Pull-Down with a c-di-GMP-Specific Capture Compound Coupled to Mass Spectrometry as a Powerful Tool to Identify Novel Effector Proteins

2017 ◽  
pp. 361-376 ◽  
Author(s):  
Benoît-Joseph Laventie ◽  
Timo Glatter ◽  
Urs Jenal
Keyword(s):  
Mass Spectrometry ◽  
Effector Proteins

scholarly journals Capture Compound Mass Spectrometry - A Powerful Tool to Identify Novel c-di-GMP Effector Proteins

10.3791/51404 ◽  
2015 ◽  
Author(s):  
Benoît-Joseph Laventie ◽  
Jutta Nesper ◽  
Erik Ahrné ◽  
Timo Glatter ◽  
Alexander Schmidt ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Effector Proteins

scholarly journals A synthetic biology approach to probing nucleosome symmetry

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Yuichi Ichikawa ◽  
Caitlin F Connelly ◽  
Alon Appleboim ◽  
Thomas CR Miller ◽  
Hadas Jacobi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Synthetic Biology ◽  
Regulatory Elements ◽  
Effector Proteins ◽  
Histone Tail ◽  
Core Histones ◽  
Cryptic Transcription ◽  
Synthetic Biology Approach

The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.

The role of mass spectrometry analysis in bacterial effector characterization

2017 ◽  
Vol 474 (16) ◽  
pp. 2779-2784 ◽  
Author(s):  
Nichollas E. Scott ◽  
Elizabeth L. Hartland
Keyword(s):  
Mass Spectrometry ◽  
Cell Biology ◽  
Critical Role ◽  
Effector Proteins ◽  
Mass Spectrometry Analysis ◽  
Protein Activity ◽  
Post Translational Modifications ◽  
Spectrometry Analysis ◽  
New Generation

Many secreted bacterial effector proteins play a critical role in host–pathogen interactions by mediating a variety of post-translational modifications, some of which do not occur natively within the eukaryotic proteome. The characterization of bacterial effector protein activity remains an important step to understanding the subversion of host cell biology during pathogen infection and although molecular biology and immunochemistry remain critical tools for gaining insights into bacterial effector functions, increasingly mass spectrometry (MS) and proteomic approaches are also playing an indispensable role. The focus of this editorial is to highlight the strengths of specific MS approaches and their utility for the characterization of bacterial effector activity. With the capability of new generation MS instrumentation, MS-based technologies can provide information that is inaccessible using traditional molecular or immunochemical approaches.

scholarly journals A synthetic biology approach to probing nucleosome symmetry

2017 ◽  
Author(s):  
Yuichi Ichikawa ◽  
Caitlin F. Connelly ◽  
Alon Appleboim ◽  
Thomas C. Miller ◽  
Hadas Jacobi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Synthetic Biology ◽  
Regulatory Elements ◽  
Effector Proteins ◽  
Histone Tail ◽  
Core Histones ◽  
Cryptic Transcription ◽  
Synthetic Biology Approach

ABSTRACTThe repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.

How SIMS microscopy can be used in medicine

1992 ◽  
Vol 50 (2) ◽  
pp. 1602-1603
Author(s):  
Philippe Fragu
Keyword(s):  
Mass Spectrometry ◽  
Biomedical Applications ◽  
Secondary Ion Mass Spectrometry ◽  
Chemical Elements ◽  
Biological Applications ◽  
The Past ◽  
Potential Source ◽  
Secondary Ion ◽  
Chemical Integrity ◽  
Scientific Endeavour

The identification, localization and quantification of intracellular chemical elements is an area of scientific endeavour which has not ceased to develop over the past 30 years. Secondary Ion Mass Spectrometry (SIMS) microscopy is widely used for elemental localization problems in geochemistry, metallurgy and electronics. Although the first commercial instruments were available in 1968, biological applications have been gradual as investigators have systematically examined the potential source of artefacts inherent in the method and sought to develop strategies for the analysis of soft biological material with a lateral resolution equivalent to that of the light microscope. In 1992, the prospects offered by this technique are even more encouraging as prototypes of new ion probes appear capable of achieving the ultimate goal, namely the quantitative analysis of micron and submicron regions. The purpose of this review is to underline the requirements for biomedical applications of SIMS microscopy.Sample preparation methodology should preserve both the structural and the chemical integrity of the tissue.

Imaging of Al-Li-Cu alloys with a Scanning Ion Microprobe

1990 ◽  
Vol 48 (2) ◽  
pp. 314-315
Author(s):  
K.K. Soni ◽  
D.B. Williams ◽  
J.M. Chabala ◽  
R. Levi-Setti ◽  
D.E. Newbury
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Equilibrium Phase ◽  
Icosahedral Symmetry ◽  
Ion Microprobe ◽  
X Ray ◽  
Cu Alloys ◽  
Two Phases ◽  
The University ◽  
Secondary Ion

In contrast to the inability of x-ray microanalysis to detect Li, secondary ion mass spectrometry (SIMS) generates a very strong Li+ signal. The latter’s potential was recently exploited by Williams et al. in the study of binary Al-Li alloys. The present study of Al-Li-Cu was done using the high resolution scanning ion microprobe (SIM) at the University of Chicago (UC). The UC SIM employs a 40 keV, ∼70 nm diameter Ga+ probe extracted from a liquid Ga source, which is scanned over areas smaller than 160×160 μm2 using a 512×512 raster. During this experiment, the sample was held at 2 × 10-8 torr.In the Al-Li-Cu system, two phases of major importance are T1 and T2, with nominal compositions of Al2LiCu and Al6Li3Cu respectively. In commercial alloys, T1 develops a plate-like structure with a thickness <∼2 nm and is therefore inaccessible to conventional microanalytical techniques. T2 is the equilibrium phase with apparent icosahedral symmetry and its presence is undesirable in industrial alloys.

Applications of Time-OF-Flight Secondary Ion Mass Spectrometry (TOF-SIMS)

1990 ◽  
Vol 48 (2) ◽  
pp. 308-309
Author(s):  
Bruno Schueler ◽  
Robert W. Odom
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Structural Information ◽  
Time Of Flight ◽  
Biological Tissues ◽  
Polymer Surfaces ◽  
Tof Sims ◽  
Secondary Ions ◽  
Ion Mass Spectrometry ◽  
Secondary Ion

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) provides unique capabilities for elemental and molecular compositional analysis of a wide variety of surfaces. This relatively new technique is finding increasing applications in analyses concerned with determining the chemical composition of various polymer surfaces, identifying the composition of organic and inorganic residues on surfaces and the localization of molecular or structurally significant secondary ions signals from biological tissues. TOF-SIMS analyses are typically performed under low primary ion dose (static SIMS) conditions and hence the secondary ions formed often contain significant structural information.This paper will present an overview of current TOF-SIMS instrumentation with particular emphasis on the stigmatic imaging ion microscope developed in the authors’ laboratory. This discussion will be followed by a presentation of several useful applications of the technique for the characterization of polymer surfaces and biological tissues specimens. Particular attention in these applications will focus on how the analytical problem impacts the performance requirements of the mass spectrometer and vice-versa.

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