scholarly journals Neocortical microdissection at columnar and laminar resolution for molecular interrogation

2017 ◽  
Author(s):  
Koen Kole ◽  
Tansu Celikel
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Barrel Cortex ◽  
Brain Slices ◽  
High Quality ◽  
Living Slices ◽  
Physiological Processes ◽  
Molecular Studies ◽  
The Brain

AbstractThe heterogeneous organization of the mammalian neocortex poses a challenge to elucidate the molecular mechanisms underlying its physiological processes. Although high-throughput molecular methods are increasingly deployed in neuroscience, their anatomical specificity is often lacking. Here we introduce a targeted microdissection technique that enables extraction of high-quality RNA and proteins at high anatomical resolution from acutely prepared brain slices. We exemplify its utility by isolating single cortical columns and laminae from the mouse primary somatosensory (barrel) cortex. Tissues can be isolated from living slices in minutes, and the extracted RNA and protein are of sufficient quantity and quality to be used for RNA-sequencing and mass spectrometry. This technique will help to increase the anatomical specificity of molecular studies of the neocortex, and the brain in general as it is applicable to any brain structure that can be identified using optical landmarks in living slices.

scholarly journals Protein SUMOylation modification and its associations with disease

Open Biology ◽  
2017 ◽  
Vol 7 (10) ◽  
pp. 170167 ◽  
Author(s):  
Yanfang Yang ◽  
Yu He ◽  
Xixi Wang ◽  
Ziwei liang ◽  
Gu He ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cell Growth ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Cellular Responses ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Sumoylation Site ◽  
Signal Crosstalk ◽  
Protein Sumoylation

SUMOylation, as a post-translational modification, plays essential roles in various biological functions including cell growth, migration, cellular responses to stress and tumorigenesis. The imbalance of SUMOylation and deSUMOylation has been associated with the occurrence and progression of various diseases. Herein, we summarize and discuss the signal crosstalk between SUMOylation and ubiquitination of proteins, protein SUMOylation relations with several diseases, and the identification approaches for SUMOylation site. With the continuous development of bioinformatics and mass spectrometry, several accurate and high-throughput methods have been implemented to explore small ubiquitin-like modifier-modified substrates and sites, which is helpful for deciphering protein SUMOylation-mediated molecular mechanisms of disease.

scholarly journals “Multiomics” Approaches to Understand and Treat COVID-19: Mass Spectrometry and Next-Generation Sequencing

BioChem ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 210-237
Author(s):  
Diane Appiasie ◽  
Daniel J. Guerra ◽  
Kyle Tanguay ◽  
Steven Jelinek ◽  
Damian D. Guerra ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Lipid Metabolism ◽  
Next Generation Sequencing ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Viral Proteins ◽  
Next Generation ◽  
Sources Of Information ◽  
Generation Sequencing

In the race against COVID-19 for timely therapeutic developments, mass spectrometry-based high-throughput methods have been valuable. COVID-19 manifests an extremely diverse spectrum of phenotypes from asymptomatic to life-threatening, drastic elevations in immune response or cytokine storm, multiple organ failure and death. These observations warrant a detailed understanding of associated molecular mechanisms to develop therapies. In this direction, high-throughput methods that generate large datasets focusing on changes in protein interactions, lipid metabolism, transcription, and epigenetic regulation of gene expression are extremely beneficial sources of information. Hence, mass spectrometry-based methods have been employed in several studies to detect changes in interactions among host proteins, and between host and viral proteins in COVID-19 patients. The methods have also been used to characterize host and viral proteins, and analyze lipid metabolism in COVID-19 patients. Information obtained using the above methods are complemented by high-throughput analysis of transcriptomic and epigenomic changes associated with COVID-19, coupled with next-generation sequencing. Hence, this review discusses the most recent studies focusing on the methods described above. The results establish the importance of mass spectrometry-based studies towards understanding the infection process, immune imbalance, disease mechanism, and indicate the potential of the methods’ therapeutic developments and biomarker screening against COVID-19 and future outbreaks.

scholarly journals Selenium, Selenoproteins, and Immunity

Nutrients ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 1203 ◽  
Author(s):  
Joseph Avery ◽  
Peter Hoffmann
Keyword(s):  
Immune System ◽  
Immune Responses ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
Biological Effects ◽  
Cell Functions ◽  
Experimental Systems ◽  
Physiological Processes

Selenium is an essential micronutrient that plays a crucial role in development and a wide variety of physiological processes including effect immune responses. The immune system relies on adequate dietary selenium intake and this nutrient exerts its biological effects mostly through its incorporation into selenoproteins. The selenoproteome contains 25 members in humans that exhibit a wide variety of functions. The development of high-throughput omic approaches and novel bioinformatics tools has led to new insights regarding the effects of selenium and selenoproteins in human immuno-biology. Equally important are the innovative experimental systems that have emerged to interrogate molecular mechanisms underlying those effects. This review presents a summary of the current understanding of the role of selenium and selenoproteins in regulating immune cell functions and how dysregulation of these processes may lead to inflammation or immune-related diseases.

scholarly journals High-Throughput Mass Spectrometry Screening for Inhibitors of Phosphatidylserine Decarboxylase

2007 ◽  
Vol 12 (5) ◽  
pp. 628-634 ◽  
Author(s):  
Chris D. Forbes ◽  
Joshuaine G. Toth ◽  
Can C. Özbal ◽  
William A. Lamarr ◽  
Jennifer A. Pendleton ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Catalytic Activity ◽  
High Throughput ◽  
High Throughput Screening ◽  
Lipid Synthesis ◽  
High Quality ◽  
Compound Libraries ◽  
Z Value ◽  
Large Compound ◽  
Mass Spectrometry Assay

A high-throughput mass spectrometry assay to measure the catalytic activity of phosphatidylserine decarboxylase (PISD) is described. PISD converts phosphatidylserine to phosphatidylethanolamine during lipid synthesis. Traditional methods of measuring PISD activity are low throughput and unsuitable for the high-throughput screening of large compound libraries. The high-throughput mass spectrometry assay directly measures phosphatidylserine and phosphatidylethanolamine using the RapidFire™ platform at a rate of 1 sample every 7.5 s. The assay is robust, with an average Z′ value of 0.79 from a screen of 9920 compounds. Of 60 compounds selected for confirmation, 54 are active in dose-response studies. The application of high-throughput mass spectrometry permitted a high-quality screen to be performed for an otherwise intractable target. ( Journal of Biomolecular Screening 2007:628-634)

scholarly journals Epitranscriptomic regulation by m6A RNA methylation in brain development and diseases

2020 ◽  
Vol 40 (12) ◽  
pp. 2331-2349
Author(s):  
Anil K Chokkalla ◽  
Suresh L Mehta ◽  
Raghu Vemuganti
Keyword(s):  
Gene Expression ◽  
Brain Cancer ◽  
Molecular Mechanisms ◽  
The Body ◽  
Fine Tuning ◽  
Rna Methylation ◽  
Mrna Metabolism ◽  
Physiological Processes ◽  
M6a Rna Methylation ◽  
The Brain

Cellular RNAs are pervasively tagged with diverse chemical moieties, collectively called epitranscriptomic modifications. The methylation of adenosine at N6 position generates N6-methyladenosine (m6A), which is the most abundant and reversible epitranscriptomic modification in mammals. The m6A signaling is mediated by a dedicated set of proteins comprised of writers, erasers, and readers. Contrary to the activation–repression binary view of gene regulation, emerging evidence suggests that the m6A methylation controls multiple aspects of mRNA metabolism, such as splicing, export, stability, translation, and degradation, culminating in the fine-tuning of gene expression. Brain shows the highest abundance of m6A methylation in the body, which is developmentally altered. Within the brain, m6A methylation is biased toward neuronal transcripts and sensitive to neuronal activity. In a healthy brain, m6A maintains several developmental and physiological processes such as neurogenesis, axonal growth, synaptic plasticity, circadian rhythm, cognitive function, and stress response. The m6A imbalance contributes to the pathogenesis of acute and chronic CNS insults, brain cancer, and neuropsychiatric disorders. This review discussed the molecular mechanisms of m6A regulation and its implication in the developmental, physiological, and pathological processes of the brain.

154: Integration of TPSA and High-Throughput Mass Spectrometry Data Improves Prostate Cancer Prediction

2007 ◽  
Vol 177 (4S) ◽  
pp. 52-53
Author(s):  
Stefano Ongarello ◽  
Eberhard Steiner ◽  
Regina Achleitner ◽  
Isabel Feuerstein ◽  
Birgit Stenzel ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Mass Spectrometry ◽  
High Throughput ◽  
Mass Spectrometry Data ◽  
Cancer Prediction

A Mucin-Specific Protease Enables Molecular and Functional Analysis of Human Cancer-Associated Mucins

2018 ◽  
Author(s):  
Stacy A. Malaker ◽  
Kayvon Pedram ◽  
Michael J. Ferracane ◽  
Elliot C. Woods ◽  
Jessica Kramer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Mechanisms ◽  
Cultured Cells ◽  
High Resolution Mass Spectrometry ◽  
Human Cancer ◽  
Glycosylation Sites ◽  
Bacterial Protease ◽  
Specific Protease ◽  
To Come ◽  
And Function

<div> <div> <div> <p>Mucins are a class of highly O-glycosylated proteins that are ubiquitously expressed on cellular surfaces and are important for human health, especially in the context of carcinomas. However, the molecular mechanisms by which aberrant mucin structures lead to tumor progression and immune evasion have been slow to come to light, in part because methods for selective mucin degradation are lacking. Here we employ high resolution mass spectrometry, polymer synthesis, and computational peptide docking to demonstrate that a bacterial protease, called StcE, cleaves mucin domains by recognizing a discrete peptide-, glycan-, and secondary structure- based motif. We exploited StcE’s unique properties to map glycosylation sites and structures of purified and recombinant human mucins by mass spectrometry. As well, we found that StcE will digest cancer-associated mucins from cultured cells and from ovarian cancer patient-derived ascites fluid. Finally, using StcE we discovered that Siglec-7, a glyco-immune checkpoint receptor, specifically binds sialomucins as biological ligands, whereas the related Siglec-9 receptor does not. Mucin-specific proteolysis, as exemplified by StcE, is therefore a powerful tool for the study of glycoprotein structure and function and for deorphanizing mucin-binding receptors. </p> </div> </div> </div>

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