Biology subjects

Baggerman, G.

Publications and source records attributed to Baggerman, G..

4 recordsLinked to original sources

bioRxiv2025

Degradation rather than disassembly of necrotic debris is essential to enhance recovery after acute liver injury

Necrotic cell death causes loss of membrane integrity, release of intracellular contents and deposition of necrotic cell debris. Effective clearance of this debris is crucial for resolving inflammation and promoting tissue recovery. While leukocyte phagocytosis plays a major role, soluble factors in the bloodstream also contribute to debris removal. Our study examined whether enzymatic degradation or disassembly of necrotic debris enhances clearance and improves outcomes in a mouse model of drug-induced liver injury. Using intravital microscopy and proteomic profiling, we demonstrated that necrotic debris is more complex than anticipated, containing DNA, filamentous actin, histones, complement C3, fibrin(ogen) and plasmin(ogen), among many other components. DNase 1 treatment facilitated recovery significantly by enhancing the clearance of DNA from necrotic areas, reducing circulating nucleosomes and actin, and lowering the associated inflammatory response. However, its effect on actin and other damage-associated molecular patterns in necrotic regions was limited. Treatment with short synthetic peptides, specifically 20-amino acid-long positively charged PLK and negatively charged PLE, which displace histones from debris in vitro, did not inhibit liver injury or promote recovery. Moreover, activating plasmin to disrupt fibrin encapsulation via tissue plasminogen activator (tPa) led to increased circulating actin levels and worsening of injury parameters. These findings suggest that fibrin encapsulation is important for containing necrotic debris and that enzymatic degradation of necrotic debris is a more effective strategy to enhance tissue recovery than targeting debris disassembly. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/633891v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1d324e6org.highwire.dtl.DTLVardef@11b9de7org.highwire.dtl.DTLVardef@1bcc23org.highwire.dtl.DTLVardef@f71a32_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Whitefly effector G4 interacts with tomato proteins of which MIPDB141 affects whitefly performance

The phloem-feeding insect Bemisia tabaci is an important pest, responsible for the transmission of several crop-threatening virus species. While feeding, the insect secretes a cocktail of effectors to modulate defense responses. Here, we present a set of proteins that was identified in artificial diet on which B. tabaci was salivating. We studied whether these candidate effectors can play a role in plant immune suppression. Effector G4 was the most robust suppressor of the flg22-induced ROS response when transiently expressed in Nicotiana benthamiana. In addition, G4 was able to supress ROS in Solanum lycopersicum (tomato) and Capsicum annuum (pepper). Fused to a fluorescence tag, G4 localized in the cytoplasm in N. benthamiana. A yeast two-hybrid screen combined with a luciferase bimolecular complementation and co-localization assays resulted in the identification of two target proteins in tomato: REF-like stress related protein 1 (RSP1) and meloidogyne-induced giant cell protein DB141 (MIPDB141). Silencing of MIPDB141 in tomato, using virus-induced gene silencing, reduced whitefly fecundity up to 40% demonstrating that the protein is involved in susceptibility to B. tabaci. Together our data demonstrate that effector G4 impairs tomato immunity to whiteflies by interfering with the ROS production and via a direct interaction with tomato susceptibility protein MIPDB141.

plant biology↗

bioRxiv2021

Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania

Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but the molecular and functional consequences for the pathogen remain poorly understood. Here, we addressed this question in vitro and present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analyses unambiguously establish that aneuploidy in Leishmania proportionally impacts the average transcript- and protein abundance levels of affected chromosomes, ultimately correlating with the degree of metabolic differences between strains. This proportionality was present in both proliferative and non-proliferative in vitro promastigotes. However, protein complex subunits and non-cytoplasmic proteins, showed dosage compensation, responding less or even not at all to aneuploidy-induced dosage changes. In contrast to other Eukaryotes, we did not observe the widespread regulation at the transcript level that typically modulates some of the negative effects of aneuploidy. Further, the majority of differentially expressed proteins between aneuploid strains were encoded by non-aneuploid chromosomes and were not driven by a significant underlying transcript change, suggesting that aneuploidy is accompanied by extensive post-transcriptional protein-level modulation. This makes Leishmania a unique Eukaryotic model for elucidating post-transcriptional protein-abundance modulation in the context of aneuploidy.

systems biology↗

bioRxiv2019

A combined strategy of neuropeptide predictions and tandem mass spectrometry identifies evolutionarily conserved ancient neuropeptides in the sea anemone Nematostella vectensis

Neuropeptides are a class of bioactive peptides and are responsible for various physiological processes including metabolism, development and reproduction. Although accumulated genome and transcriptome data have reported a number of neuropeptide candidates, it still remains difficult to obtain a comprehensive view of neuropeptide repertoires due to their small and variable nature. Neuropeptide prediction tools usually work only for those peptides for which sequentially related homologs have previously been identified. Recent peptidomics technology has enabled systematic structural identification of neuropeptides by using the combination of liquid chromatography and tandem mass spectrometry. However, obtaining reliable identifications of endogenous peptides is still difficult using a conventional tandem mass spectrometry-based peptide identification approach using protein database because a large search space has to be scanned due to the absence of a cleavage enzyme specification. We developed a pipeline consisting of the prediction of in silico cleaved endogenous neuropeptides followed by peptide-spectrum matching enabling highly sensitive and reliable neuropeptide identification. This approach effectively reduces the search space of peptide-spectrum matching, and thus increases search sensitivity. To identify neuropeptides in Nematostella vectensis, a basal eumetazoan having one of the most primitive nervous systems, we scanned the Nematostella protein database for sequences displaying structural hallmarks of metazoan neuropeptides, including C/N-terminal structures and modifications. Peptide-spectrum matching was performed against the in silico cleaved peptides and successfully identified dozens of neuropeptides at high confidence. The identification of Nematostella neuropeptides structurally related the tachykinin, GnRH/AKH, neuromedin-U/pyrokinin peptide families indicate that these peptides already originated in the eumetazoan ancestor of all animal species, most likely concomitantly with the development of a nervous system.

biochemistry↗