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Rasmussen, A.

Publications and source records attributed to Rasmussen, A..

At least 19 recordsLinked to original sources
bioRxiv2026

The Structure of Escherichia coli MscL and its dimer formation in Nanodiscs

Mechanosensitive channels of large conductance (MscL) are essential bacterial safety valves that prevent osmotic lysis by releasing solutes in response to membrane tension. Despite extensive functional studies on Escherichia coli MscL (EcMscL), its high-resolution structure remained unknown. Using cryo-electron microscopy, we present an experimental structure of EcMscL reconstituted in nanodiscs at 3.1 [A] resolution. The structure reveals a pentameric assembly with a narrow hydrophobic gate at the cytosolic side and a periplasmic cavity, consistent with the canonical MscL-fold. Differences to earlier published crystal structures of MscL from other organisms are in the less conserved periplasmic loop. We observe a previously unreported dimeric association of EcMscL pentamers, mediated by residues 61-63 in the periplasmic loop. This dimeric interface is located at the periplasmic side and provides a structural basis for the formation of higher-order clusters. The observed arrangement enables a fluid-like, mosaic packing of channels with center-to-center distances of 5.9-9 nm, consistent with biophysical and imaging data. These findings provide a structural framework for understanding cluster organization of EcMscL that modulates its activity in cellular stress response.

molecular biology↗
bioRxiv2026

Slow to Start, Free at Last: Dual Effects of Mucin on Escherichia coli Phage T4

Bacteriophages traversing the gastrointestinal tract are exposed to extreme physicochemical stresses that may rapidly compromise virion integrity and shape infection dynamics. While some phages bind to host-derived mucins at mucosal surfaces, the functional consequences of soluble mucin glycans for phage-host interactions remain incompletely understood. Here, we show that soluble mucin glycans exert dual effects on the Escherichia coli phage T4 by delaying infection initiation while simultaneously providing environmental virion stability. Mucin-coated T4 exhibits a lag in the onset of productive infection, consistent with transient steric occlusion from E. coli, yet without impairing overall phage progeny production once infection was established. We further show that E. coli can metabolize purified mucin, supporting a model in which dynamic remodeling of the mucin matrix gradually releases T4 and enables infection. Importantly, mucin coating substantially increases T4 survival under gastrointestinal-like stresses, including acidic pH and protease exposure. Moreover, we find that in a murine gut colonization model, a single oral dose of mucin-coated T4 displayed enhanced fecal persistence over a two-week period, which correlated with prolonged suppression of E. coli populations and delayed resolution of phage-associated functional shifts in the gut microbiome. Together, we find that that soluble mucin glycans actively shape T4 phage infection kinetics, virion stability, and ecological impact in the murine gut, and support mucin-based formulations as a strategy to extend the persistence and efficacy of orally delivered phages.

microbiology↗
bioRxiv2026

Ancestry-specific rewiring of BCR-MAPK signaling in sarcoidosis B cells

Sarcoidosis is a heterogenous disease of unknown etiology characterized by non-caseating granulomas. Disease prevalence and presentation vary significantly by ancestry and ranges from acute, self-resolving disease to severe, chronic disease. Following previous reports suggesting B cells in the development and pathogenesis of sarcoidosis, we present here results of single-cell RNA sequencing, supporting B cell involvement in sarcoidosis through altered immediate early response, rewiring of MAPK signaling, and ancestry-specific preferential expansion of B cell receptors. Peripheral blood mononuclear cells were obtained from individuals of African or European Ancestry (AA and EA, respectively) including 48 healthy controls, 59 sarcoidosis patients, and 28 systemic lupus erythematosus (SLE) patients. SLE samples were used as a disease control. Differential expression analysis highlighted many differentially expressed genes (DEGs) with almost 5x more in the AA sarcoidosis versus AA control group compared to the EA sarcoidosis versus EA control group. B cells had the most DEGs of all cell types and expression patterns were similar between ancestries, however, sarcoidosis had an opposite transcription pattern than SLE, demonstrating an alternative immune response to acute activation than that seen in a prototypical autoinflammatory disease. This trend was maintained when examining specialized B cell subsets, with the most pronounced effect in the AA sarcoidosis versus AA control comparison. Our results strongly support further investigation of the role of humoral immune response in sarcoidosis and the potential to highlight patient groups likely to benefit from existing B cell therapies.

immunology↗
bioRxiv2025

MPXV Clade IIb virus infection in mice leads to prolonged viral replication, macrophage infiltration, and decreased spermatogenesis in the testes.

Mpox (formerly monkeypox) is caused by monkeypox virus (MPXV) and has prompted two recent global health emergencies. Clade IIb MPXV, a recently recognized subclade, has been associated with oral and genital lesions and transmission among men who have sex with men (MSM); however, mechanisms of genital pathogenesis and sexual transmission are not understood. We investigated several routes of MPXV Clade IIb virus infection (intranasal, oral, anal, and intraperitoneal) and found high and prolonged viral titres in the testes after IP inoculation still detectable at 21 days. The testes had significant changes to tissue architecture including loss of spermatogenesis, disorganization of spermatozoa, loss of Leydig cells, and breakdown of the seminiferous tubule membranes. Viral antigen positive cells were present in the interstitial spaces between the seminiferous tubules with macrophage infiltration also evident. This work provides insights into potential of sexual transmission for MPXV viruses as well as mechanisms of Mpox disease which may significantly impact long-term fertility or sex organ health of infected males. Author SummaryMpox (formerly monkeypox) is a painful disease similar to smallpox caused by the monkeypox virus (MPXV) which is an emerging/re-emerging virus. Recently the WHO has declared two global health emergencies due to human-to-human transmission of MPXV. Clade IIb MPXV is a newly recognized subclade that has been associated with genital lesions and sexual transmission/contact; however, how the virus causes disease in sex-organs or how it is passed from person-to-person is not understood. We investigated several routes of MPXV Clade IIb inoculation and found IP inoculation in male mice led to high and prolonged viral titres in testes. Additionally, the testes were significantly affected having loss of sperm and cellular organization. Evidence of inflammatory cell infiltration, specifically, macrophages, are suspected to be the cause of testes specific disease. This work provides insights into potential of sexual transmission for MPXV viruses as well as mechanisms of Mpox disease.

microbiology↗
bioRxiv2025

Sensitive Transcriptomics and Genotyping reveals function of genetic variants in immunity

Advancements in genomics have revolutionized human genetics by defining the genetic architecture of disease. However, identifying causal variants and their mechanisms of action remains a challenge in translating genetics into therapeutic interventions. Here, we developed Sensitive Transcriptomics And Genotyping by sequencing (STAG-seq), a high-throughput platform designed to define mechanistic genotype-phenotype relationships through simultaneous single-cell measurements of genomic DNA and RNA transcripts. Combined with base-editing, STAG-seq enables functionalization of variants in relevant cellular contexts. We demonstrate the applicability of this approach in several settings. First, we screened genetic perturbations to identify monoallelic and biallelic variant effects in primary human macrophages treated with innate immune stimuli. Next, we phenotyped clinically relevant missense variants associated with immunodeficiency and autoimmunity. Finally, we defined a noncoding variant in a pleiotropic autoimmunity locus that governs TNRC18 expression in primary T cells. STAG-seq thus enables variant phenotyping at scale to advance functional genomics and disease biology.

genomics↗
bioRxiv2024

YnaI exemplifies the diversity of structural gating mechanisms in mechanosensitive channels of small conductance

Osmotically varying environments are challenging for bacterial cells. Sudden drops in osmolytes cause an increased membrane tension and rupture the cells in the absence of protective mechanisms. One family of protective proteins are mechanosensitive channels of small conductance that open in response to membrane tension. Although these channels have a common architecture, they vary widely in the number of transmembrane helices, conductivity, and gating characteristics. Despite of several structures of channels in the open and closed state, the underlying common principles of the gating mechanism are not well understood. Here we show that YnaI opens by radial relocation of the transmembrane sensor paddles together with a shortening of the pore. This contrasts the prototypic smaller MscS which tilts the sensor paddles and retains the pore length. A chimera of both channels with the YnaI sensor paddles and the pore containing C-terminal part of MscS has the conductivity of the pore donor and the tension response of the paddle donor together with the conformational changes of the respective donor. Our research shows that elements with different types of structural rearrangements can be mixed and matched within one channel as long as they support the common area expansion on the periplasmic side.

biochemistry↗
bioRxiv2024

What if...? Computational anatomy in the cerebellar microzone, the middle layer of the cerebellar network

The cerebellum is a large brain structure. Most of the mass and volume of the cerebellum is made up by the cerebellar cortex. The outer layer of the cerebellar cortex is divided functionally into long, thin strips called microzones. We argue that the cerebellar microzone computation is the aggregate of simple unit computations and a passive effect of anatomy, unaided and unlearned, which we recreate in silico. This is likely to polarise opinion. In the traditional view, data processing by the cerebellum (stated very briefly) is the effect of learned synaptic changes. However, this has become difficult to reconcile with evidence that rate information is linearly conserved in cerebellar signalling. We present an alternative interpretation of cell morphologies and network architecture in the light of linear communication. Parallel fibre synaptic memory has a supporting role in the network computation. Lay summaryIt is not fully understood how the cerebellum represents information and uses it to generate motor outputs, and how outputs are coordinated to control movement. We model the cerebellar network computation, with a focus on the microzone computation, the middle layer of the network. The main proposal is the contentious idea that the core computation is a passive and unlearned effect of neuroanatomy, unit functions are linear, and the computation is mathematically unsophisticated. To provide functional context, we propose that the topography of input and output of cerebellar motor circuits could be a functional extension of modular cerebellar wiring which automates motor sequences. To illustrate how that could work, we present a simple model of anguilliform (eel-like) swimming.

neuroscience↗
bioRxiv2023

scDiffEq: drift-diffusion modeling of single-cell dynamics with neural stochastic differential equations

Single-cell sequencing measurements facilitate the reconstruction of dynamic biology by capturing snapshot molecular profiles of individual cells. Cell fate decisions in development and disease are orchestrated through an intricate balance of deterministic and stochastic regulatory events. Drift-diffusion equations are effective in modeling single-cell dynamics from high-dimensional single-cell measurements. While existing solutions describe the deterministic dynamics associated with the drift term of these equations at the level of cell state, diffusion is modeled as a constant across cell states. To fully understand the dynamic regulatory logic in development and disease, models explicitly attuned to the balance between deterministic and stochastic biology are required. To address these limitations, we introduce scDiffEq, a generative framework for learning neural stochastic differential equations that approximate biologys deterministic and stochastic dynamics. Using lineage-traced single-cell data, we demonstrate that scDiffEq offers an improved reconstruction of cell trajectories and prediction of cell fate from multipotent progenitors during hematopoiesis. By imparting in silico perturbations to multipotent progenitor cells, we find that scDiffEq accurately recapitulates the dynamics of CRISPR-perturbed hematopoiesis. We generalize this approach beyond lineage-traced or multi-time point datasets to model the dynamics of single-cell data from a single time point. Using scDiffEq, we simulate high-resolution developmental cell trajectories, which can model their drift and diffusion, enabling us to study their time-dependent gene-level dynamics.

bioinformatics↗
bioRxiv2023

Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland

Fine mapping and bioinformatic analysis of the DDX6-CXCR5 genetic risk association in Sjogrens Disease (SjD) and Systemic Lupus Erythematosus (SLE) identified five common SNPs with functional evidence in immune cell types: rs4938573, rs57494551, rs4938572, rs4936443, rs7117261. Functional interrogation of nuclear protein binding affinity, enhancer/promoter regulatory activity, and chromatin-chromatin interactions in immune, salivary gland epithelial, and kidney epithelial cells revealed cell type-specific allelic effects for all five SNPs that expanded regulation beyond effects on DDX6 and CXCR5 expression. Mapping the local chromatin regulatory network revealed several additional genes of interest, including lnc-PHLDB1-1. Collectively, functional characterization implicated the risk alleles of these SNPs as modulators of promoter and/or enhancer activities that regulate cell type-specific expression of DDX6, CXCR5, and lnc-PHLDB1-1, among others. Further, these findings emphasize the importance of exploring the functional significance of SNPs in the context of complex chromatin architecture in disease-relevant cell types and tissues.

genetics↗
bioRxiv2023

Low-resolution neuronal code: a theory

We present a theory of the inner layer of the cerebellar cortex, the granular layer, where the main excitatory input to the cerebellum is received. We ask how input signals are converted into an internal code and what form that has. While there is a computational element, and the ideas are quantified with a computer simulation, the approach is primarily evidence-led and aimed at experimenters rather than the computational community. Network models are often simplified to provide a noiseless medium for sophisticated computations. We propose, with evidence, the reverse: physiology is highly adapted to provide a noiseless medium for straightforward computations. We find that input data are converted to a hyper low-resolution internal code. Information is coded in the joint activity of large cell groups and therefore has minimum spatial dimensions - the dimensions of a code group. The conversion exploits statistical effects of random sampling. Code group dimensions are an effect of topography, cell morphologies and granular layer architecture. The activity of a code group is the smallest unit of information but not the smallest unit of code - the same information is coded in any random sample of signals. Code in this form is unexpectedly wasteful - there is a huge sacrifice of resolution - but may be a solution to fundamental problems involved in the biological representation of information.

neuroscience↗
bioRxiv2022

Bigger is better: Thicker maize brace roots are advantageous for both strength and nitrogen uptake.

Plant root systems provide critical functions to enable plant survival. From anchoring the plant in the soil to finding and acquiring water and nutrients, these organs are essential for plant productivity. Despite a variety of root functions, research typically focuses on defining only one function. In this study, we explore a trade-off hypothesis, that the optimization of one root function (i.e. anchorage) may negatively impact another root function (i.e. nitrogen uptake). Previous work has demonstrated that larger roots are stronger, but may also have a diminished capacity for nutrient acquisition due to a reduced surface area to volume ratio. Using maize brace roots that had entered the soil, we show here that larger roots are both stronger and take up more nitrogen. Despite this general relationship, there are subtle trade-offs between mechanics and uptake that occur when assessing individual genotypes. These trade-offs represent an opportunity to optimize one root function without compromising other root functions. Together these data demonstrate that our original trade-off hypothesis was incorrect for maize brace roots, and that larger roots are both stronger and take up more nitrogen.

plant biology↗
bioRxiv2021

Natural history of nonhuman primates after conjunctival exposure to Ebola virus

Transmission of Ebola virus (EBOV) primarily occurs via contact exposure of mucosal surfaces with infected body fluids. Historically, nonhuman primate (NHP) challenge studies have employed intramuscular or small particle aerosol exposure, which are uniformly lethal routes of infection, but mimic worst-case scenarios such as a needlestick. When exposed by more likely routes of natural infection, limited NHP studies have shown delayed onset of disease and reduced mortality. Here we performed a series of systematic natural history studies in cynomolgus macaques with a range of conjunctival exposure doses. Challenge with 10,000 plaque forming units (PFU) of EBOV was uniformly lethal, whereas 5/6 subjects survived low and moderate dose challenges (100 or 500 PFU). Conjunctival challenge resulted in a protracted time-to death. Asymptomatic disease was observed in survivors with limited detection of EBOV replication. Inconsistent seropositivity in survivors may suggest physical or natural immunological barriers are sufficient to prevent widespread viral dissemination.

microbiology↗
bioRxiv2021

The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations

Data cataloguing viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open collation, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically-maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static datasets and integration of dynamically-updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength are also available in a harmonized format. In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus "species" (of which 1,661 are ICTV ratified), 3,692 resolved vertebrate host species, and 23,147 unique interactions between taxonomically-valid organisms. Together, these data cover roughly a quarter of mammal diversity, a tenth of bird diversity, and ~6% of the estimated total diversity of vertebrates, and a much larger proportion of their virome than any previous database. We show how these data can be used to test hypotheses about microbiology, ecology, and evolution, and make suggestions for best practices that address the unique mix of evidence that coexists in these data.

microbiology↗
bioRxiv2020

Effects of working memory load and CS-US intervals on delay eyeblink conditioning

BackgroundEyeblink conditioning is used in many different species to study motor learning and make inferences about cerebellar function. However, considerable discrepancies in performance between different species combined with evidence that awareness of stimulus contingencies affects performance indicates that eyeblink conditioning in part reflects activity in non-cerebellar regions. This questions whether eyeblink conditioning can be used as a pure measure of cerebellar function in humans. MethodsHere we explored two ways to reduce non-cerebellar influences on performance in eyeblink conditioning: (1) using a short interstimulus interval, and (2) having participants do working memory tasks during the conditioning. Data were analyzed, and the influence of the interstimulus interval and working memory tasks was assessed using a linear mixed effects model. ResultsOur results show that subjects trained with a short interstimulus interval (150ms and 250ms) produce few conditioned responses after 100 trials. For subjects trained with a longer interstimulus interval (500ms), those who did working memory tasks produced fewer conditioned responses and had a more gradual learning curve - more akin to those reported in the animal literature. ConclusionsOur results suggest that having subjects perform working memory tasks during eyeblink conditioning can be a viable strategy to reduce non-cerebellar interference in the learning.

neuroscience↗
bioRxiv2020

Substitutional landscape of a split fluorescent protein fragment

Split fluorescent proteins have wide applicability as biosensors for protein-protein interactions, genetically encoded tags for protein detection and localization, as well as fusion partners in super-resolution microscopy. We have established and validated a novel platform for functional analysis of leave-one-out split fluorescent proteins (LOO-FPs) in high throughput and with rapid turnover. We have screened more than 12,000 strand 10 variants using high-density peptide microarrays for binding and functional complementation in Green Fluorescent Protein. We studied the effect of peptide length and the effect of different linkers to the solid support and mapped the effect of all possible amino acid substitutions on each position as well as in the context of some single and double amino acid substitutions. As all peptides were tested in 12 duplicates, the analysis rests on a firm statistical basis allowing determination of robustness and precision of the method. We showed that the microarray fluorescence correlated with the affinity in solution between the LOO-FP and peptides. A double substitution yielded a peptide with 9-fold higher affinity than the starting peptide.

synthetic biology↗
bioRxiv2020

Quantitative properties of the creation and activation of a cell-intrinsic engram

The conditional pause in the spontaneous firing of the cerebellar Purkinje, which determines the timing of the conditional eyeblink response, is mediated by a cell-intrinsic engram (Johansson, et al. 2014) that encodes the interstimulus interval. Our trial-by-trial analysis of the pause parameters reveals that it consists of a single unusually long interspike interval, whose onset and offset latencies are stochastically independent scalar functions of the interstimulus interval. The coefficients of variation are comparable to those observed in the timing of the overt conditional eyeblink. The onsets of the long interspike interval are step changes; there is no prior build-up of inhibition. A single spike volley in the parallel fiber input triggers the read-out of the engram into the long interspike interval; subsequent volleys have no effect on the pause. The high spontaneous firing rate on which the one-interval firing pause supervenes is markedly non-stationary (Fano factors >> 1).

bioinformatics↗
bioRxiv2019

Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation

Biological and biochemical functions of immunity transcription factor NF-{kappa}B in basal metazoans are largely unknown. Herein, we characterize transcription factor NF-{kappa}B from the demosponge Amphimedon queenslandica (Aq), in the phylum Porifera. Structurally and phylogenetically, the Aq-NF-{kappa}B protein is most similar to NF-{kappa}B p100 and p105 among vertebrate proteins, with an N-terminal DNA-binding/dimerization domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile more similar to human NF-{kappa}B proteins than Rel proteins. Aq-NF-{kappa}B also resembles the mammalian NF-{kappa}B protein p100 in that C-terminal truncation results in translocation of Aq-NF-{kappa}B to the nucleus and increases its transcriptional activation activity. Overexpression of a human or sea anemone I{kappa}B kinase (IKK) can induce C-terminal processing of Aq-NF-{kappa}B in vivo, and this processing requires C-terminal serine residues in Aq-NF-{kappa}B. Unlike human NF-{kappa}B p100, however, the C-terminal sequences of Aq-NF-{kappa}B do not effectively inhibit its DNA-binding activity when expressed in human cells. Tissue of another demosponge, a black encrusting sponge, contains NF-{kappa}B site DNA-binding activity and an NF-{kappa}B protein that appears mostly processed and in the nucleus of cells. NF-{kappa}B DNA-binding activity and processing is increased by treatment of sponge tissue with LPS. By transcriptomic analysis of A. queenslandica we identified likely homologs to many upstream NF-{kappa}B pathway components. These results present a functional characterization of the most ancient metazoan NF-{kappa}B protein to date, and show that many characteristics of mammalian NF-{kappa}B are conserved in sponge NF-{kappa}B, but the mechanism by which NF-{kappa}B functions and is regulated in the sponge may be somewhat different.

cell biology↗