Biology subjects

Schwarz, L.

Publications and source records attributed to Schwarz, L..

7 recordsLinked to original sources

bioRxiv2026

qg: Configuration-Driven, Multi-Vendor Acquisition Queue Generation with Reproducible Run-Order and QC Control for Mass Spectrometry

Mass spectrometry laboratories must turn lists of submitted samples into acquisition queues. The run order and the placement of quality-control (QC) injections determine whether a design controls batch effects and signal drift, and whether those effects stay correctable afterward. Yet operators usually set them by hand in vendor worklist editors that neither randomize run order nor offer configurable, pattern-driven QC. We present qg, an open-source tool that builds acquisition queues with systematic run-order handling: four run-order modes (none, simple, blocked/randomized-complete-block, and group-uniform blocked), pattern-driven QC and standard injections, and sampler- and plate-aware positioning. Unlike plate-design tools that stop at a generic sample sheet, qg writes the native vendor acquisition file directly, for three instrument ecosystems (Thermo Fisher XCalibur, Axel Semrau Chronos, Bruker HyStar) across proteomics, metabolomics, and lipidomics. It separates a small, stateless generation pipeline from a declarative configuration layer, so a laboratory adapts instruments, QC patterns, layouts, and naming by editing version-controlled configuration through a validating editor rather than changing code. qg runs from a reactive web interface or a scripted command-line interface, integrated with a LIMS (B-Fabric) or standalone from uploaded tables; randomized runs record their seed and reproduce from exported parameters. On an unbalanced design, group-uniform blocked randomization spreads biological groups evenly across acquisition time, whereas textbook block randomization leaves a tail of the largest group and can track acquisition time worse than a plain shuffle. qg is released under the Apache-2.0 license.

bioinformatics↗

bioRxiv2026

Lactate-dependent metabolic rewiring is associated with CD163+ macrophage polarization in human pyelonephritis

Chronic pyelonephritis is characterized by persistent bacterial infection of the kidney and a dysregulated immune response that promotes disease progression. Macrophages are central regulators of antibacterial immunity in the urinary tract. However, the mechanisms underlying their functional reprogramming in chronic infection remain poorly understood. Here, we identify lactate as a key metabolic determinant of macrophage polarization in human pyelonephritis. Proteomic analysis of human kidney tissue revealed extensive metabolic remodelling, including upregulation of enzymes involved in glycolysis. Consistent with this, lactate levels were significantly elevated in urine and plasma of pyelonephritis patients. Concomitantly, we observed a pronounced accumulation of CD163 macrophages in infected kidneys, representing a distinct macrophage subset with immunomodulatory function. Correlation-based network analysis revealed a strong association between CD163 and lactate dehydrogenase A, supporting a functional association between lactate metabolism and macrophage polarization. Mechanistically, exposure of murine bone marrow-derived macrophages to lactate induced intracellular protein lactylation and promoted polarization toward a CD163 phenotype, defining a metabolically imprinted macrophage state distinct from classical activation paradigms. Proteomic profiling demonstrated extensive remodelling of macrophage protein expression in response to lactate with significant alteration of mediators of phagocytosis, Toll-like receptor signalling, and interferon response. Together, these findings identify lactate as a potent metabolic driver of macrophage reprogramming and establish a foundation for investigating lactylation-dependent immune dysfunction in chronic pyelonephritis.

immunology↗

bioRxiv2024

prolfquapp - A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics

AbstractMass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis (DEA) of proteins. As experiments grow in complexity, involving more samples, groups, and identified proteins, traditional interactive data analysis methods become impractical. The prolfquapp addresses this challenge by providing a command-line interface that simplifies DEA, making it accessible to non-programmers and seamlessly integrating it into workflow management systems. Prolfquapp streamlines data processing and result visualization by generating dynamic HTML reports that facilitate the exploration of differential expression results. These reports allow for investigating complex experiments, such as those involving repeated measurements and multiple explanatory variables. Additionally, prolfquapp supports various output formats, including XLSX files, SummarizedExperiment objects and rank files, for further interactive analysis using spreadsheet software, the exploreDE Shiny application, or gene set enrichment analysis software. By leveraging advanced statistical models from the prolfqua R package, prolfquapp offers a user-friendly, integrated solution for large-scale quantitative proteomics studies, combining efficient data processing with insightful, publication-ready outputs. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/617391v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@10930a2org.highwire.dtl.DTLVardef@57f5dborg.highwire.dtl.DTLVardef@ce0d73org.highwire.dtl.DTLVardef@1d531da_HPS_FORMAT_FIGEXP M_FIG C_FIG This visual table of contents illustrates the workflow and key features of the prolfquapp tool for differential expression analysis in proteomics. On the left are the inputs, like the CSV for annotation and quantification results, YAML for parameters, and FASTA files for protein information. In the center are the prolfquapp and prolfqua R packages and supporting tools like crosstalk and knitr, representing the core processing components. On the right side, the figure highlights the various outputs generated by prolfquapp O_LIXLSX files containing protein abundances, group summaries, and differential expression results. C_LIO_LIHTML reports with text, graphs, interactive volcano plots, and dynamic tables for data exploration. C_LIO_LIPDF documents with detailed protein boxplots and peptide-level matrix plots. C_LIO_LIIntegration with exploreDE for interactive data visualization. C_LI This diagram concisely summarizes the flow from data input to the creation of analysis-ready outputs, offering a clear overview of the prolfquapp toolset.

bioinformatics↗

bioRxiv2023

Proteomic adaptations in the kidney reveal orchestration of local and secreted antimicrobial peptides in human pyelonephritis

Pyelonephritis (PN) is a frequent bacterial infection of the kidney and is often associated with severe diseases, organ loss and sepsis. Antibiotics are the cornerstone of therapy, however, increasing antibiotic resistance threatens therapy success and necessitates novel treatment strategies. Various proteins, such as antimicrobial peptides (AMPs), are key molecules of the innate immune response and insights into their regulation may help overcome multi-drug resistance and severe diseases. Using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS), several cellular, biological, and metabolic processes important for the antimicrobial response were identified, including a significant increase in previously undescribed proteins in human PN with antimicrobial function. Among others, we observed elevation of AMPs, such as calprotectin, azurocidin-1, and cathepsin G in the kidney, which we validated in the urine. Additionally, we observed a negative correlation of azurocidin-1 with plasma levels of C-reactive protein suggesting that the presence in the kidney may protect from severe diseases and systemic inflammation. This study represents the first renal proteomic dataset of human PN, enabling novel insights into the expression of AMPs in the context of PN. Lay SummaryGrowing antimicrobial resistance necessitates a better understanding of the expression of proteins that are critical for the immune response. Using mass spectrometry we identified AMPs in the kidney and urine of PN patients. Elevated levels of the AMP azurocidin-1 was associated with reduced systemic inflammation, indicated by lower C-reactive protein. Overall, this study identified expression of previously undescribed AMPs in the context of human PN. These proteins may play a pivotal role in protection from severe diseases and systemic inflammation.

immunology↗

bioRxiv2022

Action prediction error: a value-free dopaminergic teaching signal that drives stable learning

Animals choice behavior is characterized by two main tendencies: taking actions that led to rewards and repeating past actions. Theory suggests these strategies may be reinforced by different types of dopaminergic teaching signals: reward prediction error (RPE) to reinforce value-based associations and movement-based action prediction errors to reinforce value-free repetitive associations. Here we use an auditory-discrimination task in mice to show that movement-related dopamine activity in the tail of the striatum encodes the hypothesized action prediction error signal. Causal manipulations reveal that this prediction error serves as a value-free teaching signal that supports learning by reinforcing repeated associations. Computational modeling and experiments demonstrate that action prediction errors alone cannot support reward-guided learning but when paired with the RPE circuitry they serve to consolidate stable sound-action associations in a value-free manner. Together we show that there are two types of dopaminergic prediction errors that work in tandem to support learning.

neuroscience↗

bioRxiv2022

The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs

Abstract/SummarySpecialized chromatin-binding proteins are required for DNA-based processes during development. We recently established PWWP2A as direct histone variant H2A.Z interactor involved in mitosis and cranial-facial development. Here, we identify the H2A.Z/PWWP2A-associated protein HMG20A as part of several chromatin-modifying complexes including NuRD, and show that it localizes to genomic regulatory regions. Hmg20a depletion causes severe head and heart developmental defects in Xenopus laevis. Our data indicate that craniofacial malformations are caused by defects in neural crest cell (NCC) migration and cartilage formation. These developmental defects are pheno-copied in HMG20A-depleted mESCs, which show inefficient differentiation into NCCs and cardiomyocytes (CMs). Accordingly, loss of HMG20A caused striking deregulation of transcription programs involved in epithelial- mesenchymal transition (EMT) and cardiac differentiation, thereby providing insights into the regulatory circuits controlled by HMG20A. Collectively, our findings implicate HMG20A as part of the H2A.Z/PWWP2A/NuRD-axis and reveal it as a key modulator of the intricate developmental transcription programs that guide NCC and cardiomyocyte differentiation.

molecular biology↗

bioRxiv2019

PINK1 Regulates Dopamine and Lipids at Mitochondria to Maintain Synapses and Neuronal Function

Mitochondrial dysfunction contributes to the pathogenesis of Parkinsons disease but it is not clear why inherent mitochondrial defects lead specifically to the death of dopaminergic neurons of the mid brain. PINK1 is mitochondrial kinase and PINK1 mutations cause early onset Parkinsons disease.\n\nWe found that in neuronal progenitors, PINK1 regulates mitochondrial morphology, mitochondrial contact to the endoplasmic reticulum (ER) and the phosphorylation of Miro1. A compensatory metabolic shift towards lipid synthesis provides mitochondria with the components needed for membrane renewal and oxidative phosphorylation, maintaining the mitochondrial network once mature.\n\nCholesterol is increased by loss of PINK1, promoting overall membrane rigidity. This alters the distribution of phosphorylated DAT at synapses and impairs dopamine uptake. PINK1 is required for the phosphorylation of tyrosine hydroxylase at Ser19, dopamine and calcium homeostasis and dopaminergic pacemaking.\n\nWe suggest a novel mechanism for PINK1 pathogenicity in Parkinsons disease in addition to but not exclusive of mitophagy. We also provide a basis for potential therapeutics by showing that low doses of the cholesterol depleting drug {beta}-cyclodextrin reverse PINK1-specific phenotypes.

neuroscience↗