Biomedical subjects

Elke Hammer

Publications and source records attributed to Elke Hammer.

14 recordsLinked to original sources

PubMed2026

Interleukin-1α Mediates Pancreatic Fibroblast Activation, Regulates Immune Cell Recruitment and Fibrosis in Acute and Chronic Pancreatitis.

Pancreatitis is a life-threatening inflammatory disease of the pancreas. The cytokine interleukin-1α has been demonstrated to act as an alarmin released by necrotic cells. In the present study, we investigated the influence of IL-1α on the immune response during acute and chronic pancreatitis. Following tissue injury, pancreatic acinar cells released IL-1α, which activates tissue-resident fibroblasts to differentiate toward a pro-inflammatory phenotype. By secreting chemokines and cytokines such as CXCL5, CCL2, and IL-6, these fibroblasts recruit immune cells to the pancreas. The absence of IL-1α reduces disease severity in acute pancreatitis and chemokine release. Furthermore, IL-1α primes fibroblasts to enhance the production of extracellular matrix-components by the up-regulation of pro-fibrotic receptors such as Il4ra, Il13ra1, and Tgfbr3. Therefore, the deletion of IL-1α significantly reduced the development of tissue fibrosis. A therapeutic blockade of the IL1R1-signaling by i.p. administration of the IL-1-receptor antagonist Anakinra showed the same effect; the severity of acute pancreatitis and fibrogenesis during chronic pancreatitis were reduced. In conclusion, the crosstalk between necrotic acinar cells and fibroblasts mediated by IL-1α plays a crucial role in acute inflammation of the pancreas and fibrogenic signaling. Blockade of IL1R1-signaling by Anakinra is therefore a promising therapeutic intervention for both acute and chronic pancreatitis.

Anakinra↗

PubMed2026

Disease-driven post-transcriptional alterations and alternative splicing in podocytes in focal segmental glomerulosclerosis.

Focal segmental glomerulosclerosis (FSGS) is a major cause of nephrotic syndrome and progression to end-stage renal disease, yet its molecular pathogenesis remains still incompletely defined. While transcriptional alterations in podocytes have been extensively characterized, the contribution of post-transcriptional regulatory mechanisms is poorly understood. Here, we combined a zebrafish podocyte-specific injury model with glomerulus-resolved transcriptomic profiling to dissect RNA regulatory alterations during FSGS progression. Integrated analyses of bulk RNA sequencing, small RNA profiling, and alternative splicing revealed pronounced, time-dependent remodeling of the glomerular transcriptome. We demonstrate that podocyte injury is associated with loss of key podocyte-specific proteins, activation of inflammatory pathways, remodeling of the extracellular matrix, and altered microRNA expression, such as miR-21 and miR-193. Moreover, we found that alternative splicing influences key podocyte gene expression, affecting genes critical for slit diaphragm integrity, actin cytoskeleton organization, and glomerular basement membrane stability. Isoform analyses identified FSGS-associated isoform switches in SRSF3 and EPB41L5. Importantly, these changes were also evident in glomeruli from FSGS patients, demonstrating that the zebrafish model recapitulates key molecular features of human disease and highlighting alternative splicing as a central regulatory mechanism in FSGS.

Animals↗

PubMed2025

Alternative Splicing in Mechanically Stretched Podocytes as a Model of Glomerular Hypertension.

KEY POINTS: Mechanical stretch induced over 3000 alternative splicing events in podocytes, affecting gene expression and protein abundance. Seventeen genes showed consistent splicing events across multiple analysis tools, with key isoform changes. Shroom3 and Myl6 underwent isoform switches under mechanical stretch, altering the C-terminal sequence and interaction properties of Myl6. BACKGROUND: Alterations in pre-mRNA splicing are crucial to the pathophysiology of various diseases. However, the effects of alternative splicing of mRNA on podocytes in hypertensive nephropathy are still unknown. The Sys_CARE project aimed to identify alternative splicing events involved in the development and progression of glomerular hypertension. METHODS: Murine podocytes were exposed to mechanical stretch, after which proteins and mRNA were analyzed by proteomics, RNA sequencing, and several bioinformatic alternative splicing tools. RESULTS: Using transcriptomic and proteomic analysis, we identified significant changes in gene expression and protein abundance because of mechanical stretch. RNA-Seq identified over 3000 alternative spliced genes after mechanical stretch, including all types of alternative splicing events. Among these, 17 genes exhibited an alternative splicing event across four different splicing analysis tools. From this group, we focused on Myl6, a component of the myosin protein complex, and Shroom3, an actin-binding protein essential for podocyte function. We identified two Shroom3 isoforms with significant expression changes under mechanical stretch, which was validated by quantitative RT-PCR and in situ hybridization. In addition, we observed an expression switch of two Myl6 isoforms after mechanical stretch, accompanied by an alteration in the C-terminal amino acid sequence. CONCLUSIONS: A comprehensive RNA-Seq analysis of mechanically stretched podocytes identified novel potential podocyte-specific biomarkers and highlighted significant alternative splicing events, notably in the mRNA of Shroom3 and Myl6.

podocyte↗

PubMed2025

SpectroPipeR-a streamlining post Spectronaut® DIA-MS data analysis R package.

SUMMARY: Proteome studies frequently encounter challenges in down-stream data analysis due to limited bioinformatics resources, rapid data generation, and variations in analytical methods. To address these issues, we developed SpectroPipeR, an R package designed to streamline data analysis tasks and provide a comprehensive, standardized pipeline for Spectronaut® DIA-MS data. This novel package automates various analytical processes, including XIC plots, ID rate summary, normalization, batch and covariate adjustment, relative protein quantification, multivariate analysis, and statistical analysis, while generating interactive HTML reports for e.g. ELN systems. AVAILABILITY AND IMPLEMENTATION: The SpectroPipeR package (manual: https://stemicha.github.io/SpectroPipeR/) was written in R and is freely available on GitHub (https://github.com/stemicha/SpectroPipeR).

Software↗

PubMed2006

Decolorization of synthetic dyes by the deuteromycete Pestalotiopsis guepinii CLPS no. 786 strain.

The ability of Pestalotiopsis guepinii CLPS no. 786 to decolorize 13 dyes of varied structure was analyzed and compared with that of the basidiomycete Phanerochaete chrysosporium . Nine dyes representing anthrapyridone, azo, N-heterocyclic and triphenylmethane chromophores, but none with the O-heterocyclic group, were decolorized by P. guepinii when added to an agar medium. Studies with liquid cultures revealed that P. guepinii transformed both crystal violet and methylene blue B dyes, and adsorbed different chromophores onto its mycelium.

Anthraquinones↗

PubMed2006

Direct mass spectrometric identification of ABCB1 (P-glycoprotein/MDR1) from the apical membrane fraction of human placenta using fourier transform ion cyclotron mass spectrometry.

Identification and quantification of proteins from human tissue by electrophoresis and subsequent mass spectrometry (MS) has been mainly restricted to high abundance, non-membrane-bound molecules. Pharmacologically relevant structures such as cytochrome P450 enzyme, drug transporters and receptors were not accessible by this technology. We developed a method to identify an integral membrane-bound protein (ABCB1) from human placenta using Fourier transform ion cyclotron (FTICR)-MS. Apical and basal membrane fractions were enriched from term human placenta using differential centrifugation. Following SDS-page these fractions were cleaved with trypsin, separated by nano-HPLC and subjected to FTICR-MS. We identified a total of 70 and 89 proteins in the apical and basal membranes, respectively. Among these proteins, and restricted to the apical membrane, was the transport protein ABCB1, with 10 peptides identified by MS, covering a total of 10% of the entire protein. The study describes a method suitable for direct monitoring of membrane-bound proteins from human tissue using FTICR-MS.

ATP Binding Cassette Transporter, Subfamily B↗

PubMed2006

Novel penicillins synthesized by biotransformation using laccase from Trametes spec.

Eight novel penicillins were synthesized by heteromolecular reaction of ampicillin or amoxicillin with 2,5-dihydroxybenzoic acid derivatives using a laccase from Trametes spec. All products inhibited the growth of several gram positive bacterial strains in the agar diffusion assay, among them methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. The products protected mice against an infection with Staphylococcus aureus lethal to the untreated animals. Cytotoxicity and acute toxicity of the new compounds were neglectable. The results show the usefulness of laccase for the synthesis of potential new antibiotics. The biological activity of the new compounds stimulates intensified pharmacological tests.

Animals↗

PubMed2005

Oxidative ring cleavage of low chlorinated biphenyl derivatives by fungi leads to the formation of chlorinated lactone derivatives.

The yeast Trichosporon mucoides and the filamentous fungus Paecilomyces lilacinus as biphenyl oxidizing organisms are able to oxidize chlorinated biphenyl derivatives. Initial oxidation of derivatives chlorinated at C4 position started at the non-halogenated ring and went on up to ring cleavage. The products formed were mono- and dihydroxylated 4-chlorobiphenyls, muconic acid derivatives 2-hydroxy-4-(4-chlorophenyl)-muconic acid and 2-hydroxy-5-(4-chlorophenyl)-muconic acid as well as the corresponding lactones 4-(4-chlorophenyl)-2-pyrone-6-carboxylic acid and 3-(4-chlorophenyl)-2-pyrone-6-carboxylic acid. Altogether T. mucoides formed 12 products and P. lilacinus accumulated five products. Whereas the rate of the first oxidation step at 4-chlorobiphenyl seems to be diminished by the decreased bioavailability of the compound, no considerable differences were observed between the degradation of 4-chloro-4'-hydroxybiphenyl and 4-hydroxybiphenyl. Twofold chlorinated biphenyl derivatives did not serve as substrates for oxidation by either organism with the exception of 2,2'-dichlorobiphenyl, transformed by the yeast Trichosporon mucoides to two monohydroxylated derivatives. The results show, that soil fungi may contribute to the aerobic degradation of low chlorinated biphenyls accumulating from anaerobic dehalogenation of PCB by bacteria.

Aerobiosis↗

PubMed2004

Production of aromatic compounds during methanogenic degradation of straw in rice field soil.

Production of CH(4) in anoxic rice field soil is stimulated by the addition of rice straw. Previous experiments showed that acetate and propionate are the most important intermediates of the carbon flow to CH(4), and accumulate if CH(4) production is inhibited by 2-bromoethanesulfonate (BES). However, some unidentified compounds were found to accumulate in addition. We now identified them as benzoate, phenylpropionate, and phenylacetate by comparison of the retention times in HPLC chromatograms with authentic standards and by mass spectrometry. These aromatic compounds accumulated only to concentrations <100 microM, especially in soil amended with rice straw (stem, sheath or blade straw). Phenylpropionate and benzoate were the most abundant aromatic intermediates contributing up to 4% to total CH(4) production. Phenylacetate, on the other hand, contributed very little (<0.3%). Gibbs free energies (DeltaG) were calculated for different anaerobic degradation pathways of the aromatic compounds at the actual incubation conditions. Conversion of benzoate to acetate, CO(2) and H(2) was strongly exergonic (DeltaG = -86 kJ mol(-1)) under methanogenic conditions, but became less exergonic (DeltaG = -30 kJ mol(-1)) when CH(4) production was inhibited. The primary oxidation of phenylpropionate was only exergonic for alpha-oxidation (i.e. phenylacetate as product) but not for beta-oxidation (i.e. benzoate as product). However, the DeltaG values for the complete degradation of phenylpropionate to acetate, CO(2) and H(2) were similar for both pathways and were also similar to those of benzoate degradation. Collectively, the results suggest that aromatic compounds are minor intermediates of anaerobic degradation of organic matter in rice field soil, and are syntrophically degraded by coupling to methanogenesis.

Bacteria, Anaerobic↗

PubMed2004

Oxidation and ring cleavage of dibenzofuran by the filamentous fungus Paecilomyces lilacinus.

The ability of the imperfect soil fungus Paecilomyces lilacinus to transform the environmental pollutant dibenzofuran was investigated. Transformation of dibenzofuran and related derivatives lead to 14 products, which were identified by UV spectroscopy, mass spectrometry, and proton nuclear magnetic resonance spectroscopy. Biotransformation was initiated by two separate hydroxylation steps, leading to the accumulation of 4-monohydroxylated and 4-dihydroxylateddibenzofurans. Hydroxylation at both aromatic rings produced 2,7-dihydroxydibenzofuran, 3,7-dihydroxydibenzofuran, and 2,8-dihydroxydibenzofuran. Further oxidation yields ring cleavage of dibenzofuran, which has not been described before for filamentous fungi. The ring fission products were identified as benzo[ b]furo[3,2-d]-2-pyrone-6-carboxylic acid and [2-(1-carboxy-methylidene)-benzofuran-3-ylidene]-hydroxy-acetic acid and its derivatives hydroxylated at carbon 7 and 8 at the non-cleaved ring. Other metabolites were riboside-conjugates of 2-hydroxydibenzofuran and 3-hydroxydibenzofuran. The results showed that P. lilacinus transforms the hydrophobic compound dibenzofuran by phase I/phase II reactions to produce hydroxylated products and excretable sugar conjugates.

Benzofurans↗

PubMed2004

Mono-allelic expression of the IGF-I receptor does not affect IGF responses in human fibroblasts.

OBJECTIVE: It has been suggested that mono-allelic deletion of the IGF-I receptor gene is causally related to severe intrauterine and postnatal growth deficiency whereas no IGF-I resistance was observed in the patients' fibroblasts. The expression and regulation of the growth-modulating IGF binding proteins (IGFBPs) have been investigated in serum and fibroblasts of a short girl with mono-allelic loss of the distal long arm of chromosome 15 (15q26.1-qter). PATIENT AND METHODS: The mono-allelic loss of the IGF-I receptor (IGF1R) gene was confirmed in a child with prenatal and severe postnatal growth retardation by fluorescence in situ hybridization, and was evaluated on the protein level in fibroblasts of the patient by FACS analysis and IGF cross-linkage. Additionally, expression of IGFBPs and cell-mediated degradation of IGFBP-3 were examined in the patient's fibroblasts. RESULTS: Levels of GH, IGF-I, and IGFBP-3 were above the 95th percentile in the serum of the 3-year-old girl with a mono-allelic deletion of the IGF1R gene, suggesting IGF-I resistance. In the patient's fibroblasts the IGF-I receptor concentration was half that in control cells. Whereas the pattern of secreted IGFBPs in response to IGFs was not altered, the abundance of secreted IGFBPs was higher in the patient's cells than in controls. Moreover, fibroblast-mediated degradation of 125I-labeled IGFBP-3 appears to be reduced in the patient's fibroblasts. The higher abundance of IGFBPs in the patient's fibroblasts might be responsible for the lack of IGF-I-stimulated [alpha-1-14C]methylaminoisobutyric acid transport. CONCLUSION: Our results suggest that the expression and regulation of IGFBPs in tissues from patients with mono-allelic deletion of the IGF-I receptor gene may lead to IGF sequestration and contribute to IGF-I resistance and growth retardation.

Body Height↗

PubMed2003

Synthesis of imidazol-2-yl amino acids by using cells from alkane-oxidizing bacteria.

Sixty-one strains of alkane-oxidizing bacteria were tested for their ability to oxidize N-(2-hexylamino-4-phenylimidazol-1-yl)-acetamide to imidazol-2-yl amino acids applicable for pharmaceutical purposes. After growth with n-alkane, 15 strains formed different imidazol-2-yl amino acids identified by chemical structure analysis (mass and nuclear magnetic resonance spectrometry). High yields of imidazol-2-yl amino acids were produced by the strains Gordonia rubropertincta SBUG 105, Gordonia terrae SBUG 253, Nocardia asteroides SBUG 175, Rhodococcus erythropolis SBUG 251, and Rhodococcus erythropolis SBUG 254. Biotransformation occurred via oxidation of the alkyl side chain and produced 1-acetylamino-4-phenylimidazol-2-yl-6-aminohexanoic acid and the butanoic acid derivative. In addition, the acetylamino group of these products and of the substrate was transformed to an amino group. The product pattern as well as the transformation pathway of N-(2-hexylamino-4-phenylimidazol-1-yl)-acetamide differed in the various strains used.

Acetamides↗

PubMed2002

Isolation and characterization of biarylic structure-degrading yeasts: hydroxylation potential of dibenzofuran.

Yeast communities from heavily polluted sediments that received the discharge from oil refineries and other industries were studied. Yeast species were isolated from these sediments and their ability to degrade dibenzofuran were determined. Twenty-four different yeast strains were isolated and cultured on aromatic medium; two Candida krusei strains. Candida tenuis, Candida tropicalis, two Pichia anomala strains, Pichia haplophila, two Rhodotorula glutinis strains, Rhodotorula mucilaginosa, two Trichosporon pullulans strains and Yarrowia lipolytica were able to hydroxylate dibenzofuran. Three metabolites were identified by HPLC analysis: 3-hydroxydibenzofuran was in all the cases the most abundant isomer, and while 4-hydroxydibenzofuran was also common, 2-hydroxydibenzofuran was detected in very small quantities and with few species. In the R. glutinis and Y. lipolytica cultures a ring cleavage product was also found. While in the R. gluttinis assays the hydroxydibenzofuran was detected earlier, at 2 days' incubation time, in the other yeast experiments they were observed at the 4-5th incubation days with the maximum amounts at the 7th day. Our results confirmed the ability of autochthonous yeast species to hydroxylate dibenzofuran and to cleave the rings, and it is the first report for C. krusei, C. tenuis, P. anomala, P. haplophila and R. mucilaginosa. The ecological relevance of this study is based on the fact that dibenzofuran is a xenobiotic not easily transformed, so the catabolic activities observed in authochonous yeasts contribute to broadening the biodegradable substrate spectrum.

Benzofurans↗

PubMed2002

Biotransformation of biarylic compounds by yeasts of the genus trichosporon.

The biotransformation of biphenyl, dibenzofuran, and diphenyl ether by 24 strains belonging to 18 species of the genus Trichosporon was investigated to assess the taxonomic relevance of this property at species and genus level. With the exceptions of T. brassicae and T. porosum CBS 2040, all other strains were able to transform the parent compounds to monohydroxylated intermediates. A second hydroxylation on the same aromatic ring was carried out by fewer strains and depended on the substrate. It appears that this step is the rate-limiting one in the biotransformation of the biarylic compounds tested. Ring fission of dihydroxylated derivatives of biphenyl was observed within 12 species. The aromatic ring system of dihydroxylated dibenzofuran was cleaved by strains of 5 species, while strains of 13 species were able to cleave the aromatic ring system of dihydroxylated diphenyl ether. Only 4 strains out of 18 species were able to cleave the aromatic ring system of all three parent compounds. These most active yeasts belong to the species T. coremiiforme, T. montevideense, T. mucoides, and T. sporotrichoides. In addition, strains of the species Cryptococcus curvatus and Cryptococcus humicola, closely related to the genus Trichosporon, were tested in parallel.

Benzofurans↗