Biology subjects

Hansen, C.

Publications and source records attributed to Hansen, C..

14 recordsLinked to original sources

bioRxiv2026

Multimodal Alignment of MicroCT Imaging to Vibroacoustic Signals to Validate Soft Tissue Needle Transitions in Manduca sexta

ObjectiveRobotic-assisted needle insertions lack haptic feedback, a key sensory cue for detecting tissue transitions and regulating puncture force. Modeling this feedback requires an understanding of soft-tissue biomechanics during insertion. Vibroacoustic signals generated by needle-tissue interactions may provide an additional sensing modality, but their interpretation requires validation against anatomical ground truth. MethodsA multimodal framework was developed to correlate vibroacoustic signals with high-resolution post-puncture microCT ({micro}CT) imaging in Manduca sexta, an insect model containing interconnected soft-tissue layers. A custom clip-on prototype recorded vibroacoustic signals during manual needle insertions. Three trajectory-marking strategies were evaluated to determine 3D coordinates of soft-tissue layer crossings and to assess correlations between acoustic events and anatomical transitions. Distances between layer crossings and needle displacement were used for spatiotemporal alignment of vibroacoustic and {micro}CT data. ResultsA {micro}CT-compatible nylon string preserved puncture trajectories without artifacts and enabled high-resolution 3D reconstruction of anatomy and needle paths. Fusion of vibroacoustic and imaging data allowed identification of acoustic events associated with tissue entry, exit, and transitions. ConclusionBy integrating high-resolution {micro}CT imaging with vibroacoustic sensing, this study establishes a biologically grounded framework for validating the relationship between vibroacoustic signals and anatomical tissue transitions during needle insertion, providing a basis for future quantitative analyses. SignificanceThis work provides initial evidence for correlating vibroacoustic signals recorded during needle insertion with corresponding {micro}CT-identified tissue barriers. Because vibroacoustics offers substantially higher temporal and spatial resolution than most imaging modalities, it has the potential to improve tissue sensing and procedural accuracy in future needle-based interventions.

biophysics↗

bioRxiv2024

Entamoeba histolytica extracellular vesicles drive pro-inflammatory monocyte signaling

The parasitic protozoan Entamoeba histolytica secretes extracellular vesicles (EVs), but so far little is known about their function in the interaction with the host immune system. Infection with E. histolytica trophozoites can lead to formation of amebic liver abscesses (ALAs), in which pro-inflammatory immune responses of Ly6Chi monocytes contribute to liver damage. Men exhibit a more severe pathology as the result of higher monocyte recruitment and a stronger immune response. To investigate the role of EVs and pathogenicity in the host immune response, we studied the effect of EVs secreted by low pathogenic EhA1 and highly pathogenic EhB2 amebae on monocytes. Size and quantity of isolated EVs from both clones were similar. However, they differed in their proteome and miRNA cargo, providing insight into factors potentially involved in amebic pathogenicity. In addition, EVs were enriched in proteins with signaling peptides compared with the total protein content of trophozoites. Exposure to EVs from both clones induced monocyte activation and a pro-inflammatory immune response as evidenced by increased surface presentation of the activation marker CD38 and upregulated gene expression of key signaling pathways (including NF-{kappa}B, IL-17 and TNF signaling). The release of pro-inflammatory cytokines was increased in EV-stimulated monocytes and more so in male-than in female-derived cells. While EhA1 EV stimulation caused elevated myeloperoxidase (MPO) release by both monocytes and neutrophils, EhB2 EV stimulation did not, indicating the protective role of MPO during amebiasis. Collectively, our results suggest that parasite-released EVs contribute to the male-biased immunopathology mediated by pro-inflammatory monocytes during ALA formation. Author summaryParasites communicate with their host via small membranous extracellular vesicles (EVs) that can shuttle cargo and thus information between cells. The protozoan parasite Entamoeba histolytica releases EVs but not much is known about their role in the interaction with the host immune system. Infection with E. histolytica can lead to amebic liver abscess (ALA) formation. Innate immune cells, particularly monocytes, contribute to liver damage by releasing microbicidal factors. Men have a more severe ALA pathology as the result of a stronger monocyte immune response. In this study, we analyzed the effect of EVs from differently virulent E. histolytica clones on monocytes to better understand their interaction. EVs of both clones were similar in size and quantity but differed in their cargo, which provides information on factors potentially involved in pathogenicity. Monocytes responded to EVs of both clones in a pro-inflammatory manner that reflected the immune processes occurring during ALA in vivo, including the bias towards the male sex. Only EVs of amebae with low pathogenicity, and not those released by the highly pathogenic clone, elicited secretion of the granular enzyme myeloperoxidase, which plays a protective role during ALA. Overall, our data suggest that EVs may contribute to liver injury.

immunology↗

bioRxiv2024

Context-driven interaction retrieval and classification for modeling, curation, and reuse

Automated extraction of molecular interactions from scientific literature has outpaced the development of systematic methods for integrating this information with curated models and knowledge graphs. Here we present VIOLIN (Versatile Interaction Organizing to Leverage Information in Networks), a configurable, attribute-aware reconciliation framework that formally compares newly extracted interaction lists against structured baseline graphs. VIOLIN classifies each interaction as a corroboration, contradiction, flagged case, or extension, and supports configurable attribute inclusion strategies and mismatch semantics to adjust reconciliation strictness. We evaluate VIOLIN using interaction lists generated by two traditional NLP systems (REACH, INDRA) and two large language models (GPT-4.1, Llama 3) across multiple literature corpora and structurally distinct baseline graphs. Across all conditions, reconciliation outcomes were stable and interpretable, with extensions dominating and corroboration-contradiction balance reflecting intrinsic structural relationships between baseline graphs and extracted evidence. Sensitivity analyses demonstrate that attribute inclusion and classification scheme selection shift category boundaries predictably. Benchmark evaluations confirm high algorithmic correctness and alignment with expert curation. VIOLIN is publicly available as a Python package and through web-based interface (https://nmzlab.github.io/Tools-UI).

systems biology↗

bioRxiv2024

The BioRECIPE Knowledge Representation Format

AO_SCPLOWBSTRACTC_SCPLOWThe BioRECIPE (Biological system Representation for Evaluation, Curation, Interoperability, Preserving, and Execution) knowledge representation format was introduced to facilitate seamless human-machine interaction while creating, verifying, evaluating, curating, and expanding executable models of intra- and intercellular signaling. This format allows a human user to easily preview and modify any model component, while it is at the same time readable by machines and can be processed by a suite of model development and analysis tools. The BioRECIPE format is compatible with multiple representation formats, natural language processing tools, modeling tools, and databases that are used by the systems biology community. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/579694v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@76a130org.highwire.dtl.DTLVardef@505cb4org.highwire.dtl.DTLVardef@1f64e68org.highwire.dtl.DTLVardef@195bd03_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa

BackgroundGene editing in induced pluripotent stem (iPS) cells has been hailed to enable new cell therapies for various monogenetic diseases including dystrophic epidermolysis bullosa (DEB). However, manufacturing, efficacy and safety roadblocks have limited the development of genetically corrected, autologous iPS cell-based therapies. MethodsWe developed Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a new generation GMP-compatible (cGMP), reproducible, and scalable platform to produce autologous clinical-grade iPS cell-derived organotypic induced skin composite (iSC) grafts to treat incurable wounds of patients lacking type VII collagen (C7). DEBCT uses a combined high-efficiency reprogramming and CRISPR-based genetic correction single step to generate genome scar- free, COL7A1 corrected clonal iPS cells from primary patient fibroblasts. Validated iPS cells are converted into epidermal, dermal and melanocyte progenitors with a novel 2D organoid differentiation protocol, followed by CD49f enrichment and expansion to minimize maturation heterogeneity. iSC product characterization by single cell transcriptomics was followed by mouse xenografting for disease correcting activity at 1 month and toxicology analysis at 1-6 months. Culture-acquired mutations, potential CRISPR-off targets, and cancer-driver variants were evaluated by targeted and whole genome sequencing. FindingsiPS cell-derived iSC grafts were reproducibly generated from four recessive DEB patients with different pathogenic mutations. Organotypic iSC grafts onto immune-compromised mice developed into stable stratified skin with functional C7 restoration. Single cell transcriptomic characterization of iSCs revealed prominent holoclone stem cell signatures in keratinocytes and the recently described Gibbin-dependent signature in dermal fibroblasts. The latter correlated with enhanced graftability. Multiple orthogonal sequencing and subsequent computational approaches identified random and non-oncogenic mutations introduced by the manufacturing process. Toxicology revealed no detectable tumors after 3-6 months in DEBCT- treated mice. InterpretationDEBCT successfully overcomes previous roadblocks and represents a robust, scalable, and safe cGMP manufacturing platform for production of a CRISPR-corrected autologous organotypic skin graft to heal DEB patient wounds.

bioengineering↗

bioRxiv2023

Extensive profiling of histidine-containing dipeptides reveals species-specific distribution and metabolism in mice, rats and humans

Histidine-containing dipeptides (HCDs) are pleiotropic homeostatic molecules linked to inflammatory, metabolic and neurological diseases, as well as exercise performance. Using a sensitive UHPLC-MS/MS approach and an optimized quantification method, we performed a systematic and extensive profiling of HCDs in the mouse, rat, and human body (in n=26, n=25, n=19 tissues, respectively). Our data show that tissue HCD levels are uniquely regulated by carnosine synthase (CARNS1), an enzyme that was preferentially expressed by fast-twitch skeletal muscle fibers and brain oligodendrocytes. Cardiac HCD levels are remarkably low compared to other excitable tissues. Carnosine is unstable in human plasma, but is preferentially transported within red blood cells in humans but not rodents. The low abundant carnosine analog N-acetylcarnosine is the most stable plasma HCD, and is enriched in human skeletal muscles. Here, N-acetylcarnosine is continuously secreted into the circulation, which is further induced by acute exercise in a myokine-like fashion. Collectively, we provide a novel basis to unravel tissue-specific, paracrine, and endocrine roles of HCDs in human health and disease. Significance statementBy extensively profiling the pluripotent histidine-containing dipeptides across three species, we generated many new insights into species- and tissue-specific histidine-containing dipeptide metabolism. For instance, the only stable analog that is specific for the human circulation (N-acetylcarnosine) is continuously released from muscle tissue and is positively regulated by physical exercise. The great number of analyses and experiments involving humans establishes great translational value of the findings. These new data open exciting opportunities to study histidine-containing dipeptide metabolism, including paracrine and/or endocrine signaling of these dipeptides, possibly contributing to the potent health-promoting exercise effects.

physiology↗

bioRxiv2021

Essential elements of radical pair magnetosensitivity in Drosophila

Many animals use the Earths magnetic field (geoMF) for navigation1. The favored mechanism for magnetosensitivity involves a blue-light (BL) activated electron transfer reaction between flavin adenine dinucleotide (FAD) and a chain of tryptophan (Trp) residues within the photoreceptor protein, CRYPTOCHROME (CRY). The spin-state of the resultant radical pair (RP), and hence the concentration of CRY in its active state, is influenced by the geoMF2. The canonical CRY-centric radical pair mechanism (RPM) does not, however, explain many physiological and behavioural observations2-8. Here, using electrophysiology and behavioural analyses, we assay magnetic field (MF) responses at single neuron and organismal level. We show that the 52 C-terminal (CT) amino acids of CRY, which are missing the canonical FAD binding domain and Trp chain, are sufficient to facilitate magnetoreception. We also show that increasing intracellular FAD potentiates both BL-induced and MF-dependent effects on the activity mediated by the CT. Additionally, high levels of FAD alone are sufficient to cause BL neuronal sensitivity and, remarkably, potentiation of this response in the co-presence of a MF. These unexpected results reveal the essential components of a primary magnetoreceptor in flies, providing strong evidence that non-canonical (i.e., non-CRY-dependent) RPs can elicit MF responses in cells.

physiology↗

bioRxiv2021

TNF increases Tyrosine Hydroxylase expression in human monocytes

Most, if not all, peripheral immune cells in humans and animals express tyrosine hydroxylase (TH), the rate limiting enzyme in catecholamine synthesis. Since TH is typically studied in the context of brain catecholamine signaling, little is known about changes in TH production and function in peripheral immune cells. This knowledge gap is due, in part, to the lack of an adequately sensitive assay to measure TH in immune cells expressing lower TH levels compared to other TH expressing cells. Here, we report the development of a highly sensitive and reproducible Bio-ELISA to quantify picogram levels of TH in multiple model systems. We have applied this assay to monocytes isolated from blood of persons with Parkinsons disease (PD) and to age-matched, healthy controls. Our study unexpectedly revealed that PD patients monocytes express significantly higher levels of TH protein in peripheral monocytes relative to healthy controls. Tumor necrosis factor (TNF{delta}), a pro-inflammatory cytokine, has also been shown to be increased in the brains and peripheral circulation in human PD, as well as in animal models of PD. Therefore, we investigated a possible connection between higher levels of TH protein and the known increase in circulating TNF{delta} in PD. Monocytes isolated from healthy donors were treated with TNF{delta} or with TNF{delta} in the presence of an inhibitor. Tissue plasminogen activator (TPA) was used as a positive control. We observed that TNF{delta} stimulation increased both the number of TH+ monocytes and the quantity of TH per monocyte, without increasing the total numbers of monocytes. These results revealed that TNF{delta} could potentially modify monocytic TH production and serve a regulatory role in peripheral immune function. The development and application of a highly sensitive assay to quantify TH in both human and animal cells will provide a novel tool for further investigating possible PD immune regulatory pathways between brain and periphery.

neuroscience↗

bioRxiv2020

Registration-free Distortion Correction of Diffusion Weighted MRI

Diffusion magnetic resonance images may suffer from geometric distortions due to susceptibility induced off resonance fields, which cause geometric mismatch with anatomical images and ultimately affect subsequent quantification of microstructural or connectivity indices. State-of-the art diffusion distortion correction methods typically require data acquired with reverse phase encoding directions, resulting in varying magnitudes and orientations of distortion, which allow estimation of an undistorted volume. Alternatively, additional field maps acquisitions can be used along with sequence information to determine warping fields. However, not all imaging protocols include these additional scans and cannot take advantage of state-of-the art distortion correction. To avoid additional acquisitions, structural MRI (undistorted scans) can be used as registration targets for intensity driven correction. In this study, we aim to (1) enable susceptibility distortion correction with historical and/or limited diffusion datasets that do not include specific sequences for distortion correction and (2) avoid the computationally intensive registration procedure typically required for distortion correction using structural scans. To achieve these aims, we use deep learning (3D U-nets) to synthesize an undistorted b0 image that matches geometry of structural T1w images and intensity contrasts from diffusion images. Importantly, the training dataset is heterogenous, consisting of varying acquisitions of both structural and diffusion. We apply our approach to a withheld test set and show that distortions are successfully corrected after processing. We quantitatively evaluate the proposed distortion correction and intensity-based registration against state-of-the-art distortion correction (FSL topup). The results illustrate that the proposed pipeline results in b0 images that are geometrically similar to non-distorted structural images, and more closely match state-of-the-art correction with additional acquisitions. In addition, we show generalizability of the proposed approach to datasets that were not in the original training / validation / testing datasets. These datasets included varying populations, contrasts, resolutions, and magnitudes and orientations of distortion and show efficacious distortion correction. The method is available as a Singularity container, source code, and an executable trained model to facilitate evaluation.

bioengineering↗

bioRxiv2019

Diffusion tubes: a method for the mass culture of ctenophores and other pelagic marine invertebrates

The culture of pelagic marine invertebrates, especially the ctenophore Mnemiopsis leidyi, has been demonstrated in past studies dating back to the 1960s, however the mass culture of delicate pelagic invertebrates has remained elusive. By using a pair of acrylic tubes and enabling water diffusion between them, we have been able to reliably and cost effectively mass culture several genera of ctenophores (Pleurobrachia, Hormiphora, Bolinopsis, Mnemiopsis, and Leucothea), one species of siphonophore (Nanomia) and one species of larvacean (Oikopleura). The simple, compact method is effective enough to support two permanent exhibits of ctenophores at the Monterey Bay Aquarium while minimizing live food culture requirements with the potential to support further investigation of pelagic marine invertebrate ontogeny, ecology and genomics.

developmental biology↗

bioRxiv2019

Housing laboratory mice in a natural environment uncovers genetic and environmental contributions to immune variation.

The relative contributions of genetic and environmental factors to variation in immune responses are still poorly understood. Here, we performed a deep phenotypic analysis of immunological parameters of laboratory mice released into an outdoor enclosure, carrying susceptibility genes (Nod2 and Atg16l1) implicated in the development of inflammatory bowel diseases. Variations of immune cell populations were largely driven by environment, whereas cytokine production in response to stimulation was affected more by genetic mutations. Multi-omic models identified transcriptional signatures associated with differences in T cell populations. Subnetworks associated with responses against Clostridium perfringens, Candida albicans and Bacteroides vulgatus were also coupled with rewilding. Hence, exposing laboratory mice carrying different genetic mutations to a natural environment uncovered important contributors to immune variation. One sentence summaryNatural environment exposure in laboratory mice primarily promotes variation in population frequencies of immune cells, whereas cytokine responses to stimulation are affected more by genetic susceptibility to inflammatory bowel disease.

immunology↗

bioRxiv2019

Altered immunity of laboratory mice in the natural environment is associated with fungal colonization

The immune systems of free-living mammals such as humans and wild mice display a heightened degree of activation compared with laboratory mice maintained under artificial conditions. Here, we demonstrate that releasing inbred laboratory mice into an outdoor enclosure to mimic life in a natural environment alters the state of immunity. In addition to enhancing the differentiation of T cell populations previously associated with pathogen exposure, we found that outdoor release of mice led to an increase in circulating granulocytes. However, rewilded mice were not infected by pathogens previously implicated in immune activation. Rather, changes to the immune system were associated with an altered composition of the microbiota, and fungi isolated from rewilded mice were sufficient to increase circulating granulocytes. These findings establish an experimental procedure to investigate the impact of the natural environment on immune development and identify a role for sustained fungal exposure in determining granulocyte numbers.

immunology↗

bioRxiv2018

Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires

Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes at scale and high fidelity. Using an amplification-free single-cell genome sequencing approach implemented on commodity hardware (DLP+) coupled with a cloud-based computational platform, we define a resource of 40,000 single-cell genomes characterized by their genome states, across a wide range of tissue types and conditions. We show that shallow sequencing across thousands of genomes permits reconstruction of clonal genomes to single nucleotide resolution through aggregation analysis of cells sharing higher order genome structure. From large-scale population analysis over thousands of cells, we identify rare cells exhibiting mitotic mis-segregation of whole chromosomes. We observe that tissue derived scWGS libraries exhibit lower rates of whole chromosome anueploidy than cell lines, and loss of p53 results in a shift in event type, but not overall prevalence in breast epithelium. Finally, we demonstrate that the replication states of genomes can be identified, allowing the number and proportion of replicating cells, as well as the chromosomal pattern of replication to be unambiguously identified in single-cell genome sequencing experiments. The combined annotated resource and approach provide a re-implementable large scale platform for studying lineages and tissue heterogeneity.

genomics↗

bioRxiv2018

Limits to anatomical accuracy of diffusion tractography using modern approaches

Diffusion MRI fiber tractography is widely used to probe the structural connectivity of thebrain, with a range of applications in both clinical and basic neuroscience. Despite widespread use, tractography has well-known pitfalls that limits the anatomical accuracy of this technique. Numerous modern methods have been developed to address these shortcomings through advances in acquisition, modeling, and computation. To test whether these advances improve tractography accuracy, we organized the ISBI 2018 3D Validation of Tractography with Experimental MRI (3D-VoTEM) challenge. We made available three unique independent tractography validation datasets - a physical phantom and two ex vivo brain specimens - resulting in 176 distinct submissions from 9 research groups. By comparing results over a wide range of fiber complexities and algorithmic strategies, this challenge provides a more comprehensive assessment of tractographys inherent limitations than has been reported previously. The central results were consistent across all sub-challenges in that, despite advances in tractography methods, the anatomical accuracy of tractography has not dramatically improved in recent years. Taken together, our results independently confirm findings from decades of tractography validation studies, demonstrate inherent limitations in reconstructing white matter pathways using diffusion MRI data alone, and highlight the need for alternative or combinatorial strategies to accurately map the fiber pathways of the brain.

neuroscience↗