scholarly journals Proteome Characterization of BALF Extracellular Vesicles in Idiopathic Pulmonary Fibrosis: Unveiling Undercover Molecular Pathways

2021 ◽  
Vol 22 (11) ◽  
pp. 5696
Author(s):  
Enxhi Shaba ◽  
Claudia Landi ◽  
Alfonso Carleo ◽  
Lorenza Vantaggiato ◽  
Eugenio Paccagnini ◽  
...  
Keyword(s):  
Disease Pathogenesis ◽  
Isolation Technique ◽  
C Peptide ◽  
Complex Samples ◽  
Fluid Component ◽  
Protein Functions ◽  
Proteomic Investigation ◽  
Scatter Plots ◽  
Cytoskeleton Remodeling

In the longtime challenge of identifying specific, easily detectable and reliable biomarkers of IPF, BALF proteomics is providing interesting new insights into its pathogenesis. To the best of our knowledge, the present study is the first shotgun proteomic investigation of EVs isolated from BALF of IPF patients. Our main aim was to characterize the proteome of the vesicular component of BALF and to explore its individual impact on the pathogenesis of IPF. To this purpose, ultracentrifugation was chosen as the EVs isolation technique, and their purification was assessed by TEM, 2DE and LC-MS/MS. Our 2DE data and scatter plots showed considerable differences between the proteome of EVs and that of whole BALF and of its fluid component. Analysis of protein content and protein functions evidenced that EV proteins are predominantly involved in cytoskeleton remodeling, adenosine signaling, adrenergic signaling, C-peptide signaling and lipid metabolism. Our findings may suggest a wider system involvement in the disease pathogenesis and support the importance of pre-fractioning of complex samples, such as BALF, in order to let low-abundant proteins-mediated pathways emerge.

scholarly journals Proteome Characterization of BALF Extracellular Vesicles in Idiopathic Pulmonary Fibrosis: Unveiling Undercover Molecular Pathways

2021 ◽  
Author(s):  
Enxhi Shaba ◽  
Claudia Landi ◽  
Alfonso Carleo ◽  
Lorenza Vantaggiato ◽  
Eugenio Paccagnini ◽  
...  
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Lavage Fluid ◽  
Isolation Technique ◽  
Complex Samples ◽  
Protein Functions ◽  
Proteomic Investigation ◽  
Scatter Plots ◽  
Cytoskeleton Remodeling

In the longtime challenge of identifying specific, easily-detectable and reliable biomarkers of Idiopathic Pulmonary Fibrosis (IPF), bronchoalveolar lavage fluid (BALF) proteomics is providing interesting new insights into its pathogenesis. To the best of our knowledge, the present study is the first shotgun proteomic investigation of EVs isolated from BALF of IPF patients. Our main aim was to characterize the proteome of the vesicular component of BALF and to explore its individual impact on the pathogenesis of IPF. To this purpose, ultracentrifugation was chosen as EVs isolation technique and their purification was assessed by TEM, 2DE and LC-MS/MS. Our 2DE data and scatter plots showed considerable differences between the proteome of EVs and that of whole BALF and of its fluid component. Analysis of protein content and protein functions evidenced that EV proteins are predominantly involved in cytoskeleton remodeling, adenosine signaling, adrenergic signaling, C-peptide signaling and lipid metabolism. Our findings may suggest a wider system involvement in the disease pathogenesis and support the importance of pre-fractioning of complex samples, like BALF, in order to let low-abundant proteins-mediated pathways to emerge.

scholarly journals Isolation and Characterization of Proinsulin C-Peptide from Bovine Pancreas

1971 ◽  
Vol 246 (5) ◽  
pp. 1365-1374
Author(s):  
Donald F. Steiner ◽  
Sooja Cho ◽  
Philip E. Oyer ◽  
Susan Terris ◽  
James D. Peterson ◽  
...  
Keyword(s):  
C Peptide ◽  
Isolation And Characterization ◽  
Bovine Pancreas

scholarly journals Simple and Efficient Protocol for Subcellular Fractionation of Normal and Apoptotic Cells

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 852
Author(s):  
Viacheslav V. Senichkin ◽  
Evgeniia A. Prokhorova ◽  
Boris Zhivotovsky ◽  
Gelina S. Kopeina
Keyword(s):  
Subcellular Fractionation ◽  
Nuclear Fraction ◽  
Apoptotic Cells ◽  
Apoptotic Bodies ◽  
Functional Studies ◽  
Ionic Detergents ◽  
Protein Functions ◽  
Indispensable Tool ◽  
Cell Fragments

Subcellular fractionation approaches remain an indispensable tool among a large number of biochemical methods to facilitate the study of specific intracellular events and characterization of protein functions. During apoptosis, the best-known form of programmed cell death, numerous proteins are translocated into and from the nucleus. Therefore, suitable biochemical techniques for the subcellular fractionation of apoptotic cells are required. However, apoptotic bodies and cell fragments might contaminate the fractions upon using the standard protocols. Here, we compared different nucleus/cytoplasm fractionation methods and selected the best-suited approach for the separation of nuclear and cytoplasmic contents. The described methodology is based on stepwise lysis of cells and washing of the resulting nuclei using non-ionic detergents, such as NP-40. Next, we validated this approach for fractionation of cells treated with various apoptotic stimuli. Finally, we demonstrated that nuclear fraction could be further subdivided into nucleosolic and insoluble subfractions, which is crucial for the isolation and functional studies of various proteins. Altogether, we developed a method for simple and efficient nucleus/cytoplasm fractionation of both normal and apoptotic cells.

Characterization Of Complex Samples By Laser-Excited Matrix-Isolation Fluorescence Spectrometry

1983 ◽  
Vol 22 (5) ◽  
Author(s):  
E. L. Wehry ◽  
Vincent B. Conrad ◽  
John L. Hammons ◽  
Jon R. Maple ◽  
Mildred B. Perry
Keyword(s):  
Matrix Isolation ◽  
Fluorescence Spectrometry ◽  
Complex Samples

Otelixizumab Anti-CD3 Monoclonal Antibody DEFEND-1 Study: Characterization of C-Peptide Levels in New-Onset Type 1a Diabetes Mellitus

2011 ◽  
pp. P3-474-P3-474
Author(s):  
Tom Donner ◽  
Jens Sandahl Christiansen ◽  
Paul Miller ◽  
Wei Liu ◽  
Aoife M Brennan
Keyword(s):  
Diabetes Mellitus ◽  
Monoclonal Antibody ◽  
C Peptide ◽  
Onset Type ◽  
Type 1A Diabetes ◽  
New Onset

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

scholarly journals White matter changes in Huntington’s disease and the demyelination hypothesis: a critical review

2019 ◽  
Author(s):  
chiara casella ◽  
Claudia Metzler-Baddeley ◽  
Derek Jones ◽  
Ilona Lipp
Keyword(s):  
White Matter ◽  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Neurodegenerative Disorder ◽  
Biological Properties ◽  
Disease Pathogenesis ◽  
Tissue Modeling ◽  
Cortical Grey Matter ◽  
Neuroimaging Techniques

Huntington’s disease (HD) is a genetic neurodegenerative disorder, characterised by atrophy of the neostriatum, and cortical grey matter abnormalities. White matter (WM) alterations have recently been identified as a relevant pathophysiological feature of HD, but the etiology of WM degeneration, and its role in disease pathogenesis and progression remain unclear. An increasing body of research suggests that WM changes in HD are due to alterations in myelin-associated biological processes at the cellular and molecular level. This review first discusses evidence from neurochemical studies lending support to the ‘De-myelination hypothesis’ of HD, and pointing towards a role for aberrant myelination and changes in oligodendrocytes in HD WM. Next, evidence from neuroimaging studies is reviewed, the limitations of the described methodologies are discussed and suggested interpretations of findings from published studies are challenged. Although our understanding of HD-associated pathological changes in the brain will increasingly rely on neuroimaging techniques, the shortcomings of these methodologies must not be forgotten. Advances in MRI techniques and tissue modeling will enable a better characterization of the biological properties of WM microstructure, and will allow more specific monitoring of longitudinal changes noninvasively. This, in turn, will provide insight into disease pathogenesis and progression and facilitate the identification of disease-related biomarkers and the specification of outcome measures in clinical trials.

Myeloperoxidase deficiency in dogs observed with the ADVIA®120

2010 ◽  
Vol 38 (03) ◽  
pp. 139-146 ◽  
Author(s):  
J. Richartz ◽  
N. Bauer ◽  
A. Moritz ◽  
S. Klenner
Keyword(s):  
Screening Tool ◽  
High Standard ◽  
Pancreatic Abscess ◽  
High Standard Deviation ◽  
Diagnostic Use ◽  
Cellular Volume ◽  
Myeloperoxidase Deficiency ◽  
Scatter Plots ◽  
The Mean

Summary Objective: In contrast to humans, neutrophil myeloperoxidase deficiency (MPOD) has been rarely investigated in dogs. The hematology analyzer ADVIA®120 differentiates leukocytes based on the cellular volume and their myeloperoxidase concentration. The aim of this study was the characterization of myeloperoxidase deficiency in dogs and the evaluation of the diagnostic use of the ADVIA®120 Myeloperoxidase Index (MPXI). Material and methods: ADVIA® peroxidase scatter plots indicative of MPOD were reviewed. Severity of MPOD was classified semiquantitatively in three groups (MPOD grade 1–3): MPOD grade 1 (MPOD-1): neutrophils showing an abnormal shift of the population, < 25% extending in the monocyte cluster and therefore misclassified, MPOD-2: ~25–50% of neutrophils misclassified, MPOD-3: 50–100% of the neutrophils misclassified due to their location in the monocyte cluster. Sex, age, and breed of the dogs as well as diagnosis, and MPXI were recorded. Results: 29 dogs (nine females and 20 males belonging to 23 breeds) with 38 analyses consistent with MPOD were found. Diseases were characterized by severe leukocyte consumption and included mainly parvovirosis (8/29), DIC/sepsis (3/29), pyometra, pyothorax, pneumonia, pancreatic abscess, and cystitis. A significantly lower mean MPXI in MPOD-3 was present in comparison to the mean MPXI of MPOD-1 (p < 0.05), however, there was a great overlap between the groups. Conclusion: Diseases associated with neutrophil consumption may show an acquired MPOD in dogs. High standard deviation limits the diagnostic use of the MPXI for detection of MPOD. Clinical relevance: The ADVIA®120 cytograms are a good screening tool for detection of MPOD in dogs, but the use of the MPXI is impaired in this species.

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