The use of a silica-based heat sink to “uncouple” the matrix-assisted laser desorption/ionization (MALDI) mechanism

2011 ◽  
Vol 89 (4) ◽  
pp. 446-460 ◽  
Author(s):  
E. Lourantos ◽  
O. M. Ramirez ◽  
A. E. Giannakopulos ◽  
K. A. Beran ◽  
Peter J. Derrick ◽  
...  
Keyword(s):  
Gas Phase ◽  
Heat Sink ◽  
Model System ◽  
Model Systems ◽  
Laser Desorption Ionization ◽  
System A ◽  
The Matrix ◽  
Pass Through ◽  
Maldi Mechanism ◽  
Silicon Based

The relationships between ion yield(s) as a function of desorption alone and (or) ionization was investigated using two model systems. In the first model system, a carbohydrate (2,3,6-tri-O-methyl-β-cyclodextrin, TMBCD), which could be directly laser desorbed, was analyzed with and without a silicon-based heat sink compound (HSC). The HSC allowed heat to pass through but obstructed the flow of charge. In the second model system, a peptide (substance P), which ccould not be laser desorbed, was analyzed under similar conditions. The ion yield of TMBCD under either system of heat conductivity was similar, whereas the ion yield of the peptide with the heat sink was negligible. Compounds that are predominately cationized either in the gas phase or preformed in solution give an ion yield that is not dependent upon the surface conditions, whereas compounds that are not ordinarily cationized are affected by the emission of electrons from the metal surface.

scholarly journals Overview of Arabidopsis as a Genetics Model System and Its Limitation, Leading to the Development of Emerging Plant Model Systems

2021 ◽  
Author(s):  
Madhabendra Mohon Kar ◽  
Ayan Raichaudhuri
Keyword(s):  
Molecular Biology ◽  
Genetic Basis ◽  
Model System ◽  
Model Systems ◽  
Plant Model ◽  
New Model ◽  
Plant System ◽  
Model Plant ◽  
System A ◽  
Plant Process

Model plant systems make it easier to perform experiments with them. They help to understand and expand our knowledge about the genetic basis behind different plant process. Also, it is easier to design and perform genetic and genomic experiments using a model plant system. A. thaliana was initially chosen as the model plant system, and remains to this date, one of the most widely studied plant. With the advent of better molecular biology and sequencing tools and to understand the genetic basis for the unique processes in different plant species, there is emergence of several new model systems.

scholarly journals Photochemistry and UV/Vis Spectroscopy of Hydrated Vanadium Cations, V+(H2O)n, n = 1–41, a Model System for Photochemical Hydrogen Evolution

2021 ◽  
Author(s):  
Jakob Heller ◽  
Tobias F. Pascher ◽  
Dominik Muß ◽  
Christian van der Linde ◽  
Martin K. Beyer ◽  
...  
Keyword(s):  
Metal Ions ◽  
Gas Phase ◽  
Hydrogen Evolution ◽  
Light Harvesting ◽  
Model System ◽  
Model Systems ◽  
Ideal Model ◽  
Elementary Steps ◽  
Vis Spectroscopy

Photochemical hydrogen evolution provides fascinating perspectives for light harvesting. Hydrated metal ions in the gas phase are ideal model systems to study elementary steps of this reaction on a molecular...

Fundamental study of hydrogen-attachment-induced peptide fragmentation occurring in the gas phase and during the matrix-assisted laser desorption/ionization process

2018 ◽  
Vol 20 (18) ◽  
pp. 13057-13067 ◽  
Author(s):  
Daiki Asakawa ◽  
Hidenori Takahashi ◽  
Shinichi Iwamoto ◽  
Koichi Tanaka
Keyword(s):  
Gas Phase ◽  
Laser Desorption ◽  
Peptide Fragmentation ◽  
Laser Desorption Ionization ◽  
Fundamental Study ◽  
The Matrix ◽  
Fragmentation Techniques ◽  
Hydrogen Radical ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

Mass spectrometry with hydrogen-radical-mediated fragmentation techniques has been used for the sequencing of proteins/peptides.

scholarly journals Comparison of Automation Equipment in High Throughput Screening

1998 ◽  
Vol 3 (4) ◽  
pp. 305-311 ◽  
Author(s):  
Michelle E. Stevens ◽  
Peter J. Bouchard ◽  
Ilona Kariv ◽  
Thomas D.Y. Chung ◽  
Kevin R. Oldenburg
Keyword(s):  
High Throughput Screening ◽  
Model Systems ◽  
Liquid Handling ◽  
System A ◽  
Accuracy And Precision ◽  
Gene Assay ◽  
The Matrix ◽  
Automation Equipment ◽  
A Cell ◽  
Time Accuracy

This report compares several types of liquid handling equipment presently used in HTS. The devices include 96-well automated pipettors such as the Carl Creative PlateTrac™ (Harbor City, CA), Matrix PlateMate™ (Hudson, NH), Tomtec Quadra-96T? (Hamden, CT) and a Zymark RapidPlate-96™ (Hopkinton, MA) integrated into a full robotic system. A general set of considerations including ease of programming, assay-completion time, accuracy and precision of liquid dispensing, and low-volume pipetting were evaluated. Both a protease screen and a cell-based reporter gene assay were used as model systems for comparison. The data indicate that the Carl Creative PlateTrac has an advantage in several areas. These include the ease in programming, reduction in assay run time, and increased accuracy and precision in liquid dispensing, especially for volumes of 1 μl or less. However, both the Matrix Platemate and Zymark robotic systems may be used to perform complicated multi-step tasks involving multidirectional plate transfer, which is not possible on the current PlateTrac. Advantages and limitations of each piece of equipment are discussed further in this report.

Florida Activity Mobility Simulator

2005 ◽  
Vol 1921 (1) ◽  
pp. 123-130 ◽  
Author(s):  
Ram M. Pendyala ◽  
Ryuichi Kitamura ◽  
Akira Kikuchi ◽  
Toshiyuki Yamamoto ◽  
Satoshi Fujii
Keyword(s):  
Travel Demand ◽  
Demand Forecasting ◽  
Model Development ◽  
Model System ◽  
Model Systems ◽  
Development Effort ◽  
Transportation Demand ◽  
New Era ◽  
System A ◽  
Preliminary Validation

The development of modeling systems for activity-based travel demand ushers in a new era in transportation demand forecasting and planning. A comprehensive multimodal activity-based system for forecasting travel demand was developed for implementation in Florida and resulted in the Florida Activity Mobility Simulator (FAMOS). Two main modules compose the FAMOS microsimulation model system for modeling activity–travel patterns of individuals: the Household Attributes Generation System and the Prism-Constrained Activity–Travel Simulator. FAMOS was developed and estimated with household activity and travel data collected in southeast Florida in 2000. Results of the model development effort are promising and demonstrate the applicability of activity-based model systems in travel demand forecasting. An overview of the model system, a description of its features and capabilities, and preliminary validation results are provided.

scholarly journals A new dynamic model system for the study of capture reactions for diffusable compounds in cytochemistry. I. Description of the model with special attention to phosphate capture in acid phosphatase cytochemistry.

1978 ◽  
Vol 26 (5) ◽  
pp. 331-339 ◽  
Author(s):  
A S de Jong ◽  
T J Hak ◽  
P van Duijn ◽  
W T Daems
Keyword(s):  
Acid Phosphatase ◽  
Model System ◽  
Phosphate Concentration ◽  
Model Studies ◽  
System A ◽  
Phosphate Ions ◽  
The Matrix ◽  
Phosphatase Cytochemistry ◽  
Trapping Reactions ◽  
Bone Calcification

A model system is described for the investigation of the dynamics of precipitation processes in a matrix. In this system a solution containing the molecular species to be precipitated and the precipitating medium are pumped along opposite sides of a polyacrylamide film. The solutions flowing continuously along the film, interact and can form a precipitate inside the film. The applicability of the model was tested on the capture reaction for phosphate ions by the Gomori type medium for acid phosphatase. Precipitation of lead phosphate in the film occurred only at a phosphate concentration above a certain value. The dependence of this minimal phosphate concentration on various parameters was studied and the results were compared with values found in earlier model studies and calculations concerning phosphate concentrations that can be built up in lysosomes during the Gomori reaction. The system seems promising for obtaining fundamental data about other cytochemical enzyme trapping reactions as well as for the matrix facotrs involved in bone calcification and shell formation.

scholarly journals Singularly Perturbed Oscillators with Exponential Nonlinearities

2021 ◽  
Author(s):  
S. Jelbart ◽  
K. U. Kristiansen ◽  
P. Szmolyan ◽  
M. Wechselberger
Keyword(s):  
Limit Cycles ◽  
Space Dimension ◽  
Blow Up ◽  
Exponential Convergence ◽  
Model System ◽  
Piecewise Smooth ◽  
Singularly Perturbed ◽  
Model Systems ◽  
Smooth System ◽  
Unique Limit

AbstractSingular exponential nonlinearities of the form $$e^{h(x)\epsilon ^{-1}}$$ e h ( x ) ϵ - 1 with $$\epsilon >0$$ ϵ > 0 small occur in many different applications. These terms have essential singularities for $$\epsilon =0$$ ϵ = 0 leading to very different behaviour depending on the sign of h. In this paper, we consider two prototypical singularly perturbed oscillators with such exponential nonlinearities. We apply a suitable normalization for both systems such that the $$\epsilon \rightarrow 0$$ ϵ → 0 limit is a piecewise smooth system. The convergence to this nonsmooth system is exponential due to the nonlinearities we study. By working on the two model systems we use a blow-up approach to demonstrate that this exponential convergence can be harmless in some cases while in other scenarios it can lead to further degeneracies. For our second model system, we deal with such degeneracies due to exponentially small terms by extending the space dimension, following the approach in Kristiansen (Nonlinearity 30(5): 2138–2184, 2017), and prove—for both systems—existence of (unique) limit cycles by perturbing away from singular cycles having desirable hyperbolicity properties.

scholarly journals The Relevance of the SH2 Domain for c-Src Functionality in Triple-Negative Breast Cancer Cells

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 462
Author(s):  
Víctor Mayoral-Varo ◽  
María Pilar Sánchez-Bailón ◽  
Annarica Calcabrini ◽  
Marta García-Hernández ◽  
Valerio Frezza ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Sh2 Domain ◽  
Model Systems ◽  
System A ◽  
Promising Therapeutic Target ◽  
Relevant Role ◽  
Inactivating Mutation

The role of Src family kinases (SFKs) in human tumors has been always associated with tyrosine kinase activity and much less attention has been given to the SH2 and SH3 adapter domains. Here, we studied the role of the c-Src-SH2 domain in triple-negative breast cancer (TNBC). To this end, SUM159PT and MDA-MB-231 human cell lines were employed as model systems. These cells conditionally expressed, under tetracycline control (Tet-On system), a c-Src variant with point-inactivating mutation of the SH2 adapter domain (R175L). The expression of this mutant reduced the self-renewal capability of the enriched population of breast cancer stem cells (BCSCs), demonstrating the importance of the SH2 adapter domain of c-Src in the mammary gland carcinogenesis. In addition, the analysis of anchorage-independent growth, proliferation, migration, and invasiveness, all processes associated with tumorigenesis, showed that the SH2 domain of c-Src plays a very relevant role in their regulation. Furthermore, the transfection of two different aptamers directed to SH2-c-Src in both SUM159PT and MDA-MB-231 cells induced inhibition of their proliferation, migration, and invasiveness, strengthening the hypothesis that this domain is highly involved in TNBC tumorigenesis. Therefore, the SH2 domain of c-Src could be a promising therapeutic target and combined treatments with inhibitors of c-Src kinase enzymatic activity may represent a new therapeutic strategy for patients with TNBC, whose prognosis is currently very negative.

scholarly journals The Meaning of the Matrix: Towards a Cybernetic Critical Theory of Capitalism

2018 ◽  
Vol 6 (1) ◽  
pp. 1
Author(s):  
Shay Hershkovitz
Keyword(s):  
Social Systems ◽  
Theoretical Concept ◽  
Social Actors ◽  
System A ◽  
The Social ◽  
Social Entity ◽  
Key Concepts ◽  
The Matrix ◽  
Critical Approaches ◽  
Operational Logic

Marxist criticism is most discernible; despite the oft-repeated claim that it is now irrelevant, belonging to an age now past. This essay assumes that criticism originating in the Marxist school of thought continue to be relevant also in this present time; though it may need to be further developed and improved by integrating newer critical approaches into the classic Marxist discourse. This essay therefore integrates basic Marxist ideas with key concepts from ‘social systems theory’; especially the theory of the German sociologist Niklas Luhmann's. In this light, capitalism is conceptualized here as a ‘super (social) system’: a meaning-creating social entity, in which social actors, behaviors and structures are realized. This theoretical concept and terminology emphasizes the social construction of control and stability, when discussing the operational logic of capitalism.

scholarly journals Paracoccus denitrificans: a genetically tractable model system for studying respiratory complex I

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Owen D. Jarman ◽  
Olivier Biner ◽  
John J. Wright ◽  
Judy Hirst
Keyword(s):  
Complex I ◽  
Paracoccus Denitrificans ◽  
Model System ◽  
Proton Pumping ◽  
Model Systems ◽  
Metabolic Enzyme ◽  
Nadh:Ubiquinone Oxidoreductase ◽  
Mitochondrial Complex I ◽  
Mitochondrial Complex ◽  
Inner Mitochondrial Membrane

AbstractMitochondrial complex I (NADH:ubiquinone oxidoreductase) is a crucial metabolic enzyme that couples the free energy released from NADH oxidation and ubiquinone reduction to the translocation of four protons across the inner mitochondrial membrane, creating the proton motive force for ATP synthesis. The mechanism by which the energy is captured, and the mechanism and pathways of proton pumping, remain elusive despite recent advances in structural knowledge. Progress has been limited by a lack of model systems able to combine functional and structural analyses with targeted mutagenic interrogation throughout the entire complex. Here, we develop and present the α-proteobacterium Paracoccus denitrificans as a suitable bacterial model system for mitochondrial complex I. First, we develop a robust purification protocol to isolate highly active complex I by introducing a His6-tag on the Nqo5 subunit. Then, we optimize the reconstitution of the enzyme into liposomes, demonstrating its proton pumping activity. Finally, we develop a strain of P. denitrificans that is amenable to complex I mutagenesis and create a catalytically inactive variant of the enzyme. Our model provides new opportunities to disentangle the mechanism of complex I by combining mutagenesis in every subunit with established interrogative biophysical measurements on both the soluble and membrane bound enzymes.

Sign in / Sign up

Export Citation Format

Share Document