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Schmidt, S.

Publications and source records attributed to Schmidt, S..

At least 37 records · Page 2Linked to original sources

A Numerical Alternative to MR Thermometry for Safety Validation of Multi-Channel RF Transmit Coils

PurposeThis study proposes an alternative approach to MR thermometry (MRT) for the safety validation of multi-channel RF transmit coils and demonstrates its use to enable human studies at 10.5T. MethodsTo ensure patient safety, specific absorption rate (SAR) limits established under international guidelines must not be exceeded. Predicting SAR on state-of-the-art parallel transmit systems relies on electromagnetic simulations, which require extensive experimental validation. Despite a well-established validation workflow, SAR prediction errors are unavoidable and must be quantified as a safety margin. While MRT tests are commonly used for this purpose, their technical challenges necessitate an alternative. The proposed technique propagates the error between experimentally and numerically acquired B+distributions to the uncertainty in simulated peak local SAR using Monte-Carlo simulations without the need for MRT. This method was validated using a 16-channel transceiver coil for imaging the human torso (henceforth referred to as a "body" coil) at 10.5T with two excitation scenarios, as well as an 8-channel 10.5T head coil with four excitation scenarios. ResultsThe proposed numerical technique proved more conservative than existing MRT-based SAR error quantification methods across all tested scenarios. Its application to validate three state-of-the-art head coils (16Tx/32Rx, 16Tx/80Rx, and 16Tx/128Rx) led to regulatory approval for human head imaging and high-quality functional as well as diffusion MRI results at 10.5T. ConclusionA numerical alternative to MRT requires only the experimental acquisition of B+ maps for comparison with simulations, enabling the quantification of uncertainty in SAR prediction. This technique was applied to three 16-channel transmit arrays, each used in conjunction with high-channel-count receive arrays for in vivo imaging.

neuroscience↗

SOX2 and SOX9 as Transcriptional Regulators of human Galectin-3 in SW1353 Cells: Potential Implications for Osteoarthritis

Galectin-3 (Gal-3), a member of the {beta}-galactoside-binding protein family, is critically involved in inflammation, extracellular matrix remodelling, and cartilage degeneration in osteoarthritis (OA). This study aims to elucidate the regulation of the human galectin-3 gene (LGALS3) promoter in SW1353 cells and its control by SOX transcription factors, known to be dysregulated during OA pathogenesis. We sought to identify key sequence elements in the LGALS3 promoter responsible for its transcriptional activity and the transcription factors (TFs) responsible for its regulation. Using luciferase reporter assays, we examined deletion variants of the 5 region (-2638 bp to +52 bp) and assessed their activation potential. We also identified potential transcription factor binding sites (TFBS) through in silico analyses and confirmed SOX9 binding in the -93/+49 region by chromatin immunoprecipitation using HaloCHIPTM. Functional assays revealed that the proximal promoter region (-97 to +52 bp) is critical for reporter gene expression in SW1353 cells. This study demonstrates that the presence of SOX2 and SOX9 leads to a dose-dependent decrease in LGALS3 promoter activity in SW1353 cells. We show that SOX9 can bind the promoter, highlighting the importance of SOX TF interactions in regulating LGALS3 expression and their potential role in chondrocytes.

molecular biology↗

Distinct druggable biological processes in early-onset prostate cancer

Despite advances in understanding and treating Prostate Cancer (PCa), there has been little effort to systematically map the biology distinguishing Early-(EOPCa) and Late-(LOPCa) onset PCa. Around 25% of EOPCa cases present with metastatic spread or aggressive disease with earlier metastatic development. Some available lines of therapy are extending treatment trajectories and prolonging lives. However, there remains a critical clinical need to identify new therapeutic targets for EOPCa where life expectancy necessitates safer, more targeted treatment options. To our knowledge, here we present the largest systematic analysis of molecular profiles in EOPCa versus LOPCa, employing machine-learning-enabled algorithms to identify distinguishing biology and druggable targets for each age group. Distinct stromal signatures are uncovered in EOPCa, which are used to propose therapeutic opportunities herein. Moreover, our analysis identifies 50 druggable targets, 11 of which we confirm in PCa cell line genetic/pharmacological perturbation data. These findings provide the first specific, testable hypotheses in EOPCa, offering avenues for experimental validation and potential therapeutic exploitation, and, more generally, shed light on the intricate and distinguished molecular profile of this aggressive, poorly understood disease. One Sentence SummaryMachine learning-enabled algorithms were utilized to identify distinguishing biology and associated druggable targets for early-onset prostate cancers.

cancer biology↗

Genetic and phenotypic diversity of wine-associated Hanseniaspora species

The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and enological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated from wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow- (SEL) and fast-evolving (FEL) lineages that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting specifically in the FEL lineage. Pangenome analysis within H. uvarum identified extensive copy number variation (CNV), particularly in genes related to xenobiotic tolerance, nutrient transport and metabolism. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the Hanseniaspora FEL lineage, with significant enrichment in genes within the lysine biosynthetic pathway, suggesting a key role for this amino acid in early FEL adaptation. In H. uvarum, signatures of recent positive selection were detected in genes linked to sulphur assimilation, sterol biosynthesis and glycerol production, indicating potential adaptation to the stresses imposed by grape and wine fermentation. Furthermore, phenotypic screening of 113 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO2, and cold tolerance. These findings provide novel insights into the genomic evolution and functional diversity of Hanseniaspora, expanding our understanding of yeast adaptation to wine fermentation and laying the foundation for targeted gene investigations within this important genus.

microbiology↗

Substrate recognition by human separase

The protein complex cohesin encircles the sister chromatids in early mitosis1. At anaphase onset, sister separation is triggered by cleavage of the cohesin subunit SCC1/RAD21 by the cysteine protease separase2-5. SCC1 contains two cleavage sites, where cleavage is stimulated by SCC1 phosphorylation5,6. The molecular mechanisms of substrate recognition and cleavage are only partly understood7. Here, we determined a series of cryoEM structures of human separase in apo-or substrate-bound forms that, together with biochemical analysis, provide novel insights into the regulation of separase cleavage activity. We verify the first SCC1 cleavage site and reassign the second site. We show that multiple substrates, including separase autocleavage sites8,9 and the two SCC1 cleavage sites, interact with several docking sites in separase, including four phosphate-binding sites. We also describe the structural basis of the interaction between the cohesin subunit SA1/A2 and separase, which promotes cleavage at the second site in SCC1. Finally, using cross-linking mass spectrometry and cryoEM, we propose a model of how cohesin is targeted by human separase. Our work provides an extensive functional and structural framework that explains one of the most fundamental events in cell division.

biochemistry↗

A biocatalytic platform for the production of substituted 2-quinolones and (thio)coumarins

2-quinolones are privileged scaffolds for drug discovery that are relatively rare in nature. Here, we characterise two promiscuous fungal polyketide synthases AthePKS and FerePKS, which we had previously found to produce quinolones in vitro. We challenged the enzymes with several substituted anthranilic acid derivatives, revealing their ability to produce precursors of pharmaceutically relevant quinolones. We also discovered that AthePKS and FerePKS accept other 2-substituted benzoic acids, leading to the formation of coumarin and thiocoumarin scaffolds. We applied AthePKS in an artificial enzymatic cascade towards an antimicrobial 4-methoxy-1-methyl-2-quinolone and demonstrated its in vivo feasibility by successfully expressing the pathway in Escherichia coli. Lastly, we determined the crystal structure of AthePKS, suggesting hotspots for enhancing its catalytic efficiency by enzyme engineering. Our results provide a framework for further engineering of enzymatic routes towards privileged heteroaromatic scaffolds and derivatives thereof.

biochemistry↗

Non-destructive transcriptomics via vesicular export

Transcriptomics enables comprehensive, multiplexed characterization of cellular states, yet prevailing methods typically require cell fixation or lysis, precluding longitudinal analysis of RNA expression in living cells. Here, we present non-destructive transcriptomics by vesicular export (NTVE), a platform for multi-time-point monitoring of RNA expression dynamics in living cells. Stabilized RNA reporter barcodes can be selectively packaged and exported from cells via virus-like particles (VLPs) bearing bioorthogonal affinity handles for convenient multichannel tracking of co-cultured cells. Using an engineered poly(A)-binding protein adapter, NTVE exports endogenous transcripts from inducible human and murine cell lines with high concordance to conventional lysate-derived RNA-seq. NTVE captures transcriptome changes in response to genetic and chemical perturbations within the same cells over time using standard sequencing workflows. NTVE can further be equipped with fusogens to deliver mRNA-encoded effectors or ribonucleoprotein gene editors from sender cells, activating gene reporters in co-cultured recipient cells. We demonstrate the utility of NTVE for monitoring hiPSC differentiation through daily non-destructive transcriptomic profiling of lineage-specific marker dynamics.

bioengineering↗

De novo design of triosephosphate isomerases using generative language models

The design of proteins with tailored functions is of immense interest to biotechnology, medicine, and the chemical industry. While protein design is rapidly evolving with the use of AI techniques, the design of complex enzymes remains a challenge. Here, we present the use of two large language models (LLMs), ZymCTRL and ProtGPT2, for the generation of de novo enzymes that catalyze the triosephosphate isomerase (TIM) reaction. Natural TIM enzymes are obligatory oligomers that catalyze a multi-step isomerization reaction near the diffusion limit. This makes TIM an ideal target to assess the generative ability of protein language models. Newly generated sequences were filtered to obtain a set of twelve candidates from each approach for experimental validation. Multiple constructs from both language models exhibit the intended function in vivo through their ability to complement a TIM-deficient E. coli strain. In-depth characterization of the best-behaving artificial enzyme reveals behavior and catalytic efficiency close to its natural counterparts. These findings support the use of conditional and fine-tuned unconditional LLMs for the generation of complex enzymes.

biochemistry↗

A 128-channel receive array with enhanced SNR performance for 10.5 tesla brain imaging

PurposeTo develop and characterize the performance of a 128-channel head array for brain imaging at 10.5 tesla and evaluate the potential of brain imaging at this unique, >10 tesla magnetic field. MethodsThe coil is composed of a 16-channel self-decoupled loop transmit/receive array with a 112-loop receive-only (Rx) insert. Interactions between the outer transmitter and the inner 112Rx insert were mitigated using coaxial cable traps placed every 1/16 of a wavelength on each feed cable, locating most preamplifier boards outside the transmitter field and miniaturizing those placed directly on individual coils. ResultsThe 128-channel array described herein achieved 77% of ultimate intrinsic SNR in the center of the brain. Transmit field maps obtained experimentally on a phantom with and without the receive array were similar and matched EM simulations, leading to FDA approval for human imaging. Anatomical and functional data, including with power demanding sequences, were acquired successfully on human volunteers. ConclusionsCounterintuitive to expectations based on magnetic fields [≤]7T, the higher channel counts provided SNR gains centrally, capturing [~]80% uiSNR. Fraction of uiSNR achieved centrally in 64Rx, 80Rx, and 128Rx arrays suggested that a plateau was being reached at 80%. At this plateau, linear to approximately quadratic B0 dependent SNR gains for the periphery and the center, respectively, were observed for 10.5T relative 7T.

neuroscience↗

Fast Single-Cell MALDI Imaging of Low-Mass Metabolites Reveals Cellular Activation Markers

Single-cell MALDI mass spectrometry imaging (MSI) of lipids and metabolites >200 Da has recently come to the forefront of biomedical research and chemical biology, but fast metabolome-preserving methods without paraformaldehyde fixation for analysis of low mass, hydrophilic metabolites (<200 Da) in large cell populations are lacking. Introducing giant unilamellar vesicles (GUVs) as MSI ground truth for cell-sized objects and Monte Carlo reference-based consensus clustering for data-dependent identification of cell subpopulations. The PRISM-MS (PRescan Imaging for Small Molecule - Mass Spectrometry) dual-scan MSI workflow is presented, enabling space-efficient and therefore faster lipid analysis in single GUVs and cells. Beyond lipids, PRISM-MS enables MSI and on-cell MS2-based identification of low-mass metabolites like amino acids or Krebs cycle intermediates involved in stimulus-dependent cell activation. The utility of PRISM-MS is demonstrated through the characterization of complex metabolome changes in lipopolysaccharide (LPS)-stimulated microglial cells and human-induced pluripotent stem cell-derived microglia. Translation of single cell results to endogenous microglia in organotypic hippocampal slice cultures indicates that LPS-activation involves changes of the itaconate-to-taurine ratio and alterations in neuron-to-glia glutamine-glutamate shuttling. The data suggests that PRISM-MS could serve as a standard method in single cell metabolomics, given its capability to characterize larger cell populations and low-mass metabolites.

bioinformatics↗

Deep learning for classifying neuronal morphologies: combining topological data analysis and graph neural networks

Neuronal shape determines how neurons process and integrate information, yet a consistent and objective classification of neuronal morphologies remains elusive. Current approaches rely heavily on subjective expert views or on predefined features, limiting reproducibility and interpretability. Here, we present an interpretable deep learning framework that unifies topological data analysis, graph neural networks, and traditional morphometrics to classify neuronal morphologies objectively and transparently. Our framework compares complementary mathematical representations of neurons to capture geometric, topological, and graph-structural information. Then it benchmarks their performance against expert-labeled datasets. We show that topology- and graph-based models achieve accuracies comparable to human experts, revealing that both global branching invariants and local connectivity patterns are essential to define morphological cell types. Using explainable artificial intelligence methods, we identify structural features driving each classification decision, bridging computational and neuroanatomical interpretations. This open source and reproducible approach provides a foundation for scalable, interpretable and biologically meaningful neuronal taxonomy, enabling consistent comparisons between data sets and species.

neuroscience↗

A rapid growth rate underpins the dominance of Hanseniaspora uvarum in spontaneous grape juice fermentations

Hanseniaspora uvarum is consistently observed as the dominant non-Saccharomyces species in spontaneous grape juice fermentations. However, the physiological mechanisms and physicochemical variables influencing the prevalence of H. uvarum over other non-Saccharomyces species remain unclear. We tested the physicochemical parameters contributing to H. uvarum dominance by inoculating a chemically diverse set of grape juices with a mock community whose composition was defined following a comprehensive microbial survey of spontaneous fermentations. Our findings indicated that the chemical composition of grape juice had minimal impact on the microbial dynamics of fermentation, with H. uvarum emerging as the dominant non-Saccharomyces species in nearly all conditions tested. Grape juice composition primarily influenced the total yeast abundance of the mock community. Flow cytometry analysis confirmed that H. uvarum has a faster growth rate than Saccharomyces cerevisiae and several other Hanseniaspora spp.. Moreover, its growth was not affected by the presence of S. cerevisiae, explaining its rapid dominance in spontaneous fermentations. The rapid growth of H. uvarum negatively impacted the growth of S. cerevisiae, with significant implications for fermentation performance and sugar consumption. The results of this study suggest that the fast growth rate of H. uvarum enables it to quickly dominate the grape juice environment during the early stages of fermentation. This physiological advantage indicates that the initial abundance of H. uvarum may be critical to the outcome of spontaneous fermentations, as evidenced by its direct impact on the growth of S. cerevisiae and fermentation performance.

microbiology↗

Harnessing early multimodal motor training to drive motor recovery and brain-wide structural reorganization after stroke

Stroke survivors often suffer from severe motor impairments, highlighting the critical need for effective rehabilitation strategies. In experimental models, extensive task-specific motor training within the first few weeks post-stroke significantly mitigates motor deficits. However, whether more multimodal motor training approaches after stroke can restore task-specific performance in non-trained motor tasks remains largely unknown. Additionally, while stroke itself triggers structural brain reorganization, the influence of early multimodal motor training on this process remains unclear. Here, we employed T2-weighted MRI to investigate brain region-specific volumetric changes over eight weeks in rats subjected to stroke and subsequent early multimodal motor training. We found that this combination not only facilitated task-specific motor function recovery, but also induced dramatic, multi-region, brain-wide volumetric changes. Specifically, over 80 locations within 50 distinct brain regions across both hemispheres exhibited substantial volumetric alterations in a predominantly bilateral symmetric pattern. In contrast, stroke or training alone resulted in changes in 8-15 locations within 7-13 brain regions, with stroke alone primarily affecting the infarcted hemisphere. Analysis of temporal volume changes revealed two distinct trajectories in post-stroke trained rats: one of initial swelling followed by shrinkage, and another of initial shrinkage followed by swelling, suggesting an early and delayed motor learning period. Overall, our findings demonstrate that multimodal motor training early after stroke effectively restores task-specific motor function and profoundly reshapes brain structure on a brain-wide scale, offering vital insights for developing optimized rehabilitation protocols to maximize recovery in stroke patients.

neuroscience↗

Protein fusion strategies for a multi-component Rieske oxygenase

Rieske oxygenases (ROs) are enzyme systems involved in microbial biodegradation or late-stage modifications during natural product biosynthesis. A major obstacle to working with ROs is their dependence on multi-component electron transfer chains (ETCs). Thereby, electrons from NAD(P)H are shuttled directly via a reductase (Red) or indirectly via an additional ferredoxin (Fd) to a terminal oxygenase (Oxy) for oxygen activation and subsequent substrate conversion. The present work evaluates potential fusion strategies to simplify the ETC of the three-component cumene dioxygenase (CDO) from Pseudomonas fluorescence. In in vitro reactions, the fusion of CDO-Red to CDO-Fd is the most suitable for activation of CDO-Oxy with product formation of approximately 22 mM (72 % conversion). Furthermore, protein fusion to CDO-Oxy was found to be feasible, highlighting the versatility of the redox partner fusion approach. Overall, this study aims to contribute to the research field of ROs by providing a promising strategy to simplify their multi-component nature.

biochemistry↗

Using Cupriavidus necator H16 to provide a roadmap for increasing electroporation efficiency in non-model bacteria

Bacteria are a treasure trove of metabolic reactions, but most industrial biotechnology applications rely on a limited set of established host organisms. In contrast, adopting non-model bacteria for the production of various chemicals of interest is often hampered by their limited genetic amenability coupled with their low transformation efficiency. In this study, we propose a series of steps that can be taken to increase electroporation efficiency in non-model bacteria. As a test strain, we use Cupriavidus necator H16, a lithoautotrophic bacterium that has been engineered to produce a wide range of products from CO2 and hydrogen. However, its low electroporation efficiency hinders the high-throughput genetic modifications required to develop C. necator into an industrially relevant host organism. First, we propose a species-independent technique based on natively methylated DNA and Golden Gate assembly to increase one-pot cloning and electroporation efficiency by 70-fold. Second, bioinformatic tools were used to predict defense systems and develop a restriction avoidance strategy that was used to introduce suicide plasmids by electroporation to obtain a domesticated strain. The results are discussed in the context of metabolic engineering of non-model bacteria. TABLE OF CONTENT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/596136v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@dfc76aorg.highwire.dtl.DTLVardef@19d130forg.highwire.dtl.DTLVardef@14e6ed3org.highwire.dtl.DTLVardef@4e0024_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

RF coil design strategies for improving SNR at theultrahigh magnetic field of 10.5 Tesla

PurposeTo develop multichannel transmit and receive arrays towards capturing the ultimate-intrinsic-SNR (uiSNR) at 10.5 Tesla (T) and to demonstrate the feasibility and potential of whole-brain, high-resolution human brain imaging at this high field strength. MethodsA dual row 16-channel self-decoupled transmit (Tx) array was converted to a 16Tx/Rx transceiver using custom transmit/receive switches. A 64-channel receive-only (64Rx) array was built to fit into the 16Tx/Rx array. Electromagnetic modeling and experiments were employed to define safe operation limits of the resulting 16Tx/80Rx array and obtain FDA approval for human use. ResultsThe 64Rx array alone captured approximately 50% of the central uiSNR at 10.5T while the identical 7T 64Rx array captured [~]76% of uiSNR at this lower field strength. The 16Tx/80Rx configuration brought the fraction of uiSNR captured at 10.5T to levels comparable to the performance of the 64Rx array at 7T. SNR data obtained at the two field strengths with these arrays displayed [Formula] dependent increases over a large central region. Whole-brain high resolution T2* and T1 weighted anatomical and gradient-recalled echo EPI BOLD fMRI images were obtained at 10.5T for the first time with such an advanced array, illustrating the promise of >10T fields in studying the human brain. ConclusionWe demonstrated the ability to approach the uiSNR at 10.5T over the human brain with a novel, high channel count array, achieving large SNR gains over 7T, currently the most commonly employed ultrahigh field platform, and demonstrate high resolution and high contrast anatomical and functional imaging at 10.5T.

neuroscience↗

Label-free Assessment of Complement-Dependent Cytotoxicity of Therapeutic Antibodies via a Whole-Cell MALDI Mass Spectrometry Bioassay

Potency assessment of monoclonal antibodies or corresponding biosimilars in cell-based assays is an essential prerequisite in biopharmaceutical research and development. However, cellular bioassays are still subject to limitations in sample throughput, speed, and often need costly reagents or labels as they are based on an indirect readout by luminescence or fluorescence. In contrast, whole-cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry (MS) has emerged as a direct, fast and label-free technology for functional drug screening being able to unravel the molecular complexity of cellular response to pharmaceutical reagents. However, this approach has not yet been used for cellular testing of biologicals. In this study, we have conceived, developed and bench-marked a label-free MALDI-MS based cell bioassay workflow for the functional assessment of complement-dependent cytotoxicity (CDC) of Rituximab antibody. By computational evaluation of response profiles followed by subsequent m/z feature annotation via fragmentation analysis and trapped ion mobility MS, we identified adenosine triphosphate and glutathione as readily MS-assessable metabolite markers for CDC and demonstrate that robust concentration-response characteristics can be obtained by MALDI-TOF MS. Statistical assay performance indicators suggest that whole-cell MALDI-TOF MS could complement the toolbox for functional cellular testing of biopharmaceuticals.

biochemistry↗

Recombinant manufacturing of multispecies biolubricants

Lubricin, a lubricating glycoprotein abundant in synovial fluid, forms a low-friction brush polymer interface in tissues exposed to sliding motion including joints, tendon sheaths, and the surface of the eye. Despite its therapeutic potential in diseases such as osteoarthritis and dry eye disease, there are few sources available. Through rational design, we developed a series of recombinant lubricin analogs that utilize the species-specific tissue-binding domains at the N- and C-termini to increase biocompatibility while replacing the central mucin domain with an engineered variant that retains the lubricating properties of native lubricin. In this study, we demonstrate the tissue binding capacity of our engineered lubricin product and its retention in the joint space of rats. Next, we present a new bioprocess chain that utilizes a human-derived cell line to produce O-glycosylation consistent with that of native lubricin and a purification strategy that capitalizes on the positively charged, hydrophobic N- and C-terminal domains. The bioprocess chain is demonstrated at 10 L scale in industry-standard equipment utilizing commonly available ion exchange, hydrophobic interaction and size exclusion chromatography resins. Finally, we confirmed the purity and lubricating properties of the recombinant biolubricant. The biomolecular engineering and bioprocessing strategies presented here are an effective means of lubricin production and could have broad applications to the study of mucins in general.

bioengineering↗