Biology subjects

Henriksen, A.

Publications and source records attributed to Henriksen, A..

5 recordsLinked to original sources

bioRxiv2026

Novel approaches to quantify defective interfering particle activity reveal a surrogate marker of interference in mammarenaviruses

Defective interfering particles (DIPs) profoundly influence viral replication and host responses yet it remains difficult to quantify their activity routinely in the laboratory. Here, using lymphocytic choriomeningitis virus (LCMV) as a model mammarenavirus, we establish complementary approaches for measuring interfering activity of DIPs across a range of experimental scales. First, we optimized plaque- and focus-based interference assays that directly quantify DIP-mediated suppression of standard infectious virus replication through a modified neutralization assay. Second, in cell monolayers saturated with both DIPs and infectious particles, we identified a complete loss of expression of the viral glycoprotein and matrix protein, which are each encoded in the positive-sense orientation of the mammarenavirus genome. Notably, this loss of protein expression mirrors the inhibition of plaque formation traditionally seen in this high DIP setting. The observed DIP-mediated loss of glycoprotein expression is a surrogate marker of interference and was used to develop an alternative assay of DIP activity. This glycoprotein expression assay recapitulated interference detected in traditional high-titer plaque assays (i.e. loss of plaques when all cells are saturated with DIPs and infectious particles) while substantially increasing scalability. These approaches enable sensitive and scalable quantification of DIP activity for LCMV as well as Junin virus and expand our experimental toolkit for studying arenavirus population dynamics, pathogenesis and immunity, and may help advance DIP-based antiviral strategies. This study also provides mechanistic details on how mammarenavirus DIPs interfere with infectious virus propagation.

microbiology↗

bioRxiv2026

Development and validation of two economical and flexible immunoassays for detecting antibodies against LCMV in mouse serum

Measurement of antibody responses to viral infection is essential for surveillance, diagnostics, epidemiological research, and natural history of infection studies. However, current methods to detect virus-specific antibodies are often resource-intensive and impractical for deployment in outbreak settings or in field-based studies. This manuscript presents two economical, high-throughput immunoassays--the cytoblot immunoassay (CBA) and strip immunoblot assay (SIA)--for detecting and quantifying anti-lymphocytic choriomeningitis mammarenavirus (LCMV) antibodies in mouse serum. To validate, we tested serum from acutely or persistently experimentally infected mice. Both assays detected LCMV-specific IgG and IgM antibodies with high sensitivity and specificity across multiple timepoints. By facilitating the study of immune responses in rodent reservoirs, these tools can enhance our understanding of zoonotic viral transmission, provide scalable platforms for outbreak preparedness, and serve as adaptable models for the development of rapid serological assays for other viral pathogens.

microbiology↗

bioRxiv2025

Rule-based mitigation of charge asymmetry-triggered monoclonal antibody self-assembly

In a pharmaceutical setting, understanding the factors governing monoclonal antibody (mAb) attractive interactions in formulations is highly warranted as many solution phenomena such as liquid-liquid phase separation (LLPS) result from their preferential self-interaction. While the effect of locally accumulated charge in the variable region has been recognized as an important factor in mediating non-specific mAb self-assembly, the effect of charge asymmetry, i.e. the distribution of oppositely charges residues, has been much less studied experimentally. Moreover, most studies restrict such analyses to the variable region of mAbs, leaving out possible contributions from the constant region of the molecule to the observed sticky behavior. Hence, the aim of this work is to correlate the charge asymmetry over the entire mAb surface to the extent of attractive self-interaction. To do so, we selected three mAbs with distinct solvent exposed surface distribution of charged residues, for which we computationally assessed the charge asymmetry and defined an apparent molecular stickiness ranking. We then tested this ranking experimentally by evaluating their ability to engage in attractive self-interaction as a function of mAb concentration and ionic strength. Experimental data included a combination of small-angle X-ray scattering, dynamic light scattering and micro-flow imaging. We show that the mAbs with oppositely charged Fab and Fc domains are characterized by overall attractive protein-protein interactions in solution amounting to diverse sub-visible morphologies, which vary non-linearly with mAb concentration and ionic strength. As a proof of concept, we also report the absence of any of such assemblies for the mAb with like-charged Fab and Fc domains, resulting in an overall repulsive behavior in solution. Altogether, we show how to utilize charge distribution analyses of full-length mAbs to rationally develop formulations that prevent problematic self-assembly. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/686261v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1c29a4dorg.highwire.dtl.DTLVardef@120644borg.highwire.dtl.DTLVardef@1989b61org.highwire.dtl.DTLVardef@12720_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Prediction of Antibody Non-Specificity using Protein Language Models and Biophysical Parameters

The development of therapeutic antibodies requires optimizing target binding affinity and pharmacodynamics, while ensuring high developability potential, including minimizing non-specific binding. In this study, we address this problem by predicting antibody non-specificity by two complementary approaches: (i) antibody sequence embeddings by protein language models (PLMs), and (ii) a comprehensive set of sequence-based biophysical descriptors. These models were trained on human and mouse antibody data from Boughter et al. (2020) and tested on three public datasets: Jain et al. (2017), Shehata et al. (2019) and Harvey et al. (2022). We show that non-specificity is best predicted from the heavy variable domain and heavy-chain complementary variable regions (CDRs). The top performing PLM, a heavy variable domain-based ESM 1v LogisticReg model, resulted in 10-fold cross-validation accuracy of up to 71%. Our biophysical descriptor-based analysis identified the isoelectric point as a key driver of non-specificity. Our findings underscore the importance of biophysical properties in predicting antibody non-specificity and highlight the potential of protein language models for the development of antibody-based therapeutics. To illustrate the use of our approach in the development of lead candidates with high developability potential, we show that it can be extended to therapeutic antibodies and nanobodies.

bioinformatics↗

bioRxiv2020

Moderate prenatal ethanol exposure increases total length of L1 axons in E15.5 mice

Public health campaigns broadcast the link between heavy alcohol consumption during pregnancy and physical, cognitive, and behavioral birth defects; however, they appear less effective in deterring moderate consumption prevalent in women who are pregnant or of childbearing age. The incidence of mild Fetal Alcohol Spectrum Disorders (FASD) is likely underestimated because the affected individuals lack physical signs such as retarded growth and facial dysmorphology and cognitive/behavioral deficits are not commonly detected until late childhood. Sensory information processing is distorted in FASD, but alcohol effects on the development of axons that mediate these functions are not widely investigated. We hypothesize that alcohol exposure alters axon growth and guidance contributing to the aberrant connectivity that is a hallmark of FASD. To test this, we administered alcohol to pregnant dams from embryonic day (E) 7.5 to 14.5, during the time that axons which form the major forebrain tracts are growing. We found that moderate alcohol exposure had no effect on body weight of E15.5 embryos, but significantly increased the length of L1+ axons. Our findings support our hypothesis. Future studies will investigate cellular, molecular, and functional mechanisms that underlie these effects.

developmental biology↗