Biology subjects

Burger, D.

Publications and source records attributed to Burger, D..

8 recordsLinked to original sources

bioRxiv2025

Isolation of Extracellular Vesicles from Minimal Volume Ascites Fluid Using Strong Anion Exchange Magnetic Beads

Ovarian cancer (OC) remains a leading cause of gynecologic cancer mortality due to late-stage diagnosis and limited early detection strategies. Ascites fluid, a pathological hallmark of OC, is a rich source of tumor-derived extracellular vesicles (EVs) that reflect the tumor microenvironment and hold promise for biomarker discovery. However, isolating EVs from minimal ascites volumes (<100 {micro}L) poses technical challenges using conventional methods like ultracentrifugation or size-exclusion chromatography (SEC). This study explores the application of strong anion exchange (SAX) magnetic beads (Mag-Net) for efficient EV isolation from as little as 2 {micro}L of ascites fluid from both murine models and a human patient with mucinous borderline tumor. We demonstrate that SAX achieves robust EV capture at 10{micro}l of input volume, enabling comprehensive proteomic profiling and single-EV surface-enhanced Raman spectroscopy (SERS) with a >2-fold increase in proteomic depth compared to raw ascites. Notably, this study was able to identify 1000 proteins not previously annotated in Vesiclepedia for OC-derived EVs, alongside distinct SERS signatures, highlighting the potential for multiomic analysis. Comparative analysis with UC revealed enhanced proteomic depth obtained with SAX beads, albeit we also observed differential detection of canonical markers (e.g., CD9, CD81) between input volumes of ascites fluid. These findings establish SAX as a scalable, low-input platform for EV-based biomarker discovery, paving the way for improved early detection and molecular insights into OC progression.

biochemistry↗

bioRxiv2025

Proteomic Signatures of Podocyte Injury Are Reflected in Urinary Extracellular Vesicles in Pediatric Nephrotic Syndrome.

Idiopathic nephrotic syndrome (NS) is a common glomerulopathy in children and presents with significant proteinuria. There are no reliable clinical or biochemical markers of disease relapse, or prognosis. Extracellular vesicles (EVs) are small, membrane-bound biological effectors released from stressed cells. We previously showed increases in podocyte-specific urinary EVs from children with disease relapse in NS, with numbers returning to near-zero in remission. Herein, we have expanded this work to evaluate puromycin aminonucleoside (PAN) injury by characterizing proteomic signatures of podocytes and their EVs in vitro. In addition, we performed data-independent proteomic analysis (DIA) to characterize changes in signatures of EVs from pediatric patients with active NS versus remission. Our key findings reveal PAN-injured podocytes increase large EV (LEV) secretion in vitro; moreover, DIA uncovered changes in cellular and LEV proteomes that were also observed in urinary LEVs from patients with active disease. Urinary LEV proteomes from children with active NS were significantly different than those in remission, highlighted by 645 and 240 unique proteins associated with disease or remission, respectively. This foundational work provides the impetus for a larger, prospective biomarker study aimed at identifying EV-specific proteins associated with relapse versus remission.

cell biology↗

bioRxiv2024

Ultrastructural diversity of alpha-Synuclein pathology in the post-mortem brain of Parkinson patients: implications for Lewy Body formation

Lewy bodies, the defining pathological feature of Parkinsons disease, are intraneuronal inclusions enriched in aggregated alpha-synuclein (Syn). We used correlative light and electron microscopy to selectively investigate phosphorylated Syn (SynpS129)-positive inclusions in the substantia nigra of end-stage postmortem Parkinsons disease brain. Here we show that somatic SynpS129 inclusions in nigral dopaminergic neurons are consistently fibrillar, whereas the membranous-type inclusions are restricted to neuritic processes. These neuritic inclusions displayed marked ultrastructural heterogeneity, ranging from predominantly membranous to mixed membranous-fibrillar forms. The selective targeting of defined inclusions enabled detailed structural characterization of Lewy pathology, rather than quantitative or disease-stage comparisons. Our findings highlight clear ultrastructural differences between somatic and neuritic SynpS129 pathology and demonstrate the structural complexity and heterogeneity of Lewy pathology in human Parkinsons disease brain.

neuroscience↗

bioRxiv2024

1.94 Angstrom structure of synthetic alpha-synuclein fibrils seeding MSA neuropathology

Summary ParagraphMultiple system atrophy (MSA) is a rapidly progressive neurodegenerative disease of unknown cause, typically affecting individuals aged 50-60 and leading to death within a decade1-3. It is characterized by glial cytoplasmic inclusions (GCIs) composed of fibrillar alpha-synuclein (aSyn)4-8, whose formation shows parallels with prion propagation9,10. While fibrils extracted from MSA brains have been structurally characterized11, their ability to replicate in a "protein-only" manner has been questioned12, and their capacity to induce GCIs in vivo remains unexplored. By contrast, the synthetic fibril strain 1B13,14, assembled from recombinant human aSyn, self-replicates in vitro and induces GCIs in mice15 - suggesting direct relevance to MSA - but awaited scrutiny at an atomic scale. Here, we report high-resolution structural analyses of 1B fibrils and of fibrils extracted from diseased mice injected with 1B that developed GCIs (1BP). We show in vivo that conformational templating enables fibril strain replication, resulting in MSA-like inclusion pathology. Remarkably, the structures of 1B and 1BP are highly similar and mimic the fold of aSyn observed in one protofilament of fibrils isolated from MSA patients11. Moreover, reinjection of crude mouse brain homogenates containing 1BP into new mice reproduces the same MSA-like pathology induced by the parent synthetic seed 1B. Our findings identify 1B as a synthetic pathogen capable of self-replication in vivo and reveal structural features of 1B/1BP that may underlie MSA pathology, offering insights for therapeutic strategies.

neuroscience↗

bioRxiv2024

A versatile correlative light and electron microscopy protocol for human brain and other biological models

Correlative light and electron microscopy (CLEM) combines light microscopy, for identifying a target via genetic labels, dyes, antibodies, and morphological features, with electron microscopy, for analyzing high-resolution subcellular ultrastructures. Here, we describe the step-by-step instructions to perform a CLEM experiment, optimized for the investigation of ultrastructural features in human brain tissue. The procedure is carried out at room-temperature and can be also adapted to other human and animal tissue samples. The procedure requires 8-days to complete and includes the stages of sample fixation for optimal ultrastructural preservation, immunofluorescence staining, image acquisition, multi-modal image correlation, and is executable within standard EM laboratories. Serving as a critical tool for characterizing human tissue and disease models, room-temperature CLEM facilitates the identification and quantification of subcellular morphological features across brain regions. Key pointsO_LIThe protocol for correlative light and electron microscopy (CLEM) is optimized for analyzing chemically fixed human brain tissues. It focuses on maintaining the integrity of ultrastructural features, thereby minimizing artifacts and structural alterations. C_LIO_LIExamining brain tissues at the ultrastructural level can provide an unprecedented amount of detail which may help advance our understanding of the mechanisms underlying neurodegenerative disorders. C_LI

neuroscience↗

bioRxiv2021

Cryo-EM structure of alpha-synuclein fibrils amplified by PMCA from PD and MSA patient brains

Synucleinopathies are neurodegenerative diseases related to the aggregation of the protein alpha-synuclein (aSyn). Among these diseases, Parkinsons disease (PD) and multiple system atrophy (MSA) are most prevalent. aSyn can readily form different fibrillar polymorphs, if exposed to an air-water interface or by templating with pre-existing fibrils. We here report the structures of three fibrillar polymorphs that were obtained after seeding monomeric aSyn with PD and MSA patients brain homogenates using protein misfolding cyclic amplification (PMCA). Seeding with a control brain homogenate did not produce fibrils, and seeding with other in vitro generated fibrillar polymorphs as a control faithfully produced polymorphs of a different type. The here determined fibril structures from PD and MSA brain tissue represent new folds, which partly resemble that of previously reported in vitro generated fibrils from Y39 phosphorylated aSyn protein. The relevance of these fibrils for synucleinopathies in humans remains to be further investigated. Impact StatementNeurodegenerative diseases such as Parkinsons disease (PD) and Multiple System Atrophy (MSA) are suspected to be causatively related to the prion-like propagation of aggregates of the protein alpha-synuclein (aSyn). The fibril structures reported here were obtained after seeding from diseased human brain homogenate and differ from all previously published aSyn fibril arrangements. In case these fibrils would turn out to be the long sought causative agents of these diseases, their structures might lead to the development of therapeutic strategies to modify these diseases and to a better understanding of the mechanistic processes that lead to neurodegeneration and spreading of the diseases.

neuroscience↗

bioRxiv2019

Effects of breed, management and personality on cortisol reactivity in sport horses

Sport horses need to fulfill high physical and psychological requirements during training and competition. These as well as certain conditions of modern husbandry may affect their wellbeing. Here we aimed to (1) evaluate effects of demographic and management factors as well as personality traits on stress reactivity of sport horses, (2) investigate if elite sport horses have elevated stress levels compared to amateur sport horses, and (3) assess whether different equestrian disciplines differentially influence horses adrenal cortex responsiveness. For this purpose, we visited 149 healthy elite (n=94) and amateur (n=54) sport horses in Switzerland and performed an adrenocorticotropic hormone (ACTH) stimulation test. Additionally, a person who was familiar with the horse completed a questionnaire about demographic and management factors and horses personality traits. Linear models were calculated to assess associations between the questionnaire data and salivary cortisol 60 and 90 minutes after ACTH stimulation. While the model at T90 was not significant, post-stimulatory cortisol after 60 min appears most informative in line with a previous study and was significantly affected by the horses breed and by three management factors: "number of riders", "hours spent outside" and "group housing" (adjusted r2 =15%, p<0.001). Thoroughbred and Warmblood horses displayed an increased adrenal response compared to Franches-Montagnes horses. Horses with several riders had a less pronounced reaction than horses with one rider, and horses that spent more time outside had a decreased response compared to horses that were stabled most of the time. Horses living in groups showed higher post-stimulatory cortisol values than horses that were housed singly. However, no significant associations of cortisol responsiveness with personality traits were found, and neither the horses use as elite or as amateur sport horses nor the discipline had an effect on the cortisol response. This suggests that optimizing husbandry conditions may be more important for improving horses welfare than changing their use.

animal behavior and cognition↗

bioRxiv2019

Engineered Retroviruses as Fluorescent Biological Reference Particles for Nanoscale Flow Cytometry

There has been renewed interest in the use of flow cytometry for single particle phenotypic analysis of particles in the nanometer size-range such as viruses, organelles, bacteria and extracellular vesicles (EVs). However, many of these particles are smaller than 200 nm in diameter, which places them at the limit of detection for many commercial flow cytometers. The use of reference particles of diameter, fluorescence, and light-scattering properties akin to those of the small biological particles being studied is therefore imperative for accurate and reproducible data acquisition and reporting across different instruments and analytical technologies. We show here that an engineered murine leukemia virus (MLV) can act as a fluorescence reference particle for other small particles such as retroviruses and EVs. More specifically, we show that engineered MLV is a highly monodisperse enveloped particle that can act as a surrogate to demonstrate the various effects of antibody labeling on the physical properties of small biological particles in a similar diameter range.

cell biology↗