Biology subjects

de Vries, I.

Publications and source records attributed to de Vries, I..

9 recordsLinked to original sources

bioRxiv2026

Life-history and connectivity shape the viromes of a migratory and river-resident galaxiid

Migration can increase population connectivity and gene flow but may also facilitate pathogen transmission among hosts and habitats. The way life-history strategies shape viral diversity in closely related freshwater fishes remains poorly understood. Here, we used metatranscriptomics to compare the viromes of two fish in the family Galaxiidae with contrasting life-history strategies: amphidromous [i]nanga (Galaxias maculatus) and river-resident Gollum galaxias (Galaxias gollumoides). We analysed 54 pooled libraries derived from 416 individuals collected across 27 sites spanning multiple catchments and fish-passage barriers in southern New Zealand. A total of 13 novel fish-associated viruses were identified from five viral families (Astroviridae, Circoviridae, Coronaviridae, Hepeviridae, and Picornaviridae). Virome composition differed markedly between species, with only a single virus-positive pool detected among [i]nanga, whereas Gollum galaxias harboured 11 novel viruses, with circoviruses dominating the virome. No fish-associated viruses were detected in post-larval juveniles of either species, and alpha diversity did not differ significantly among catchments, sites or positions relative to fish-passage barriers. However, beta diversity analyses revealed significant spatial structuring of viral communities among sites and catchments, indicating localised variation in virome composition. Contrary to our predictions, the migratory species exhibited substantially lower viral diversity than the river-resident species. The absence of detectable viruses in juveniles, combined with the greater viral richness of the longer-lived Gollum galaxias, suggests that host longevity and cumulative environmental exposure may be important drivers of virome assembly. These findings demonstrate that host life-history strategy influences virome composition and reveal unexpectedly low viral diversity in a globally widespread migratory galaxiid, providing new insights into virus-host ecology and connectivity in freshwater fishes.

ecology↗

bioRxiv2026

Co-infections and cryptic pathogens uncovered by metatranscriptomics in New Zealands severe acute respiratory infections

Severe acute respiratory infections (SARI) are a leading cause of hospitalisation and mortality globally. Many SARI cases remain undiagnosed because kit-based PCR diagnostic panels are typically limited to one or a small number of known pathogens and may fail to identify low-abundance infections or novel, poorly characterised organisms. Here, we used metatranscriptomic sequencing to profile the total infectome of 300 PCR-negative SARI nasopharyngeal samples collected through sentinel hospital-based surveillance in New Zealand between 2014-2021. Our analysis revealed actively transcribing potential pathogens in 43% of SARI cases, comprising 10 RNA viruses, three DNA viruses, nine bacterial species and four fungal species. Notably, co-infections occurred in 26% of cases, revealing polymicrobial infections missed by routine diagnostics. Human rhinoviruses were the most frequently identified, despite not being detected by PCR, and multiple common-cold coronaviruses, human parechovirus A1 and parainfluenza virus type 4, were identified, although these were not included in the PCR screening panel. We also detected a range of bacterial and fungal species and uncovered highly expressed virulence and antimicrobial resistance genes. Infectome composition and diversity were shaped by key demographic and epidemiological factors, with strongest effects observed for age and year of sample collection, indicating that host characteristics and temporal dynamics influence both microbial richness and community structure. These findings highlight the limitations of current diagnostic strategies and the value of metatranscriptomics for comprehensive microbial identification. Integrating such genomic approaches into both clinical and public health frameworks could improve diagnostic accuracy, enabling more sensitive detection and characterisation of potential pathogens while also strengthening surveillance and outbreak response.

genomics↗

bioRxiv2025

Foraging ecology drives viral community structure in New Zealand's aquatic birds

Wild migratory birds play a major role in the global spread of viruses, yet the diversity, host range and transmission patterns of viruses harboured by migratory species in Aotearoa/New Zealand remain largely unknown. This knowledge gap is critical given New Zealands position along major migratory flyways spanning Oceania, Antarctica and east Asia, where understanding viral diversity is key to assessing the risk of viral introductions such as highly pathogenic avian influenza virus and viral dispersal across these regions. To address this, we conducted the first large-scale metatranscriptomic survey of wild birds from New Zealand and its subantarctic islands, collecting 1,348 samples from 31 host species spanning four avian orders. We identified 118 avian viruses from 17 families, including 107 novel species, greatly expanding our knowledge of avian viral diversity. Viral communities differed significantly by host order and foraging behaviour, with scavenger birds harbouring more diverse viromes than non-scavengers. Although no HPAI subtypes were detected, we recovered a low-pathogenic avian influenza A/H1N9 virus from red knots (Calidris canutus) and a divergent tobanivirus from Auckland Island teal (Anas aucklandica), the first putative avian member of the Tobaniviridae. Notably, we detected 12 mammalian-associated viruses, primarily in scavenger birds, including Hedgehog hepatovirus, Rabbit haemorrhagic disease virus 2, and sea lion astroviruses, with mammalian host reads confirming their dietary origin. This study establishes the first virome baseline for New Zealands migratory birds, highlighting the ecological role of foraging in shaping viral communities and improving regional preparedness for HPAI and other emerging avian pathogens.

microbiology↗

bioRxiv2025

Halogen bonds between ligands and proteins: can we use them in validation?

Halogen bonds are polar interactions between a halogen atom and its acceptor. They have characteristic geometry induced by the positively charged {sigma}-hole on the halogen atom. Despite their importance in drug development, halogen bonds are often overlooked in the analysis and validation of ligand-protein complexes. We analysed halogen bonds between ligands and proteins in structure models from the PDB-REDO databank and defined key geometric parameters. These are the donor-acceptor distance, and two bond angles ({theta}1 and {theta}2) for interatomic halogen bonds, or in the case of halogen-{pi} interactions, the distance between the halogen and acceptor {pi}-system and a bond angle ({theta}1). Based on the distribution of these geometric parameters, we introduce a score, HalBS, that marks whether halogen bonds are adopting the preferred or allowed geometry or are an outlier and should be examined critically. A reference implementation of this score is now available in PDB-REDO. This is a first step towards improving halogen bond treatment in the analysis of macromolecular structure models.

biochemistry↗

bioRxiv2025

Chemotaxis of branched cells in complex environments

Cell migration in vivo is often guided by chemical signals. Such chemotaxis, such as performed by immune cells migrating to a wound site, is complicated by the complex geometry inside living tissues. In this study, we extend our theoretical model of branched-cell migration on a network by introducing chemokine sources to explore the cellular response. The model predicts a speed-accuracy tradeoff, whereby slow cells are significantly more accurate and able to follow efficiently a weak chemoattractant signal. We then compare the models predictions with experimental observations of neutrophils migrating to the site of laser-inflicted wound in a zebrafish larva fin, and migrating in-vitro inside a regular lattice of pillars. We find that the model captures the details of the sub-cellular response to the chemokine gradient, as well as the large-scale migration response. This comparison suggests that the neutrophils behave as fast cells, compromising their chemotaxis accuracy, which explains the functionality of these immune cells.

biophysics↗

bioRxiv2024

Disentangling the CHAOS of intrinsic disorder in human proteins

Most proteins consist of both folded domains and Intrinsically Disordered Regions (IDRs). However, the widespread occurrence of intrinsic disorder in human proteins, along with its characteristics, is often overlooked by the broader communities of structural and molecular biologists. Building on the MobiDB database of intrinsic disorder in proteins, here we develop a comprehensive dataset (Comprehensive analysis of Human proteins And their disOrdered Segments - CHAOS). We implement internally consistent definitions of disordered regions, and annotate general characteristics such as cellular location, essentiality, post-translational modifications, and predicted pathogenicity. Further, we cross-reference to structure predictions from AlphaFold. We find that most human proteins contain at least one disordered region, predominantly located at the protein termini. IDRs are less hydrophobic, enriched in post-translational modifications, and mutations in IDRs are predicted to be less pathogenic than in non-IDRs. Additionally, we discovered that proteins residing in different cellular locations possess distinct disorder profiles. Finally, the predicted AlphaFold models of proteins in CHAOS suggest that disordered regions and proteins are often predicted to adopt secondary structure. Hereby we enhance the visibility and understanding of intrinsic disorder in human proteins. Key messagesO_LIFour out of five human proteins contain one or more intrinsically disordered regions (IDRs). C_LIO_LIHalf of the IDRs are located at protein termini, but three quarters of all human proteins contain a terminal IDR. C_LIO_LIThe amount and location of disordered regions differs throughout cellular compartments. C_LIO_LIOne in five missense mutations in IDRs are likely pathogenic. C_LIO_LIAlphaFold predicts secondary structure elements within intrinsically disordered regions and fully disordered proteins. C_LI

bioinformatics↗

bioRxiv2024

Avian influenza virus surveillance across New Zealand and its subantarctic islands detects H1N9 in migratory shorebirds, but not 2.3.4.4b HPAI H5N1

Highly pathogenic avian influenza (HPAI) virus has never been detected in New Zealand. The potential impact of this virus on New Zealands wild birds would be catastrophic. To expand our knowledge of avian influenza viruses across New Zealand, we sampled wild aquatic birds from New Zealand, its outer islands and its subantarctic territories. Metatranscriptomic analysis of 700 individuals spanning 33 species revealed no detection of HPAI during the annual 2023-2024 migration. A single detection of H1N9 in red knots (Calidris canutus) was noted. This study provides a baseline for expanding avian influenza virus monitoring in New Zealand.

microbiology↗

bioRxiv2023

Distant sequence regions of JBP1 contribute to J-DNA binding

Base-J ({beta}-D-Glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J Binding Protein 1 (JBP1), that has a thymidine hydroxylase domain (THD) and a J-DNA binding domain (JDBD). How the THD synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for Molecular Dynamics (MD) simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. A high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.

biochemistry↗

bioRxiv2021

Mechanosensitivity of amoeboid cells crawling in 3D

Efficient immune-responses require migrating leukocytes to be in the right place at the right time. When crawling through the body amoeboid leukocytes must traverse complex three-dimensional tissue-landscapes obstructed by extracellular matrix and other cells, raising the question how motile cells adapt to mechanical loads to overcome these obstacles. Here we reveal the spatio-temporal configuration of cortical actin-networks rendering amoeboid cells mechanosensitive in three-dimensions, independent of adhesive interactions with the microenvironment. In response to compression, Wiskott-Aldrich syndrom protein (WASp) assembles into dot-like structures acting as nucleation sites for actin spikes that in turn push against the external load. High precision targeting of WASp to objects as delicate as collagen fibers allows the cell to locally and instantaneously deform its viscoelastic surrounding in order to generate space for forward locomotion. Such pushing forces are essential for fast and directed leukocyte migration in fibrous and cell-packed tissues such as skin and lymph nodes. In BriefWASp-driven actin spikes counter compressive loads of crowded tissue-landscapes.

cell biology↗