scholarly journals Histone sample preparation for bottom-up mass spectrometry: a roadmap to informed decisions

2021 ◽  
Author(s):  
Simon Daled ◽  
Sander Willems ◽  
Bart Van Puyvelde ◽  
Laura Corveleyn ◽  
Sigrid Verhelst ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Research Question ◽  
Stable Gene ◽  
Assessment Procedure ◽  
Bottom Up ◽  
Genome Complexity ◽  
Arginine Residues ◽  
Multicellular Organisms ◽  
Selection Of

Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic world, which makes these key regulators notoriously hard to analyze. We here provide a roadmap to enable fast and informed selection of a bottom-up mass spectrometry sample preparation protocol that matches a specific research question. We therefore propose a two-step assessment procedure: (i) visualization of the coverage that is attained for a given workflow and (ii) direct alignment-between-runs to assess potential pitfalls at the ion level. To illustrate the applicability, we compare four different sample preparation protocols, while adding a new enzyme to the toolbox, i.e., RgpB (GingisREX, Genovis), an endoproteinase that selectively and efficiently cleaves at the c-terminal end of arginine residues.

scholarly journals Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions

Proteomes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 17
Author(s):  
Simon Daled ◽  
Sander Willems ◽  
Bart Van Puyvelde ◽  
Laura Corveleyn ◽  
Sigrid Verhelst ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Research Question ◽  
Stable Gene ◽  
Assessment Procedure ◽  
Bottom Up ◽  
Genome Complexity ◽  
Arginine Residues ◽  
Multicellular Organisms ◽  
Selection Of

Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic world, which makes these key regulators notoriously hard to analyze. We here provide a roadmap to enable fast and informed selection of a bottom-up mass spectrometry sample preparation protocol that matches a specific research question. We therefore propose a two-step assessment procedure: (i) visualization of the coverage that is attained for a given workflow and (ii) direct alignment between runs to assess potential pitfalls at the ion level. To illustrate the applicability, we compare four different sample preparation protocols while adding a new enzyme to the toolbox, i.e., RgpB (GingisREX®, Genovis, Lund, Sweden), an endoproteinase that selectively and efficiently cleaves at the c-terminal end of arginine residues. Raw data are available via ProteomeXchange with identifier PXD024423.

Miniaturized sample preparation on a digital microfluidics device for sensitive bottom-up microproteomics of mammalian cells using magnetic beads and mass spectrometry-compatible surfactants

Lab on a Chip ◽  
2019 ◽  
Vol 19 (20) ◽  
pp. 3490-3498 ◽  
Author(s):  
Jan Leipert ◽  
Andreas Tholey
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Mammalian Cells ◽  
Magnetic Beads ◽  
Digital Microfluidics ◽  
Bottom Up ◽  
Polymer Surfactants

The combination of digital microfluidics and magnetic beads for removal of polymer surfactants enables sensitive LC-MS-based microproteomics analyses down to 100 mammalian cells.

The Tail Wagging the Dog? Top-down and Bottom-up Explanations for Bureaucratic Appointments in Authoritarian Regimes

2018 ◽  
Vol 3 (2) ◽  
pp. 239-259 ◽  
Author(s):  
Fabian Burkhardt ◽  
Alexander Libman
Keyword(s):  
Central Government ◽  
Research Question ◽  
Authoritarian Regimes ◽  
Political Regimes ◽  
Top Down ◽  
Bottom Up ◽  
Main Research ◽  
Self Selection ◽  
Democratic Country ◽  
Selection Of

The paper investigates the link between the sub-national variation of political regimes in a (at the federal level) non-democratic country and the appointments of federal officials in the sub-national provinces. In particular, we look at the appointment of the chief federal inspectors to the regions in Putin’s Russia in 2000–2012. Our main research question is whether appointment patterns can be explained by top-down concerns of the central government willing to keep control over the most unruly regions or by bottom-up self-selection of bureaucrats belonging to influential groups into more attractive positions more suitable for rent-seeking. The advantage of our case is that data we have at hand allow us to distinguish these two logics. Our results indicate that for the Russian chief federal inspectors in 2000–2012 bottom-up self-selection appears to be the more plausible explanation of the link between sub-national political regimes and appointment patterns.

Love Your Enemy: A Christian Response to Embrace Others

2020 ◽  
Author(s):  
Hanna Dewi Aritonang ◽  
Bestian Simangunsong ◽  
Adiani Hulu
Keyword(s):  
Jesus Christ ◽  
Research Question ◽  
Theological Reflection ◽  
Religious Communities ◽  
Religious People ◽  
Lifestyle Choice ◽  
Sustainable Peace ◽  
Research Problems ◽  
Selection Of

This article addresses the issue of conflict between religious communities that cause enmity amid society. Hostilities must be overcome and resolved in accordance with the call of Christianity to live in love and peace. The study used the qualitative paradigm as the method of the research and the descriptive-analyses as the writing method by describing the research problems based on data collected from related publications.One of the powerful messages of Jesus's teaching is "Love your enemies." It’s one of the greatest challenges in life. Jesus Christ gave an important doctrine about loving the enemy because love is more powerful than evil, hurtful deeds. Loving the enemy means canceling hostilities and violence, but instead, it promises acceptance of each other. The title of this study is "love your enemies": A Christian Response to Embrace Others. As the title of this study is "love your enemies," the reason for the selection of this article is because the author sees that "loving the enemy is a commandment from God that must be obeyed. This research question emphasizes how to realize "loving the enemy" amid hostility. This paper argues that Jesus's command to love the enemy is a proper Christian lifestyle choice in the midst of hostility. We use CS Song thoughts, which elaborated with other scholars' views on theology, loving, and embracing others. The purpose of the research was to gain understanding and build a theological reflection on Jesus' commandment to love the enemy. In this article, we first briefly discuss the portrait of life among religious people in Indonesia. Secondly, we discuss the conflict between religious people in Indonesia. Finally, we apply the command of Jesus to love our enemy as a Christian lifestyle in the midst of hostility to construct harmony amid hostility. We propose the command of Jesus to ‘love your enemy’ as a response to establishing sustainable peace by embrace others. Finally, the Christians must become a loving community because God so loved us, and we also ought to love and embrace others.

Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single Particle Cryo-EM

2020 ◽  
Author(s):  
Paul Dominic B. Olinares ◽  
Jin Young Kang ◽  
Eliza Llewellyn ◽  
Courtney Chiu ◽  
James Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Single Particle ◽  
Native Mass Spectrometry ◽  
Optimal Sample

scholarly journals Mass spectrometry‐based top‐down and bottom‐up approaches for proteomic analysis of the Moroccan Buthus occitanus scorpion venom

FEBS Open Bio ◽  
2021 ◽  
Author(s):  
Khadija Daoudi ◽  
Christian Malosse ◽  
Ayoub Lafnoune ◽  
Bouchra Darkaoui ◽  
Salma Chakir ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Scorpion Venom ◽  
Top Down ◽  
Bottom Up

scholarly journals Sample preparation strategy for the detection of steroid-like compounds using MALDI mass spectrometry imaging: pulmonary distribution of budesonide as a case study

2021 ◽  
Author(s):  
Riccardo Zecchi ◽  
Pietro Franceschi ◽  
Laura Tigli ◽  
Davide Amidani ◽  
Chiara Catozzi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Mass Spectrometry Imaging ◽  
Maldi Mass Spectrometry ◽  
Adult Rabbit ◽  
Chronic Obstructive ◽  
Ionization Mass ◽  
Obstructive Pulmonary Disease ◽  
Imaging Protocol ◽  
Girard’S Reagent

AbstractCorticosteroids as budesonide can be effective in reducing topic inflammation processes in different organs. Therapeutic use of budesonide in respiratory diseases, like asthma, chronic obstructive pulmonary disease, and allergic rhinitis is well known. However, the pulmonary distribution of budesonide is not well understood, mainly due to the difficulties in tracing the molecule in lung samples without the addition of a label. In this paper, we present a matrix-assisted laser desorption/ionization mass spectrometry imaging protocol that can be used to visualize the pulmonary distribution of budesonide administered to a surfactant-depleted adult rabbit. Considering that budesonide is not easily ionized by MALDI, we developed an on-tissue derivatization method with Girard’s reagent P followed by ferulic acid deposition as MALDI matrix. Interestingly, this sample preparation protocol results as a very effective strategy to raise the sensitivity towards not only budesonide but also other corticosteroids, allowing us to track its distribution and quantify the drug inside lung samples. Graphical abstract

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