Biology subjects

Paulsen, F.

Publications and source records attributed to Paulsen, F..

8 recordsLinked to original sources

bioRxiv2026

Ultrastructural comparison of fixation and cryopreservation methods for brain preservation

Maximizing the morphological and molecular fidelity of preserved mammalian brain tissue is essential for basic neuroscience and brain banking, where tissue quality determines the reliability of downstream analyses. Aldehyde fixation and cryogenic storage are the most powerful preservation techniques available. However, how to best combine them is incompletely characterized. Here, we tested twelve different approaches to preserve the murine brain, including standard aldehyde perfusion fixation, variants of aldehyde-stabilized cryopreservation (ASC) using ethylene glycol (EG), aldehyde fixation followed by unprotected freezing, and several cryopreservation protocols without preceding aldehyde fixation, such as interleaved equilibration with vitrification solution. Preservation quality was assessed using light microscopy, transmission electron microscopy, and patch-level feature analysis with the DINOv2 vision foundation model. We found that ASC with sodium dodecyl sulfate (SDS)-mediated blood-brain barrier permeabilization preserved nuclear morphology, myelin periodicity, and neuropil texture comparable to standard aldehyde perfusion fixation, providing the first independent replication of ASC. Omitting SDS caused severe parenchymal dehydration, due to a mismatch between water and cryoprotectant transport. Aldehyde fixation followed by unprotected slow freezing confined ice damage primarily to perivascular zones, while fast freezing led to intranuclear clefts and cavities. Among non-fixation protocols, interleaved equilibration with vitrification solution preserved myelinated axon profiles and chromatin patterns, but induced perivascular edema. High concentration glycerol perfusion caused significant osmotic dehydration. Straight freezing of unfixed tissue without cryoprotectant was followed by membrane disruption, but resulted in the visualization of more structure than expected, likely as a result of structural restitution upon thawing. Taken together, our results provide a framework for matching preservation strategies to the needs of different types of brain banking and neuroscience research.

neuroscience↗

bioRxiv2026

The Mechanical Fingerprint of Hippocampal Sclerosis Linking Neuronal Cell Loss and Gliosis to Tissue Stiffness

Hippocampal sclerosis (HS) is the most common pathology in drug-resistant temporal lobe epilepsy (TLE). However, clinical diagnosis, prevalent epileptogenicity, and drug drug-resistance in individuals with HS remain an ongoing challenge demanding multidisciplinary research efforts. In this study, we examined the mechanical properties of neurosurgically en bloc resected HS specimens (n=8) ex vivo under compression, tension, and torsional shear. We fitted a two-term Ogden hyperelastic model to the measured mechanical responses to quantify nonlinear mechanical tissue properties. The resulting parameters revealed higher strain stiffening under compression in HS compared to hippocampus obtained post mortem (n=7). The distinction was most noticeable in the large-strain regime, which has important implications for using mechanical tissue properties as valuable diagnostic biomarker. Furthermore, we correlated the tissue microstructure with mechanical parameters. We trained a deep-learning histopathology classifier to detect and classify neurons and glial cells from hematoxylin-stained whole slide images (WSI). We identified a strong association between the small-strain stiffness (shear modulus {micro}) and the overall cell density as well as the glial cell density. The negative relationship between the neuron-to-glia ratio and shear modulus is consistent with the hypothesis that neuronal cell loss and gliosis drives tissue stiffening, respectively. Magnetic resonance imaging (MRI) analysis of the specimens confirmed the previously reported negative association between MRI-derived fractional anisotropy and shear modulus {micro}. Taken together, our study establishes a direct link between tissue mechanics and microstructure, suggesting nonlinear continuum mechanics models as promising new tools for clinical diagnosis and novel research strategies.

bioengineering↗

bioRxiv2026

Fractional Anisotropy as a Surrogate Marker of Brain Mechanics

Understanding the mechanical properties of brain tissue may provide crucial insights into brain development, injury, disease and surgical planning. Conventionally, these properties are measured ex vivo or in vivo during surgical procedures, while non-invasive in vivo alternatives are sparse. This study investigates whether fractional anisotropy (FA) derived from diffusion-weighted magnetic resonance imaging can serve as a surrogate marker for brain tissue stiffness in healthy human brains. MRI data were collected from three body donor brains, 28 healthy adults, and a publicly available independent dataset of 26 adults. FA values were compared with mechanical properties from ex vivo mechanical testing of brain tissue. Statistical analysis revealed a strong negative correlation between FA and the mechanical response for small strains expressed as shear modulus of a one-term hyperelastic Ogden model, indicating that higher FA values are associated with lower tissue stiffness. The nonlinearity parameter alpha exhibited a qualitatively similar, but considerably weaker correlation with FA. These findings were consistent across datasets. The findings suggest that FA can be a robust, non-invasive marker for estimating mechanical properties of brain tissue, with potential applications in clinical diagnosis and computational modeling of brain mechanics and the study of brain development. Further research is needed to clarify the relationship in lesional tissues and to optimize clinical utility.

neuroscience↗

bioRxiv2024

Characterization of a new lacrimal gland cell line in 2D and 3D cell culture models

The lacrimal gland produces the tear films aqueous component, which moistens and nourishes the ocular surface to maintain eye health. Reduced production of this component leads to dry eye disease, which affects over 250 million people worldwide. Despite the impact on patients, the availability of primary human material to study underlying disease mechanisms is severely limited and there is no cell model available for human lacrimal gland epithelial cells. After insertion of an SV40 antigen into primary human lacrimal gland epithelial cells, we selected, expanded, and characterized three epithelial cell clones from a female lacrimal gland donor. We show their epithelial character at genomic (PCR and RNAseq) and protein (immunofluorescence) levels and grow these cells in a 3D cell spheroid model. Here, we report the development of an immortalized human lacrimal gland epithelial cell line that improves accessibility to study the molecular pathogenesis mechanisms of dry eye disease and link them to causal treatments. We show the expression of typical lacrimal gland epithelial cell marker genes (e.g. PAX6, FOXC1, AQP5, CSTB, and CST6) and describe the feasibility of the cells to form 2D cell sheets and 3D cell spheroids. We successfully established immortalized human lacrimal gland cells with epithelial character. In the future, the integration of these cells into larger studies holds great potential for advancing our understanding of dry eye disease and its underlying cellular mechanisms.

cell biology↗

bioRxiv2022

Inverse identification of region-specific hyperelastic material parameters for human brain tissue

The identification of material parameters accurately describing the region-dependent mechanical behavior of human brain tissue is crucial for computational models used to assist, e.g., the development of safety equipment like helmets or the planning and execution of brain surgery. While the division of the human brain into different anatomical regions is well established, knowledge about regions with distinct mechanical properties remains limited. Here, we establish an inverse parameter identification scheme using a hyperelastic Ogden model and experimental data from multi-modal testing of tissue from 19 anatomical human brain regions to identify mechanically distinct regions and provide the corresponding material parameters. We assign the 19 anatomical regions to nine governing regions based on similar parameters and microstructures. Statistical analyses confirm differences between the regions and indicate that at least the corpus callosum and the corona radiata should be assigned different material parameters in computational models of the human brain. We provide a total of four parameter sets based on the two initial Poissons ratios of 0.45 and 0.49 as well as the pre- and unconditioned experimental responses, respectively. Our results highlight the close interrelation between the Poissons ratio and the remaining model parameters. The identified parameters will contribute to more precise computational models enabling spatially resolved predictions of the stress and strain states in human brains under complex mechanical loading conditions.

bioengineering↗

bioRxiv2021

Decomposition of the SARS-CoV-2-ACE2 interface reveals a common trend among emerging viral variants

New viral variants of the SARS-CoV-2 virus show enhanced infectivity compared to wild type, resulting in an altered pandemic situation in affected areas. These variants are the B.1.1.7 (United Kingdom), B.1.1.7 with the additional E484K mutation, the B.1.351 variant (South Africa) and the P.1 variant (Brazil). Understanding the binding modalities between these viral variants and the host cell receptor ACE2 allows depicting changes, but also common motifs of virus-host cell interaction. The trimeric spike protein expressed at the viral surface contains the receptor-binding domain (RBD) that forms the molecular interface with ACE2. All the above-mentioned variants carry between one and three amino acid exchanges within the interface-forming region of the RBD, thereby altering the binding interface with ACE2. Using molecular dynamics simulations and decomposition of the interaction energies between the RBD and ACE2, we identified phenylalanine 486, glutamine 498, threonine 500 and tyrosine 505 as important interface-forming residues across viral variants. We also suggest a reduced binding energy between RBD and ACE2 in viral variants with higher infectivity, attributed to residue-specific differences in electrostatic interaction energy. Importantly, individual amino acid exchanges not only influence the affected position, but also alter the conformation of surrounding residues and affect their interaction potential as well. We demonstrate how computational methods can help to identify changed as well as common motifs across viral variants. These identified motifs might play a crucial role, in the strategical development of therapeutic interventions against the fast mutating SARS-CoV-2 virus. Significance StatementThe COVID-19 pandemic caused by the SARS-CoV-2 virus has significantly changed our lives. To date, there is a lack of neutralizing drugs that specifically target SARS-CoV-2. Hope lies in newly developed vaccines that effectively prevent severe cases of acute respiratory syndrome. However, emerging viral variants escape vaccine-induced immune-protection. Therefore, identification of appropriate molecular targets across viral variants is important for the development of second- and third-generation vaccines and inhibitory antibodies. In this study, we identify residues across viral variants that are important for viral binding to the host cell. As such residues cannot be replaced without diminishing infectivity of the virus, these residues represent primary targets for intervention, for example by neutralizing antibodies.

bioinformatics↗

bioRxiv2021

Mutations in the B.1.1.7 SARS-CoV-2 spike protein reduce receptor-binding affinity and induce a flexible link to the fusion peptide

The B.1.1.7 variant of the SARS-CoV-2 virus shows enhanced infectiousness over the wild type virus, leading to increasing patient numbers in affected areas. A number of single amino acid exchanges and deletions within the trimeric viral spike protein characterize this new SARS-CoV-2 variant. Crucial for viral entry into the host cell is the interaction of the spike protein with the cell surface receptor angiotensin-converting enzyme 2 (ACE2) as well as integration of the viral fusion peptide into the host membrane. Respective amino acid exchanges within the SARS-CoV-2 variant B.1.1.7 affect inter-monomeric contact sites within the spike protein (A570D and D614G) as well as the ACE2-receptor interface region (N501Y), which comprises the receptor-binding domain (RBD) of the viral spike protein. However, the molecular consequences of mutations within B.1.1.7 on spike protein dynamics and stability, the fusion peptide, and ACE2 binding are largely unknown. Here, molecular dynamics simulations comparing SARS-CoV-2 wild type with the B.1.1.7 variant revealed inter-trimeric contact rearrangements, altering the structural flexibility within the spike protein trimer. In addition to reduced flexibility in the N-terminal domain of the spike protein, we found increased flexibility in direct spatial proximity of the fusion peptide. This increase in flexibility is due to salt bridge rearrangements induced by the D614G mutation in B.1.1.7 found in pre- and post-cleavage state at the S2 site. Our results also imply a reduced binding affinity for B.1.1.7 with ACE2, as the N501Y mutation restructures the RBD-ACE2 interface, significantly decreasing the linear interaction energy between the RBD and ACE2. Our results demonstrate how mutations found within B.1.1.7 enlarge the flexibility around the fusion peptide and change the RBD-ACE2 interface, which, in combination, might explain the higher infectivity of B.1.1.7. We anticipate our findings to be starting points for in depth biochemical and cell biological analyses of B.1.1.7, but also other highly contagious SARS-CoV-2 variants, as many of them likewise exhibit a combination of the D614G and N501Y mutation.

biophysics↗

bioRxiv2018

Examining the Role of the Surfactant Family Member SFTA3 in Interneuron Specification

The transcription factor NKX2.1, expressed at high levels in the medial ganglionic eminence (MGE), is a master regulator of cortical interneuron progenitor development. To identify gene candidates with expression profiles similar to NKX2.1, previous transcriptome analysis of human embryonic stem cell (hESC)-derived MGE-like progenitors revealed SFTA3 as the strongest candidate. Quantitative real-time PCR analysis of hESC-derived NKX2.1-positive progenitors and transcriptome data available from the Allen Institute for Brain Science revealed comparable expression patterns for NKX2.1 and SFTA3 during interneuron differentiation in vitro and demonstrated high SFTA3 expression in the human MGE. Although SFTA3 has been well studied in the lung, the possible role of this surfactant protein in the MGE during embryonic development remains unexamined. To determine if SFTA3 plays a role in MGE specification, SFTA3-/- and NKX2.1 -/-hESC lines were generated using custom designed CRISPRs. We show that NKX2.1 KOs have a significantly diminished capacity to differentiate into MGE interneuron subtypes. SFTA3 KOs also demonstrated a somewhat reduced ability to differentiate down the MGE-like lineage, although not as severe relative to NKX2.1 deficiency. These results suggest NKX2.1 and SFTA3 are co-regulated genes, and that deletion of SFTA3 does not lead to a major change in the specification of MGE derivatives.

neuroscience↗