scholarly journals Channel crosstalk correction in suspension and imaging mass cytometry

2017 ◽  
Author(s):  
Stéphane Chevrier ◽  
Helena Crowell ◽  
Vito Zanotelli ◽  
Stefanie Engler ◽  
Mark D. Robinson ◽  
...  
Keyword(s):  
Fluorescent Dyes ◽  
Expert Knowledge ◽  
Single Cells ◽  
Spillover Effects ◽  
Pure Metal ◽  
Cell Phenotype ◽  
Mass Cytometry ◽  
Complex Samples ◽  
And Function ◽  
Experimental Effort

ABSTRACTMass cytometry enables simultaneous analysis of over 40 proteins and their modifications in single cells through use of metal-tagged antibodies. Compared to fluorescent dyes, the use of pure metal isotopes strongly reduces spectral overlap among measurement channels. Crosstalk still exists, however, caused by isotopic impurity, oxide formation, and mass cytometer properties. Spillover effects can be minimized, but not avoided, by following a set of constraining rules when designing an antibody panel. Generation of such low crosstalk panels requires considerable expert knowledge, knowledge of the abundance of each marker and substantial experimental effort. Here we describe a novel bead-based compensation workflow that includes R-based software and a web tool, which enables correction for interference between channels. We demonstrate utility in suspension mass cytometry and show how this approach can be applied to imaging mass cytometry. Our approach greatly simplifies the development of new antibody panels, increases flexibility for antibody-metal pairing, improves overall data quality, thereby reducing the risk of reporting cell phenotype and function artifacts, and greatly facilitates analysis of complex samples for which antigen abundances are unknown.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

scholarly journals Impacts of HIV infection on Vγ2Vδ2 T cell phenotype and function: a mechanism for reduced tumor immunity in AIDS

2008 ◽  
Vol 84 (2) ◽  
pp. 371-379 ◽  
Author(s):  
Jean-Saville Cummings ◽  
Cristiana Cairo ◽  
Cheryl Armstrong ◽  
Charles E. Davis ◽  
C. David Pauza
Keyword(s):  
T Cell ◽  
Hiv Infection ◽  
Tumor Immunity ◽  
Cell Phenotype ◽  
And Function

scholarly journals Pathophysiology of acute respiratory syndrome coronavirus 2 infection: a systematic literature review to inform EULAR points to consider

RMD Open ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. e001549 ◽  
Author(s):  
Aurélie Najm ◽  
Alessia Alunno ◽  
Xavier Mariette ◽  
Benjamin Terrier ◽  
Gabriele De Marco ◽  
...  
Keyword(s):  
Literature Review ◽  
Systematic Literature Review ◽  
Immune Cell ◽  
Severe Disease ◽  
Cell Phenotype ◽  
Loss Of Function ◽  
Humoral And Cellular Immunity ◽  
Host Immune Responses ◽  
Disease Spectrum ◽  
And Function

BackgroundThe SARS-CoV-2 pandemic is a global health problem. Beside the specific pathogenic effect of SARS-CoV-2, incompletely understood deleterious and aberrant host immune responses play critical roles in severe disease. Our objective was to summarise the available information on the pathophysiology of COVID-19.MethodsTwo reviewers independently identified eligible studies according to the following PICO framework: P (population): patients with SARS-CoV-2 infection; I (intervention): any intervention/no intervention; C (comparator): any comparator; O (outcome) any clinical or serological outcome including but not limited to immune cell phenotype and function and serum cytokine concentration.ResultsOf the 55 496 records yielded, 84 articles were eligible for inclusion according to question-specific research criteria. Proinflammatory cytokine expression, including interleukin-6 (IL-6), was increased, especially in severe COVID-19, although not as high as other states with severe systemic inflammation. The myeloid and lymphoid compartments were differentially affected by SARS-CoV-2 infection depending on disease phenotype. Failure to maintain high interferon (IFN) levels was characteristic of severe forms of COVID-19 and could be related to loss-of-function mutations in the IFN pathway and/or the presence of anti-IFN antibodies. Antibody response to SARS-CoV-2 infection showed a high variability across individuals and disease spectrum. Multiparametric algorithms showed variable diagnostic performances in predicting survival, hospitalisation, disease progression or severity, and mortality.ConclusionsSARS-CoV-2 infection affects both humoral and cellular immunity depending on both disease severity and individual parameters. This systematic literature review informed the EULAR ‘points to consider’ on COVID-19 pathophysiology and immunomodulatory therapies.

scholarly journals STEM-17. NOT ALL GBM STEM CELLS ARE EQUAL: IMPLICATIONS FOR RESEARCH AND THERAPY

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii199-ii200
Author(s):  
Luciano Galdieri ◽  
Arijita Jash ◽  
Olga Malkova ◽  
Diane Mao ◽  
Jian Campian ◽  
...  
Keyword(s):  
Stem Cells ◽  
Phenotypic Diversity ◽  
Treatment Resistance ◽  
Surface Markers ◽  
Mass Cytometry ◽  
Pathway Activation ◽  
Almost All ◽  
And Function ◽  
Activation Status

Abstract Glioblastoma (GBM) kills almost all patients within 2 years. A subpopulation of cells, GBM stem cells (GSCs), contributes to treatment resistance and recurrence. A major therapeutic goal is to kill GSCs, but no targeted therapy yet exists. Since their discovery, GSCs have been isolated using single surface markers, such as CD15, CD44, CD133, and a-6 integrin. It remains unknown how these single surface marker-defined GSC populations compare to each other in terms of signal transduction and function and whether expression of different combinations of these markers is associated with distinct phenotypes. Using mass cytometry and fresh operating room specimens, we found that 15 distinct GSC subpopulations exist in vivo and they differ in their MEK/ERK, WNT, and AKT pathway activation status. In culture, some subpopulations were lost and previously undetectable ones materialized. GSCs highly expressing all four surface markers had the greatest self-renewal capacity and in vivo tumorigenicity as well as the strongest WNT pathway activation. This work highlights the signaling and phenotypic diversity in GSC subpopulations, together suggesting that not all GSCs are equivalent. These observations should be considered when studying GSCs in the laboratory, with implications for the development of treatments that target GSCs and prevent tumor recurrence in patients.

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