Biology subjects

van den Berg, N.

Publications and source records attributed to van den Berg, N..

6 recordsLinked to original sources

bioRxiv2025

The avocado pangenome reveals dynamic clustering and lineage-specific diversity of NLR genes

Avocado is an economically important perennial tree crop with a complex domestication history, yet modern genomic resources are limited. We present the first high-quality avocado pangenome, spanning seven diverse accessions across Mexican, Guatemalan, and West-Indian lineages. PacBio HiFi, partially phased assemblies deliver near chromosome-level continuity (N50 ~57 Mb; BUSCO >96%), and functional annotations show enrichment of immune-related families. Core-accessory partitioning indicates adaptive functions -- pathogen response and secondary metabolism -- are overrepresented in accessory genes. Nucleotide-binding Leucine-rich repeat (NLR) genes were catalogued (226-256 per accession), showing lineage-specific expansions, diverse domain architectures, and frequent chromosomal clustering. Structural variants concentrate within NLR loci, marking hotspots of pathogen-detection diversification. Comparative analyses show ~54% of NLRs are shared, with extensive functional and sequence diversity among accessions. Together, these results define the avocado NLRome and its core- accessory interplay, providing a graph-based framework to accelerate discovery of resistance loci and breeding for durable disease resistance.

plant biology↗

bioRxiv2024

What NLR you recognizing? Predicted binding affinities- and energies may be used to identify novel NLR-effector interactions

Nucleotide binding Leucine-rich repeat (NLR) proteins play a crucial role in effector recognition and activation of Effector triggered immunity in plants following pathogen infection. Advances in genome sequencing have led to the identification of a myriad NLRs in numerous agriculturally important plant species. However, deciphering which NLR proteins recognize specific pathogen effectors remains a challenge. Predicting NLR-effector interactions in silico would provide a more targeted approach for experimental validation, critical for elucidating function, and advancing our understanding of NLR-triggered immunity. In this study, NLR-effector protein complex structures were predicted using AlphaFold2-Multimer for all experimentally validated NLR-effector interactions. Binding affinities- and energies were predicted using 97 machine learning models from Area-affinity. We show that predicted structures with an AlphaFold confidence score > 0.42 have acceptable accuracy, and can be used to investigate NLR-effector interactions in silico. Binding affinities for 58 NLR-effector complexes ranged between -8.5 and -10.6 log(K), and binding energies between -11.8 and -14.4 kcal/mol, depending on the Area-Affinity model used. For 2427 "forced" NLR-effector complexes, these estimates showed larger variability, enabling the identification of novel NLR-effector complexes with 99% accuracy using an Ensemble machine learning model. The narrow range of binding energies- and affinities for true interactions suggest a specific change in Gibbs free energy, and thus conformational change, is required for NLR activation. This is the first study to provide a method for predicting NLR-effector interactions, applicable to all plant-pathogen interactions. Finally, the NLR-Effector Interaction Classification (NEIC) resource can streamline research efforts by identifying NLRs important for providing resistance against plant pathogens, advancing our understanding of plant immunity.

plant biology↗

bioRxiv2024

Cell aspect ratio is a mechanical winning strategy in microbial competition

Bacterial competition shapes community architecture, yet a universally conserved determinant remains elusive. We show that cell aspect ratio -a simple morphological feature- confers a competitive advantage. Using growth-based range expansion experiments, we show that longer bacteria conquer the expanding front, even when initially in minority. Using an agent-based model of dividing bacteria, to isolate the effect of aspect ratio, we reveal that the takeover mechanism is collective alignment: groups of locally aligned bacteria form "nematic arms" bridging the central region of the colony to the expanding front. Once at the front, bacteria align parallel to it and block shorter bacteria from access to nutrients and space. We confirm this observation with single-cell experiments and further generalise our findings by introducing a generic continuum model of alignment-dominated competition, explaining both experimental and cell-based model observations. Moreover, we extend our predictions to spherical range expansions and confirm the competitive advantage, even though the effect is less pronounced than in surface-attached colonies. Our results uncover a simple, yet hitherto overlooked, mechanical mechanism determining the outcome of bacterial competition, which is potentially ubiquitous among various bacteria. Current advances in genetic engineering enable aspect ratio tuning as a mechanism with broad implications for biofilm control.

biophysics↗

bioRxiv2023

Validating models of TMS effects with concurrent TMS/fMRI

The exact dose and spatial pattern of brain activation induced by transcranial magnetic stimulation (TMS) is of importance to all applications of TMS, both clinical and for investigational use. How TMS coils induce electrical fields has been investigated and validated by several groups, but models of how evoked currents interact with neuronal tissue and where activation is induced have hardly been validated empirically. Here we propose a detailed model of TMS induced currents in the brain building on our previous work on different TMS coil models, taking into account various electromagnetic head tissue properties with finite element modeling and several competing macroscopic models of how brain activation is achieved by the TMS induced electrical field. Importantly, we validate these models using TMS coil discharges administered to the brain of 6 healthy volunteers inside a 3T MRI scanner, while acquiring functional MRI scans at the same time. We conclude that the mere magnitude of the electric field in the cortical gray matter tissue near the stimulation site provides the best metric to predict neuronal activation as measured by BOLD fMRI, whereas models of brain activation taking into account orientation of E-fields with respect to the cortical columns and layers do not (yet) yield better predictions of neuronal activation induced by TMS. This report is relevant for neuronavigated TMS approaches attempting to take into account evoked E-fields and neuronal activation to improve precision of TMS administration for clinical and investigational purposes.

neuroscience↗

bioRxiv2019

Longevity Relatives Count score defines heritable longevity carriers and suggest case improvement in genetic studies

AbstractLongevity loci represent key mechanisms of a life-long decreased mortality and decreased/compressed morbidity. However, identifying such loci is challenging. One of the most plausible reasons is the uncertainty in defining long-lived cases with the heritable longevity trait amongst long-living phenocopies. To avoid phenocopies, family selection scores have been constructed but these have not yet been adopted as state of the art in longevity research. Here we aim to identify individuals with the heritable longevity trait by using current insights and a novel family score based on these insights. We use a unique dataset connecting living study participants to their deceased ancestors covering 37,825 persons from 1,326 five-generational families, living between 1788 and 2019. Our main finding suggests that longevity is transmitted for at least 2 subsequent generations only when at least 20% of all relatives are long-lived. This proves the importance of family data to avoid phenocopies in genetic studies.

genetics↗

bioRxiv2018

Longevity defined as top 10% survivors is transmitted as a quantitative genetic trait: results from large three-generation datasets

Survival to extreme ages clusters within families. However, identifying genetic loci conferring longevity and low morbidity in such longevous families is challenging. There is debate concerning the survival percentile that best isolates the genetic component in longevity. Here, we use three-generational mortality data from two large datasets, UPDB (US) and LINKS (Netherlands). We studied 21,046 unselected families containing index persons, their parents, siblings, spouses, and children, comprising 321,687 individuals. Our analyses provide strong evidence that longevity is transmitted as a quantitative genetic trait among survivors up to the top 10% of their birth cohort. We subsequently showed a survival advantage, mounting to 31%, for individuals with top 10% surviving first and second-degree relatives in both databases and across generations, even in the presence of non-longevous parents. To guide future genetic studies, we suggest to base case selection on top 10% survivors of their birth cohort with equally long-lived family members.

genetics↗