The role of Data-Independent Acquisition for Glycoproteomics

Molecular & Cellular Proteomics ◽

10.1074/mcp.r120.002204 ◽

2020 ◽

pp. mcp.R120.002204

Author(s):

Zilu Ye ◽

Sergey Y Vakhrushev

Keyword(s):

Early Stage ◽

Label Free ◽

Basic Principles ◽

Post Translational Modifications ◽

Full Characterization ◽

Data Independent Acquisition ◽

Stage Of Development ◽

Free Quantification

Data independent acquisition (DIA) is now an emerging method in bottom-up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications (PTM), such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the development and perspectives of DIA methodology for N- and O- glycoproteomics and posits that DIA-based glycoproteomics could be a method of choice to address some of the challenging aspects of glycoproteomics. First, the current challenges in glycoproteomics and the basic principles of DIA is briefly introduced. DIA based glycoproteomics is then summarized and described into four aspects based on the actual samples. Lastly, we discussed the important challenges and future perspectives in the field. We believe that DIA can significantly facilitate glycoproteomic studies and contribute to the development of future advanced tools and approaches in the field of glycoproteomics.

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Hybrid QconCAT-Based Targeted Absolute and Data-Independent Acquisition-Based Label-Free Quantification Enables In-Depth Proteomic Characterization of Wheat Amylase/Trypsin Inhibitor Extracts

Journal of Proteome Research ◽

10.1021/acs.jproteome.0c00752 ◽

2021 ◽

Author(s):

Malte Sielaff ◽

Valentina Curella ◽

Manjusha Neerukonda ◽

Muhammad Afzal ◽

Khaoula El Hassouni ◽

...

Keyword(s):

Trypsin Inhibitor ◽

Label Free ◽

Label Free Quantification ◽

Data Independent Acquisition ◽

Free Quantification ◽

Wheat Amylase

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A New Piano-Stool Ruthenium(II) P-Cymene-Based Complex: Crystallographic, Hirshfeld Surface, DFT, and Luminescent Studies

Crystals ◽

10.3390/cryst11010013 ◽

2020 ◽

Vol 11 (1) ◽

pp. 13

Author(s):

Mohd. Muddassir ◽

Abdullah Alarifi ◽

Mohd. Afzal

Keyword(s):

Density Functional ◽

Weak Interactions ◽

Energy Levels ◽

Hirshfeld Surface ◽

Binding Energies ◽

Orbital Energy ◽

Aminosalicylic Acid ◽

Full Characterization

A new complex (Ru(η6-p-cymene)(5-ASA)Cl2) (1) where 5-ASA is 5-aminosalicylic acid has been prepared by reacting the ruthenium arene precursors ((η6-arene)Ru(μ-Cl)Cl)2, with the 5-ASA ligands in a 1:1 ratio. Full characterization of complex 1 was accomplished by elemental analysis, IR, and TGA following the structure obtained from a single-crystal X-ray pattern. The structural analysis revealed that complex 1 shows a “piano-stool” geometry with Ru-C (2.160(5)- 2.208(5)Å), Ru-N (2.159(4) Å) distances, which is similar to equivalents sister complex. Density functional theory (DFT) was used to calculate the significant molecular orbital energy levels, binding energies, bond angles, bond lengths, and spectral data (FTIR, NMR, and UV–VIS) of complex 1, consistent with the experimental results. The IR and UV–VIS spectra of complex 1 were computed using all of the methods and choose the most appropriate way to discuss. Hirshfeld surface analysis was also executed to understand the role of weak interactions such as H⋯H, C⋯H, C-H⋯π, and vdW interactions, which play a significant role in the crystal environment’s stability. Moreover, the luminescence results at room temperature show that complex 1 gives a more intense emission band positioned at 465 nm upon excitation at 330 nm makes it a suitable candidate for the building of photoluminescent material.

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Subcellular orchestration of alpha-synuclein variants in Parkinson’s disease brains revealed by 3D multicolor STED microscopy

10.1101/470476 ◽

2018 ◽

Cited By ~ 7

Author(s):

Tim E. Moors ◽

Christina A. Maat ◽

Daniel Niedieker ◽

Daniel Mona ◽

Dennis Petersen ◽

...

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Lewy Bodies ◽

Distribution Patterns ◽

Alpha Synuclein ◽

Label Free ◽

Post Translational Modifications ◽

Sted Microscopy ◽

C Terminus

AbstractPost-translational modifications of alpha-synuclein (aSyn), particularly phosphorylation at Serine 129 (Ser129-p) and truncation of its C-terminus (CTT), have been implicated in Parkinson’s disease (PD) pathology. To gain more insight in the relevance of Ser129-p and CTT aSyn under physiological and pathological conditions, we investigated their subcellular distribution patterns in normal aged and PD brains using highly-selective antibodies in combination with 3D multicolor STED microscopy. We show that CTT aSyn localizes in mitochondria in PD patients and controls, whereas the organization of Ser129-p in a cytoplasmic network is strongly associated with pathology. Nigral Lewy bodies show an onion skin-like architecture, with a structured framework of Ser129-p aSyn and neurofilaments encapsulating CTT aSyn in their core, which displayed high content of proteins and lipids by label-free CARS microscopy. The subcellular phenotypes of antibody-labeled pathology identified in this study provide evidence for a crucial role of Ser129-p aSyn in Lewy body formation.

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A transitional stage in the commitment of mesoderm to hematopoiesis requiring the transcription factor SCL/tal-1

Development ◽

10.1242/dev.127.11.2447 ◽

2000 ◽

Vol 127 (11) ◽

pp. 2447-2459 ◽

Cited By ~ 2

Author(s):

S.M. Robertson ◽

M. Kennedy ◽

J.M. Shannon ◽

G. Keller

Keyword(s):

Transcription Factor ◽

Embryoid Body ◽

Early Stage ◽

Es Cells ◽

Blast Cell ◽

Stage Of Development ◽

Erythroid Precursors ◽

Identification And Characterization ◽

Definitive Hematopoiesis

In this report, we describe the identification and characterization of an early embryoid body-derived colony, termed the transitional colony, which contains cell populations undergoing the commitment of mesoderm to the hematopoietic and endothelial lineages. Analysis of individual transitional colonies indicated that they express Brachyury as well as flk-1, SCL/tal-1, GATA-1, (beta)H1 and (beta)major reflecting the combination of mesodermal, hematopoietic and endothelial populations. This pattern differs from that found in the previously described hemangioblast-derived blast cell colonies in that they typically lacked Brachyury expression, consistent with their post-mesodermal stage of development (Kennedy, M., Firpo, M., Choi, K., Wall, C., Robertson, S., Kabrun, N. and Keller, G. (1997) Nature 386, 488–493). Replating studies demonstrated that transitional colonies contain low numbers of primitive erythroid precursors as well as a subset of precursors associated with early stage definitive hematopoiesis. Blast cell colonies contain higher numbers and a broader spectrum of definitive precursors than found in the transitional colonies. ES cells homozygous null for the SCL/tal-1 gene, a transcription factor known to be essential for development of the primitive and definitive hematopoietic systems, were not able to form blast colonies but did form transitional colonies. Together these findings suggest that the transitional colony represents a stage of development earlier than the blast cell colony and one that uniquely defines the requirement for a functional SCL/tal-1 gene for the progression to hematopoietic commitment.

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Fungal Gut Microbiota Dysbiosis and Its Role in Colorectal, Oral, and Pancreatic Carcinogenesis

Cancers ◽

10.3390/cancers12051326 ◽

2020 ◽

Vol 12 (5) ◽

pp. 1326 ◽

Cited By ~ 1

Author(s):

Karolina Kaźmierczak-Siedlecka ◽

Aleš Dvořák ◽

Marcin Folwarski ◽

Agnieszka Daca ◽

Katarzyna Przewłócka ◽

...

Keyword(s):

Pancreatic Cancer ◽

Gut Microbiota ◽

Early Stage ◽

Saccharomyces Boulardii ◽

Cancer Development ◽

Disease Stage ◽

Fungal Microbiota ◽

Colorectal Cancer Patients

The association between bacterial as well as viral gut microbiota imbalance and carcinogenesis has been intensively analysed in many studies; nevertheless, the role of fungal gut microbiota (mycobiota) in colorectal, oral, and pancreatic cancer development is relatively new and undiscovered field due to low abundance of intestinal fungi as well as lack of well-characterized reference genomes. Several specific fungi amounts are increased in colorectal cancer patients; moreover, it was observed that the disease stage is strongly related to the fungal microbiota profile; thus, it may be used as a potential diagnostic biomarker for adenomas. Candida albicans, which is the major microbe contributing to oral cancer development, may promote carcinogenesis via several mechanisms, mainly triggering inflammation. Early detection of pancreatic cancer provides the opportunity to improve survival rate, therefore, there is a need to conduct further studies regarding the role of fungal microbiota as a potential prognostic tool to diagnose this cancer at early stage. Additionally, growing attention towards the characterization of mycobiota may contribute to improve the efficiency of therapeutic methods used to alter the composition and activity of gut microbiota. The administration of Saccharomyces boulardii in oncology, mainly in immunocompromised and/or critically ill patients, is still controversial.

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Extracellular HMGB1 Modulates Glutamate Metabolism Associated with Kainic Acid-Induced Epilepsy-Like Hyperactivity in Primary Rat Neural Cells

Cellular Physiology and Biochemistry ◽

10.1159/000460513 ◽

2017 ◽

Vol 41 (3) ◽

pp. 947-959 ◽

Cited By ~ 15

Author(s):

Yuji Kaneko ◽

Colleen Pappas ◽

Teresita Malapira ◽

Fernando Ĺ. Vale ◽

Naoki Tajiri ◽

...

Keyword(s):

Cell Viability ◽

Kainic Acid ◽

Early Stage ◽

High Mobility ◽

Mitochondrial Activity ◽

Neural Cells ◽

Glutamate Metabolism ◽

Post Translational Modifications ◽

Mhc Ii

Background/Aims: Neuroinflammatory processes have been implicated in the pathophysiology of seizure/epilepsy. High mobility group box 1 (HMGB1), a non-histone DNA binding protein, behaves like an inflammatory cytokine in response to epileptogenic insults. Kainic acid (KA) is an excitotoxic reagent commonly used to induce epilepsy in rodents. However, the molecular mechanism by which KA-induced HMGB1 affords the initiation of epilepsy, especially the role of extracellular HMGB1 in neurotransmitter expression, remains to be elucidated. Methods: Experimental early stage of epilepsy-related hyperexcitability was induced in primary rat neural cells (PRNCs) by KA administration. We measured the localization of HMGB1, cell viability, mitochondrial activity, and expression level of glutamate metabolism-associated enzymes. Results: KA induced the translocation of HMGB1 from nucleus to cytosol, and its release from the neural cells. The translocation is associated with post-translational modifications. An increase in extracellular HMGB1 decreased PRNC cell viability and mitochondrial activity, downregulated expression of glutamate decarboxylase67 (GAD67) and glutamate dehydrogenase (GLUD1/2), and increased intracellular glutamate concentration and major histocompatibility complex II (MHC II) level. Conclusions: That a surge in extracellular HMGB1 approximated seizure initiation suggests a key pathophysiological contribution of HMGB1 to the onset of epilepsy-related hyperexcitability.

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