Biology subjects

Bachmann, M.

Publications and source records attributed to Bachmann, M..

13 recordsLinked to original sources

bioRxiv2026

Genome-resolved and kinetic evidence for low-DO comammox-anammox synergy and acetate-stimulated nitrate reduction in IFAS biofilms

Mainstream anammox implementation for nitrogen removal is constrained by unstable nitrite supply and organic carbon requirements for nitrate byproduct removal. This study evaluated integrated fixed-film activated sludge (IFAS) biofilms to enhance anammox activity by coupling low-oxygen ammonium oxidation with volatile fatty acid (VFA)-driven nitrate reduction. Nanopore long-read metagenomic assembly recovered a high-quality, circular single-contig Candidatus Brocadia sapporoensis metagenome-assembled genome (MAG) from full-scale IFAS biofilms. This MAG encodes complete anammox metabolism, dissimilatory nitrate reduction to ammonium (DNRA) and acetate/propionate carbon transformation pathways. Metatranscriptomics showed that low dissolved oxygen (DO) upregulated Ca. B. sapporoensis genes involved in anammox, nitrate reduction, and carbon metabolism. Microaerobic assays established a DO level of 0.7 mg/L as optimal for sustaining near-maximal ammonium oxidation alongside anammox-driven total inorganic nitrogen (TIN) loss. Anoxic tests conducted in secondary effluent indicated that external acetate amendment promoted greater partial nitrate reduction and TIN loss than additional propionate amendment. Integrating this dissolved oxygen concentration with external acetate amendment in a two-stage microaerobic-anoxic system successfully achieved sequential ammonium oxidation, partial nitrate reduction, and anammox-mediated TIN removal. Stage-specific expression suggested Ca. B. sapporoensis could contribute to nitrite self-supplementation via nxrAB-mediated nitrate reduction. Overall, microaerobic ammonium oxidation and Ca. B. sapporoensis-driven partial nitrate reduction jointly sustain mainstream anammox activity. Furthermore, this study demonstrates that successful metabolic synergy depends fundamentally upon precise dissolved oxygen control and effective external acetate amendment.

microbiology↗

bioRxiv2026

Distinct melanoma EV subpopulations reflect immune- and stress-induced tumor states

Melanoma is the deadliest form of skin cancer, and improved non-invasive approaches to monitor tumor burden and immune dynamics are needed. Although extracellular vesicles (EVs) are increasingly explored as cancer biomarkers, how distinct EV subpopulations reflect dynamic tumor states induced by immune pressure remains insufficiently understood. Using proteomic analyses, we identified the melanoma-associated antigens gp100 (PMEL) and GPNMB in EVs derived from B16F10 melanoma cells and incorporated them into sandwich enzyme-linked immunosorbent assays (ELISAs) that capture total EVs while selectively detecting gp100 and GPNMB EV subpopulations. We subsequently evaluated these EV populations in murine models of anti-tumor vaccination and in plasma samples from melanoma patients. In vivo, melanoma-associated EV subpopulations increased in the serum of tumor-bearing mice and were further augmented following antigen-specific anti-tumor vaccination, whereas total CD81 EVs accumulated more gradually. Notably, gp100 EV levels, but not GPNMB EVs, correlated with tumor-infiltrating lymphocyte densities across multiple time points and treatment conditions. In vitro, TNF/IFN{gamma} stimulation preferentially increased total CD81 EV release, whereas gp100 EVs were promoted by IL-1{beta} stimulation. In contrast, GPNMB EVs accumulated more gradually and broadly across inflammatory, hypoxic, and cytotoxic stress conditions. Together, these findings indicate that immune and stress signals differentially remodel melanoma-associated EV composition. The assay translated to humans, revealing elevated gp100 EV levels in the plasma of melanoma patients compared with healthy donors, whereas GPNMB EVs identified a subset of melanoma patients. We describe a clinically feasible approach that enables direct detection of melanoma-associated EV subpopulations from blood without prior EV isolation. Conceptually, our findings suggest that immune and stress signals dynamically shape circulating EV composition, generating distinct EV signatures that reflect tumor state.

immunology↗

bioRxiv2026

High-accuracy hierarchical rRNA operon profiling resolves genomovar-level taxonomy and microdiversity using Nanopore sequencing.

Genomovar-level and intragenomic diversity cannot be resolved by conventional amplicon sequencing due to the limitation of fragment lengths and read accuracy, while the application of metagenomic profiling to a large number of samples can be resource intensive. Here, we report UltraRes-rrn, an integrated wet-lab and computational workflow for high-accuracy rrn (i.e., 16S- ITS-23S rRNA) operon profiling using Nanopore sequencing. By integrating ultra-long DNA recovery, long-read amplicon sequencing, and unique molecular identifiers (UMI)-based consensus correction, UltraRes-rrn obtains full-length 16S-ITS-23S rRNA operon consensus sequences with mean accuracies exceeding 99.98%. To achieve higher resolution, we propose a hierarchical rRNA operon profiling strategy in which concatenated 16S+23S rRNA genes (16S23S) serve as a primary and the internal transcribed spacer (ITS) provides a secondary marker. The 16S23S marker achieved discrimination at the genomovar level compared to either 16S or 23S rRNA genes alone, which mitigates the ITS-driven over-splitting observed with the full-length rrn operon and allows for larger proportion of data being classified at higher confidence thresholds. Further, ITS variation was strongly structured by tRNA occurrence patterns, suggesting that ITS can capture taxon microdiversity missed by either 16S or 23S rRNA gene sequences alone. The UltraRes-rrn workflow was applied to full-scale nitrogen removal reactors, revealing intraspecies diversity variation driven by different carbon regimes, which would not have been possible with a shorter gene sequence. In summary, UltraRes-rrn enables cost-effective community profiling at genomovar-level resolution in complex ecosystems.

microbiology↗

bioRxiv2025

Functional analysis of ligand-gated chloride channels in a cnidarian sheds light on the evolution of inhibitory signalling

{psi}-aminobutyric acid (GABA) is the predominant inhibitory transmitter in the vertebrate nervous system. Fast inhibitory signalling is mediated by type A GABA receptors (GABAARs), which form pentameric ligand-gated ion channels. While GABA is also present in plants and prokaryotes, it is unknown when it was first used for fast neuronal transmission. Cnidaria represent a sister group to all Bilateria and possess a variety of putative GABAARs, none of which has been functionally characterized. In this study, we surveyed putative inhibitory ion channel receptors from the model cnidarians Nematostella and Hydra. Phylogenetic analysis revealed a surprising complexity of these receptors. The majority formed a cnidarian-specific radiation with some receptors forming a basal clade. We functionally analyzed seven putative Nematostella GABAARs of this radiation and found that none was activated by GABA or glycine, whereas three were activated by glutamate. Using site-directed mutagenesis, we identified a lysine residue in the canonical ligand-binding pocket that is important for activation by glutamate. Our results identified a group of inhibitory ion channel receptors in Cnidaria that uses glutamate as a ligand. Moreover, they suggest that inhibitory ion channel receptors in Cnidaria massively diversified, which may have been instrumental in the evolution of complex behaviors and sensory processing by the cnidarian nervous system. This work lays the foundation for understanding the diversity and evolution of inhibitory receptors in Cnidaria and the evolution of inhibitory signalling in animal nervous systems.

neuroscience↗

bioRxiv2024

3D Microphysiological Tumor Model for Dual-Targeting CAR T Cell Immunotherapy

The efficiency of immunotherapy stays limited for solid tumors. It is mainly caused by the tumoral structural heterogeneity and its complex microenvironment, which impede the infiltration of immune cells into malignant tissues. Mimicking this environment in frames of microphysiological models remains a challenge, significantly increasing costs of the clinical translation for the new therapies. Here, we study a 3D multi-spheroid model incorporating prostate stem cell antigen (PSCA) modified PC3 human prostate cancer cells and fibroblast activation protein (FAP) expressing fibrosarcoma HT1080 cells embedded within the soft hydrogel microbeads. We use this model to trial the immunotherapy based on the universal chimeric antigen receptor (UniCAR) T cells, and to better understand the impact of FAP on the immunotherapeutic treatment of solid tumors. First, we demonstrate the successful chemoattraction and infiltration of UniCAR T cells into the area of solid tumors, as well as the ability of UniCAR T cells to navigate through artificial extracellular matrix barriers. We further observe the synergistic efficacy of a dual-targeting UniCAR T cell approach against FAP and PSCA antigens, which represent the tumor microenvironment and the tumor, respectively. The results of our studies offer valuable methodologies and insights for engineering different 3D tumor models and studying immunotargeting of small-sized solid tumors (e.g., metastases and residual tumors). The developed microphysiological system has great potential to advance cancer research efforts aiming to elucidate the pivotal role of microenvironment in solid tumor development, enabling therapy trials and more precise prognosis for patients.

bioengineering↗

bioRxiv2024

Metatranscriptomic analysis reveals synergistic activities of comammox and anammox bacteria in full-scale attached growth nitrogen removal system.

0-Leveraging comammox Nitrospira and anammox bacteria for shortcut nitrogen removal can drastically lower the carbon footprint of wastewater treatment facilities by decreasing aeration energy, carbon, alkalinity, and tank volume requirements while also potentially reducing nitrous oxide emissions. However, their co-occurrence as dominant nitrifying bacteria is rarely reported in full-scale wastewater treatment. As a result, there is poor understanding of how operational parameters, in particular dissolved oxygen, impact their activity and synergistic behavior. Here, we report the impact of dissolved oxygen concentration (DO = 2, 4, 6 mg/L) on the microbial communitys transcriptomic expression in a full-scale integrated fixed film activated sludge (IFAS) municipal wastewater treatment facility predominantly performed by comammox Nitrospira and anammox bacterial populations. 16S rRNA transcript compositions revealed anammox bacteria and Nitrospira were significantly more active in IFAS biofilms compared to suspended sludge biomass. In IFAS biofilms, anammox bacteria significantly increased hzo expression at lower dissolved oxygen concentrations and this increase was highly correlated with the amoA expression levels of comammox bacteria. Interestingly, the genes involved in nitrite oxidation by comammox bacteria were significantly more upregulated relative to the genes involved in ammonia oxidation with decreasing dissolved oxygen concentrations. Ultimately, our findings suggest that comammox Nitrospira supply anammox bacteria with nitrite via ammonia oxidation and that this synergistic behavior is dependent on dissolved oxygen concentrations. SynopsisComammox bacteria differentially regulate ammonia and nitrite oxidation in response to dissolved oxygen concentration suggesting dissolved oxygen dependence of their synergistic nitrogen removal with anammox bacteria in IFAS biofilms.

microbiology↗

bioRxiv2023

Akt Drives TGF-beta-induced Over-secretion of DKK1 and Impairment of Cystic Fibrosis Airway Epithelium Polarity

Epithelial polarity is fundamental in maintaining barrier integrity and tissue protection. In cystic fibrosis (CF), apicobasal polarity of the airway epithelium is lost, resulting in increased apical fibronectin deposition and enhanced susceptibility to bacterial infections. Here we show that CFTR mutation in primary human airway epithelial cells (HAECs) and CFTR knockdown in a HAEC line promote the overexpression and over-secretion of TGF-{beta}1 and DKK1 when cultured at air-liquid interface (ALI). These dynamic changes result in hyperactivation of the TGF-{beta} pathway and inhibition of the Wnt pathway through degradation of {beta}-catenin leading to imbalanced proliferation and polarization. The abnormal interplay between TGF-{beta} and Wnt signaling pathways is further enhanced by aberrant Akt signaling. Pharmacological manipulation of TGF-{beta}, Wnt, and Akt pathways restored polarization of the CF epithelium. Our data shed new insights into the signaling pathways that fine-tune apicobasal polarization and also highlight new therapeutic strategies in preventing infections in CF HAECs.

cell biology↗

bioRxiv2023

New tools to study the interaction between integrins and latent TGFbeta1

Transforming growth factor beta (TGF{beta}) 1 regulates cell differentiation and proliferation in different physiological settings, but is also involved in fibrotic progression and protects tumors from the immune system. Integrin V{beta}6 has been shown to activate latent TGF{beta}1 by applying mechanical forces onto the latency-associated peptide (LAP). While the extracellular binding between V{beta}6 and LAP1 is well characterized, less is known about the cytoplasmic adaptations that enable V{beta}6 to apply such forces. Here, we generated new tools to facilitate the analysis of this interaction. We combined the integrin-binding part of LAP1 with a GFP and the Fc chain of human IgG. This chimeric protein, sLAP1, revealed a mechanical rearrangement of immobilized sLAP1 by V{beta}6 integrin. This unique interaction was not observed between sLAP1 and other integrins. We also analyzed V{beta}6 integrin binding to LAP2 and LAP3 by creating respective sLAPs. Compared to sLAP1, integrin V{beta}6 showed less binding to sLAP3 and no rearrangement. These observations indicate differences in the binding of V{beta}6 to LAP1 and LAP3 that have not been appreciated so far. Finally, V{beta}6-sLAP1 interaction was maintained even at strongly reduced cellular contractility, highlighting the special mechanical connection between V{beta}6 integrin and latent TGF{beta}1.

cell biology↗

bioRxiv2022

Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process.

Cooperation between comammox and anammox bacteria for nitrogen removal has been recently reported in laboratory-scale systems including synthetic community construct; however, there are no reports of full-scale municipal wastewater treatment systems with such cooperation. Here, we report intrinsic and extant kinetics as well as genome-resolved community characterization of a full-scale integrated fixed film activated sludge (IFAS) system where comammox and anammox bacteria co-occur and appear to drive nitrogen loss. Intrinsic batch kinetic assays indicated that majority of the aerobic ammonia oxidation was driven by comammox bacteria (1.75 {+/-} 0.08 mg-N/g TS-h) in the attached growth phase with minimal contribution by ammonia oxidizing bacteria. Interestingly, a portion of total inorganic nitrogen ([~]8%) was consistently lost during these aerobic assays. Aerobic nitrite oxidation assays eliminated the possibility of denitrification as a cause of nitrogen loss, while anaerobic ammonia oxidation assays resulted in rates consistent with anammox stoichiometry. Full-scale experiments at different dissolved oxygen (DO = 2-6 mg/L) set points indicated persistent nitrogen loss that was partly sensitive to DO concentrations. Genome-resolved metagenomics confirmed high abundance (relative abundance 6.53 {+/-} 0.34%) of two Brocadia-like anammox populations while comammox bacteria within the Ca. Nitrospira nitrosa cluster were lower in abundance (0.37% {+/-} 0.03%) and Nitrosomonas-like ammonia oxidizers even lower (0.12% {+/-} 0.02%). Collectively, our study reports for the first time the co-occurrence and co-operation of comammox and anammox bacteria in a full-scale municipal wastewater treatment system. SynopsisComammox and anammox cooperation resulted in dissolved oxygen concentration dependent nitrogen loss in municipal wastewater treatment system.

microbiology↗

bioRxiv2022

AA-amyloidosis in cats (Felis catus) housed in shelters

Systemic AA-amyloidosis is a protein-misfolding disease that is characterized by fibril deposition of serum amyloid-A protein (SAA) in several organs in humans and many animal species. Fibril deposits originate from abnormally high serum levels of SAA during chronic inflammation. In domestic short-hair cats, AA-amyloidosis has only been anecdotally reported and is considered a rare disease. Here we report that an astonishing 57-73% of early deceased short-hair cats kept in three independent shelters suffer from amyloid deposition in the liver, spleen, or kidney. Histopathology and mass spectrometry of post-mortem extracted deposits identified SAA as the major protein source. The duration of stay in the shelters was positively associated with a histological score of AA-amyloidosis (B=0.026, CI95%=0.007-0.046; p=0.010). Presence of SAA fragments in bile secretions raises the possibility of fecal-oral transmission of the disease.

pathology↗

bioRxiv2021

Voltage-Gated Potassium Channel Kv1.3 as a Therapeutic Target for Pancreatic Ductal Adenocarcinoma

The mitochondrial voltage-gated potassium channel, Kv1.3, has been emerged as an attractive oncologic target but its function in pancreas cancer (PDAC) is unknown. In this study we evaluated tissue expression of Kv1.3 in resected PDAC from 55 patients and tumor inhibition in orthotopic mouse models using the recently developed Kv1.3 inhibitors PCARBTP and PAPTP. Immunohistochemistry of 55 human PDAC specimens showed that all tumors expressed Kv1.3 with 60% of tumor specimens having high Kv1.3 expression. In pancreas tumor models (Pan02 cells injected into C57BL/6 mice), PCARBTP and PAPTP treatment resulted in tumor reductions of 87% and 70%, respectively. When combined with gemcitabine/abraxane, this increased to 95% and 80% without resultant organ toxicity. In vivo models indicated PCARBTP-mediated cell death occurred through the p38-MAPK pathway. In vitro-generated resistant clones to PCARBTP escaped cell death through upregulation of the anti-oxidant system as determined using SWATH-MS analysis. These data show Kv1.3 is highly expressed in resected human PDAC and the use of novel mitochondrial Kv1.3 inhibitors combined with cytotoxic chemotherapies might be novel, effective treatment for PDAC.

cancer biology↗

bioRxiv2020

Phosphorylated paxillin and FAK constitute subregions within focal adhesions

Integrin-mediated adhesions are convergence points of multiple signaling pathways. Their inner structure and their diverse functions can be studied with super-resolution microscopy. We used structured illumination microscopy (SIM) to analyze spatial organization of paxillin phosphorylation (pPax) within adhesions. We found that pPax and focal adhesion kinase (FAK) form spot-like, spatially defined clusters within adhesions in several cell lines. In contrast, other adhesion proteins showed no consistent organization in such clusters. Live-cell super-resolution imaging revealed that pPax-FAK clusters persist over time but modify distance to each other dynamically. Moreover, we show that the distance between separate clusters of pPax is mechanosensitive. Thus, in this work we introduce a new structural organization within focal adhesions and demonstrate its regulation and dynamics.

cell biology↗

bioRxiv2017

Force-dependent ligand sensing enables αVβ3 integrin to differentiate between fibronectin and high-affinity ligands

V{beta}3 integrin recognizes multiple extracellular matrix proteins, including vitronectin (Vn) and fibronectin (Fn). However, cell experiments are frequently performed on homogenously coated substrates with only one integrin ligand present. Here, we employed binary-choice substrates of Fn and Vn to dissect V{beta}3 integrin-mediated binding to both ligands on the subcellular scale. Superresolution imaging revealed that V{beta}3 integrin preferred binding to Vn under various conditions. In contrast, binding to Fn required mechanical load on V{beta}3 integrin. Integrin mutations, structural analysis, and molecular dynamics simulations established a model where the extended-closed conformation of V{beta}3 integrin binds Vn but not Fn. Force-mediated hybrid domain swing-out characterizes the extended-open conformation needed for efficient Fn binding. Thus, force-dependent conformational changes in V{beta}3 integrin increase the number of available ligands and therefore the ligand promiscuity of this integrin. These findings for V{beta}3 integrin were shown to regulate cell migration and mechanotransduction differentially on Fn compared to Vn and therefore to regulate cell behavior.

cell biology↗