Stefan Schulze
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View article: Targeting Fibrotic Scars with Extracellular Vesicles Extracted from Mature Aloe vera: Enhanced Antioxidant, Anti-inflammatory, and Antifibrotic Activity through M2 Macrophage Polarization and Myofibroblasts Inhibition
Targeting Fibrotic Scars with Extracellular Vesicles Extracted from Mature Aloe vera: Enhanced Antioxidant, Anti-inflammatory, and Antifibrotic Activity through M2 Macrophage Polarization and Myofibroblasts Inhibition Open
Background Abnormal scarring and fibrotic skin disorders arise from dysregulated wound healing processes. While Aloe vera is widely recognized for its therapeutic properties, the potential of its extracellular vesicles (Av-EVs) remains und…
View article: Abstract 2043 Predicting Functions of Uncharacterized Proteins in Prokaryotes Using a Combination of Structural and Sequence-Based Approaches
Abstract 2043 Predicting Functions of Uncharacterized Proteins in Prokaryotes Using a Combination of Structural and Sequence-Based Approaches Open
View article: Abstract 1796 Uncovering Archaeal Glycoproteomes via Large-Scale Bioinformatic Analysis of Public Proteomic Data
Abstract 1796 Uncovering Archaeal Glycoproteomes via Large-Scale Bioinformatic Analysis of Public Proteomic Data Open
View article: Advancing archaeal research through FAIR resource and data sharing, and inclusive community building
Advancing archaeal research through FAIR resource and data sharing, and inclusive community building Open
View article: Quorum sensing mediates morphology and motility transitions in the model archaeon<i>Haloferax volcanii</i>
Quorum sensing mediates morphology and motility transitions in the model archaeon<i>Haloferax volcanii</i> Open
Quorum sensing (QS) is a mechanism of intercellular communication that enables microbes to alter gene expression and adapt to the environment. This cell-cell signaling is necessary for intra- and interspecies behaviors such as virulence an…
View article: Identification of structural and regulatory cell-shape determinants in Haloferax volcanii
Identification of structural and regulatory cell-shape determinants in Haloferax volcanii Open
Archaea are key players in various processes, yet little is known about their cell biology, including cell-shape determination. Haloferax volcanii is a haloarchaeon that can form both rod- and disk-shaped cells, depending on growth conditi…
View article: Identification of structural and regulatory cell-shape determinants in Haloferax volcanii
Identification of structural and regulatory cell-shape determinants in Haloferax volcanii Open
<p>Archaea are key players in various processes, yet little is known about their cell biology, including cell-shape determination. <em>Haloferax volcanii</em> is a haloarchaeon that can form both rod- and disk-shaped…
View article: Identification and characterization of structural and regulatory cell-shape determinants in<i>Haloferax volcanii</i>
Identification and characterization of structural and regulatory cell-shape determinants in<i>Haloferax volcanii</i> Open
Archaea play indispensable roles in global biogeochemical cycles, yet many critical cellular processes, including cell-shape determination, are poorly understood. Haloferax volcanii , a model haloarchaeon, forms rods and disks, depending o…
View article: PeptideForest: Semisupervised machine learning integrating multiple search engines for peptide identification
PeptideForest: Semisupervised machine learning integrating multiple search engines for peptide identification Open
The first step in bottom-up proteomics is the assignment of measured fragmentation mass spectra to peptide sequences, also known as peptide spectrum matches. In recent years novel algorithms have pushed the assignment to new heights, unfor…
View article: A Twist to the Kirby-Bauer Disk Diffusion Susceptibility Test: an Accessible Laboratory Experiment Comparing Haloferax volcanii and Escherichia coli Antibiotic Susceptibility to Highlight the Unique Cell Biology of Archaea
A Twist to the Kirby-Bauer Disk Diffusion Susceptibility Test: an Accessible Laboratory Experiment Comparing Haloferax volcanii and Escherichia coli Antibiotic Susceptibility to Highlight the Unique Cell Biology of Archaea Open
Archaea, once thought to only live in extreme environments, are present in many ecosystems, including the human microbiome, and they play important roles ranging from nutrient cycling to bioremediation. Yet this domain is often overlooked …
View article: Immersed Liquid Biofilm and Honeycomb Pattern Formations in Haloferax volcanii
Immersed Liquid Biofilm and Honeycomb Pattern Formations in Haloferax volcanii Open
Biofilms are cellular aggregates encased in extracellular polymeric substances and are commonly formed by single-celled eukaryotes, bacteria, and archaea. In addition to attaching to solid surfaces, these cellular aggregates can also be ob…
View article: Advanced understanding of prokaryotic biofilm formation using a cost-effective and versatile multi-panel adhesion (mPAD) mount
Advanced understanding of prokaryotic biofilm formation using a cost-effective and versatile multi-panel adhesion (mPAD) mount Open
Most microorganisms exist in biofilms, which comprise aggregates of cells surrounded by an extracellular matrix that provides protection from external stresses. Based on the conditions under which they form, biofilm structures vary in sign…
View article: The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics Open
Modern proteomics approaches can explore whole proteomes within a single mass spectrometry (MS) run. However, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools a…
View article: The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics Open
Modern proteomics approaches can explore whole proteomes within a single mass spectrometry (MS) run. However, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools a…
View article: The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics Open
Modern proteomics approaches can explore whole proteomes within a single mass spectrometry (MS) run. However, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools a…
View article: A proteomics sample metadata representation for multiomics integration, and big data analysis
A proteomics sample metadata representation for multiomics integration, and big data analysis Open
The amount of public proteomics data is increasing at an extraordinary rate. Hundreds of datasets are submitted each month to ProteomeXchange repositories, representing many types of proteomics studies, focusing on different aspects such a…
View article: Glycoproteomics of<i>Haloferax volcanii</i>reveals an extensive glycoproteome and concurrence of different<i>N</i>-glycosylation pathways
Glycoproteomics of<i>Haloferax volcanii</i>reveals an extensive glycoproteome and concurrence of different<i>N</i>-glycosylation pathways Open
Glycosylation is one of the most complex post-translational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility an…
View article: Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal
Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal Open
The identification of peptide sequences and their post-translational modifications (PTMs) is a crucial step in the analysis of bottom-up proteomics data. The recent development of open modification search (OMS) engines allows virtually all…
View article: Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal
Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal Open
The identification of peptide sequences and their post-translational modifications (PTMs) is a crucial step in the analysis of bottom-up proteomics data. The recent development of open modification search (OMS) engines allows virtually all…
View article: SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides
SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides Open
Protein glycosylation is a complex post-translational modification with crucial cellular functions in all domains of life. Currently, large-scale glycoproteomics approaches rely on glycan database dependent algorithms and are thus unsuitab…
View article: SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides
SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides Open
Protein glycosylation is a complex post-translational modification with crucial cellular functions in all domains of life. Currently, large-scale glycoproteomics approaches rely on glycan database dependent algorithms and are thus unsuitab…
View article: SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides
SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides Open
Motivation Protein glycosylation is a complex post-translational modification with crucial cellular functions in all domains of life. Currently, large-scale glycoproteomics approaches rely on glycan database dependent algorithms and are th…
View article: <i>Haloferax volcanii</i> immersed liquid biofilms develop independently of known biofilm machineries and exhibit rapid honeycomb pattern formation
<i>Haloferax volcanii</i> immersed liquid biofilms develop independently of known biofilm machineries and exhibit rapid honeycomb pattern formation Open
The ability to form biofilms is shared by many microorganisms, including archaea. Cells in a biofilm are encased in extracellular polymeric substances that typically include polysaccharides, proteins, and extracellular DNA, conferring prot…
View article: The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics Open
Modern proteomics approaches can explore whole proteomes within a single mass spectrometry (MS) run. However, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools a…
View article: The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics Open
Modern proteomics approaches can explore whole proteomes within a single mass spectrometry (MS) run. However, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools a…
View article: Novel Insights Into N-Glycan Fucosylation and Core Xylosylation in C. reinhardtii
Novel Insights Into N-Glycan Fucosylation and Core Xylosylation in C. reinhardtii Open
Chlamydomonas reinhardtii (C. reinhardtii) N-glycans carry plant typical β1,2-core xylose, α1,3-fucose residues, as well as plant atypical terminal β1,4-xylose and methylated mannoses. In a recent study, XylT1A was shown to act as c…
View article: LIPID ANCHORING OF ARCHAEOSORTASE SUBSTRATES AND MID-CELL GROWTH IN HALOARCHAEA
LIPID ANCHORING OF ARCHAEOSORTASE SUBSTRATES AND MID-CELL GROWTH IN HALOARCHAEA Open
The archaeal cytoplasmic membrane provides an anchor for many surface proteins. Recently, a novel membrane anchoring mechanism involving a peptidase, archaeosortase A (ArtA) and C-terminal lipid attachment of surface proteins was identifie…
View article: Novel insights into <i>N</i>-glycan fucosylation and core xylosylation in <i>C. reinhardtii</i>
Novel insights into <i>N</i>-glycan fucosylation and core xylosylation in <i>C. reinhardtii</i> Open
Chlamydomonas reinhardtii N -glycans carry plant typical β1,2-core xylose, α1,3-fucose residues as well as plant atypical terminal β1,4-xylose and methylated mannoses. In a recent study, XylT1A was shown to act as core xylosyltransferase, …
View article: pymzML v2.0: introducing a highly compressed and seekable gzip format
pymzML v2.0: introducing a highly compressed and seekable gzip format Open
Motivation In the new release of pymzML (v2.0), we have optimized the speed of this established tool for mass spectrometry data analysis to adapt to increasing amounts of data in mass spectrometry. Thus, we integrated faster libraries for …
View article: Calredoxin represents a novel type of calcium-dependent sensor-responder connected to redox regulation in the chloroplast
Calredoxin represents a novel type of calcium-dependent sensor-responder connected to redox regulation in the chloroplast Open