-7_10
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: DIGE Analysis of Immunodepleted Plasma.

Dowling, Paul / Ohlendieck, Kay

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2596, Page(s) 363–375

Abstract: This chapter focuses on upstream immunodepletion of high-abundance proteins from plasma samples and subsequent analysis by fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). The abundances of proteins in biofluid proteomes, such as ... ...

Abstract	This chapter focuses on upstream immunodepletion of high-abundance proteins from plasma samples and subsequent analysis by fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). The abundances of proteins in biofluid proteomes, such as serum, plasma, saliva, and bronchoalveolar lavage fluid (BALF), can exceed ten orders of magnitude. This substantial dynamic range is problematic for the detection of medium and low-abundance proteins by 2D-DIGE analysis. To increase the detection, quantification, and identification of medium-low-abundance proteins, the targeted depletion of known abundant proteins with antibody columns has been successfully employed. From the literature, it is clear that the performance of abundant protein depletion with immunodepletion columns has been successful in broadening the coverage of the biofluid proteome and facilitating the identification of disease-specific biomarkers. The task for a successful biomarker strategy involves the combination of a reproducible and robust fractionation method, coupled with a highly accurate quantitative method, a task that is exemplified by combining both immunodepletion and 2D-DIGE together to discover significant proteins associated with the disease phenotype.
MeSH term(s)	Blood Proteins/analysis ; Proteomics/methods ; Two-Dimensional Difference Gel Electrophoresis/methods ; Proteome/analysis ; Biomarkers ; Electrophoresis, Gel, Two-Dimensional/methods
Chemical Substances	Blood Proteins ; Proteome ; Biomarkers
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2831-7_25
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Identification of Ubiquitination-Associated Proteins Using 2D-DIGE.

Dowling, Paul / Bazou, Despina

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2596, Page(s) 83–96

Abstract: Ubiquitination is a post-translational modification, in which a small regulatory protein (~8.6 kDa) is tagged as a single moiety or as a chain to target proteins. Ubiquitination is the most versatile cellular regulatory mechanism, essential to the ... ...

Abstract	Ubiquitination is a post-translational modification, in which a small regulatory protein (~8.6 kDa) is tagged as a single moiety or as a chain to target proteins. Ubiquitination is the most versatile cellular regulatory mechanism, essential to the physiological and pathophysiological cellular events that regulate protein turnover, gene transcription, cell cycle progression, DNA repair, apoptosis, viral budding, and receptor-mediated endocytosis. Changes and abnormalities within the ubiquitination process can result in a plethora of diseases, including various cancers. The ubiquitination process is tightly controlled in a stepwise manner by four enzymes: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, E3 ubiquitin-ligating enzymes, and deubiquitinating proteases. Using fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) to detect and quantitate cellular proteins associated with the ubiquitination process will facilitate the evaluation of this post-translational modification associated with the pathophysiological phenotype.
MeSH term(s)	Two-Dimensional Difference Gel Electrophoresis ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitination ; Ubiquitin/metabolism ; Protein Processing, Post-Translational ; Ubiquitin-Protein Ligases/metabolism ; Transcription Factors/metabolism
Chemical Substances	Ubiquitin-Conjugating Enzymes (EC 2.3.2.23) ; Ubiquitin ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Transcription Factors
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2831-7_6
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: DIGE-Based Biomarker Discovery in Blood Cancers.

Dunphy, Katie / Dowling, Paul

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2596, Page(s) 105–112

Abstract: Cancer of blood or bone marrow-derived cells dysregulates normal hematopoiesis and accounts for over 6% of all cancer cases annually. Proteomic analyses of blood cancers have improved our understanding of disease mechanisms and identified numerous ... ...

Abstract	Cancer of blood or bone marrow-derived cells dysregulates normal hematopoiesis and accounts for over 6% of all cancer cases annually. Proteomic analyses of blood cancers have improved our understanding of disease mechanisms and identified numerous proteins of clinical relevance. For many years, gel-based proteomic studies have aided in the discovery of novel diagnostic, prognostic, and predictive biomarkers, as well as therapeutic targets, in various diseases, including blood cancer. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) facilitates comparative proteomic research to identify differential protein expression in a simple and reproducible manner. The versatility of 2D-DIGE as a quantitative proteomic technique has provided insight into various aspects of blood cancer pathology, including disease development, prognostic subtypes, and drug resistance. The ability to couple 2D-DIGE with additional downstream mass spectrometry-based techniques yields comprehensive workflows capable of identifying proteins of biological and clinical significance. The application of 2D-DIGE in blood cancer research has significantly contributed to the increasingly important initiative of precision medicine. This chapter will focus on the influential role of 2D-DIGE as a tool in blood cancer research.
MeSH term(s)	Humans ; Proteomics/methods ; Electrophoresis, Gel, Two-Dimensional/methods ; Two-Dimensional Difference Gel Electrophoresis/methods ; Mass Spectrometry ; Neoplasms/diagnosis ; Proteins ; Hematologic Neoplasms
Chemical Substances	Proteins
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2831-7_8
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Analysis of Cancer Cell Line Secretomes: A Complementary Source of Disease-Specific Protein Biomarkers.

Dunphy, Katie / Bazou, Despina / Dowling, Paul

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2645, Page(s) 277–287

Abstract: Various types of cancer cells enrich or condition the medium that they are cultured in by secreting or shedding proteins and small molecules. These secreted or shed factors are involved in key biological processes, including cellular communication, ... ...

Abstract	Various types of cancer cells enrich or condition the medium that they are cultured in by secreting or shedding proteins and small molecules. These secreted or shed factors are involved in key biological processes, including cellular communication, proliferation, and migration, and are represented by protein families, including cytokines, growth factors, and enzymes. The rapid development of high-resolution mass spectrometry and shotgun strategies for proteome analysis facilitates the identification of these factors in biological models and elucidation of their potential roles in pathophysiology. Hence, the following protocol provides details on how to prepare proteins present in conditioned media for mass spectrometry analysis.
MeSH term(s)	Humans ; Secretome ; Cell Line ; Proteome/metabolism ; Neoplasms ; Biomarkers/metabolism ; Biomarkers, Tumor/metabolism ; Culture Media, Conditioned/analysis
Chemical Substances	Proteome ; Biomarkers ; Biomarkers, Tumor ; Culture Media, Conditioned
Language	English
Publishing date	2023-05-19
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3056-3_18
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Prostate volume analysis in image registration for prostate cancer care: a verification study.

Bugeja, Jessica M / Mehawed, Georges / Roberts, Matthew J / Rukin, Nicholas / Dowling, Jason / Murray, Rebecca

Physical and engineering sciences in medicine

2023 Volume 46, Issue 4, Page(s) 1791–1802

Abstract: ... prostate cancer care. Paired whole-pelvis MR and CT scan data were used (n = 20). A manual prostate CTV contour ...

Abstract	Combined magnetic resonance imaging (MRI) and positron emission tomography/computed tomography (PET/CT) may enhance diagnosis, aid surgical planning and intra-operative orientation for prostate biopsy and radical prostatectomy. Although PET-MRI may provide these benefits, PET-MRI machines are not widely available. Image fusion of Prostate specific membrane antigen PET/CT and MRI acquired separately may be a suitable clinical alternative. This study compares CT-MR registration algorithms for urological prostate cancer care. Paired whole-pelvis MR and CT scan data were used (n = 20). A manual prostate CTV contour was performed independently on each patients MR and CT image. A semi-automated rigid-, automated rigid- and automated non-rigid registration technique was applied to align the MR and CT data. Dice Similarity Index (DSI), 95% Hausdorff distance (95%HD) and average surface distance (ASD) measures were used to assess the closeness of the manual and registered contours. The automated non-rigid approach had a significantly improved performance compared to the automated rigid- and semi-automated rigid-registration, having better average scores and decreased spread for the DSI, 95%HD and ASD (all p < 0.001). Additionally, the automated rigid approach had similar significantly improved performance compared to the semi-automated rigid registration across all accuracy metrics observed (all p < 0.001). Overall, all registration techniques studied here demonstrated sufficient accuracy for exploring their clinical use. While the fully automated non-rigid registration algorithm in the present study provided the most accurate registration, the semi-automated rigid registration is a quick, feasible, and accessible method to perform image registration for prostate cancer care by urologists and radiation oncologists now.
MeSH term(s)	Male ; Humans ; Prostate/diagnostic imaging ; Prostate/surgery ; Positron Emission Tomography Computed Tomography ; Tomography, X-Ray Computed/methods ; Prostatic Neoplasms/diagnostic imaging ; Prostatic Neoplasms/surgery ; Pelvis
Language	English
Publishing date	2023-10-11
Publishing country	Switzerland
Document type	Journal Article
ISSN	2662-4737
ISSN (online)	2662-4737
DOI	10.1007/s13246-023-01342-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED