Biology subjects

Strand, A.

Publications and source records attributed to Strand, A..

7 recordsLinked to original sources

bioRxiv2026

Plant cell-based 4D engineered living materials

Engineered living materials (ELMs) seek to bridge the gap between static engineered matter and dynamic biological systems. Photosynthetic ELMs have emerged as a promising route towards autonomous and sustainable material systems; however, they remain largely based on microorganisms or isolated organelles, whereas the potential of living plant cells as multifunctional, adaptive building blocks remains largely unexplored. Here we establish plant cells as a distinct chassis for engineered living materials and demonstrate that their intrinsic metabolic plasticity, cell-wall biochemistry and mechanics can be harnessed to create adaptive, evolvable and programmable materials. Using Arabidopsis thaliana suspension cells and printable pectin-alginate bioinks, we fabricate two- and three-dimensional living materials that support growth, metabolic plasticity and, long-term viability. Non-photosynthetic ELMs undergo light-induced metabolic reprogramming to acquire photosynthetic activity, demonstrating adaptive behaviour, while continuous cell growth dynamically remodels the mechanical properties of the material, enabling evolution of material properties through intrinsic biological processes. We further exploit endogenous cell wall peroxidases to catalyse the biofabrication of conducting polymers, enabling programmable acquisition of electrochemical functionality without genetic modification. By integrating living plant cells with auxetic and honeycomb architectures, we show that biological activity and structural design jointly determine emergent mechanical behaviour, revealing a principle of geometry-dependent biological reinforcement for living mechanical metamaterials. Centimetre-scale plant ELMs retain robust photosynthetic activity, with electron transport rates approaching those of native Arabidopsis tissues despite the absence of leaf architecture. Together, these findings establish plant cells as versatile building blocks for multifunctional living materials and lay the foundation for self-powered autonomous materials with potential applications in soft robotics, bioelectronics, and carbon capture.

bioengineering↗

bioRxiv2026

Identifying Novel Targets of the Stringent Response in Plants and Cyanobacteria using chemoproteomics

Survival in dynamic environments requires photosynthetic organisms to rapidly sense and respond to stress. The stringent response, mediated by the signaling molecule guanosine-3,5-bisdiphosphate (ppGpp), is crucial for acclimation to environmental changes such as darkness and nitrogen limitation. While it has been extensively characterized in heterotrophic bacteria such as Escherichia coli, the molecular mechanisms and regulatory targets of ppGpp in photosynthetic organisms remain less understood. Here, we report large-scale chemoproteomic identification of ppGpp-binding proteins across plant chloroplasts and cyanobacteria, revealing both conserved and novel targets compared to E. coli. In plants, we found that ppGpp regulates pyrimidine metabolism by inhibiting the chloroplastic enzyme aspartate transcarbamoylase (PyrB). In cyanobacteria, we found that ppGpp activates glucose-1-phosphate adenylyltransferase (GlgC) involved in glycogen synthesis, activates citrate synthase (GltA), and induces carboxysome aggregation. These findings expand the known ppGpp regulatory network in photosynthetic organisms and provide a foundation for understanding how ppGpp coordinates adaptation to nutrient and environmental stresses.

systems biology↗

bioRxiv2025

IsoformMapper: A Web Application for Protein-Level Comparison of Splice Variants through Structural Community Analysis

Alternative splicing (AS) plays a key role in numerous cellular processes by enabling the existence of different protein isoforms with potentially different functions and fine-tuning isoform abundance. However, despite its biological importance, tools to compare the domain composition of AS-derived protein isoforms have lagged as they require both structural data and an appropriate methodology for isoform comparison. Recent advances in AI-driven protein structure prediction, particularly AlphaFold2, have made accurate structural determination of splicing isoforms easily accessible, paving the way for new tools to compare their structures and asses the functional consequences of AS at the protein structure level. Here, we present IsoformMapper, a web resource that enables researchers to study alternative splicing at the protein structural level using protein network community analysis, which captures 3D physical interactions between protein regions often missed by traditional domain analysis, allowing comparisons of isoforms across any biological system. As a proof of concept, we used our tool to a case study, in which we studied how GENOMES UNCOUPLED1 (GUN1) dependent retrograde signaling regulates plant de-etiolation through alternative splicing in Arabidopsis. In response to light, we demonstrate that GUN1 regulates the expression of specific spliceosome components, consequently modifying alternative splicing of key genes encoding components essential for establishing of photosynthesis. Additionally, the gun1 mutant showed altered splice variant ratios for PNSL2, CHAOS, and SIG5. Our tool revealed that these isoforms have significantly different protein community structures, illustrating the impact of AS on protein function and demonstrating the practical value of the tool. (247 words) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/641708v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@c006dcorg.highwire.dtl.DTLVardef@1025b07org.highwire.dtl.DTLVardef@1a64bf6org.highwire.dtl.DTLVardef@c512af_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO IsoformMapper enables structural comparison of protein isoforms through a multi-step analysis pipeline. Starting with AlphaFold2 protein structure predictions of splice variants, the method generates weighted network representations for each isoform. The web application processes multiple AlphaFold predictions per isoform, with the conformational variability between predictions represented as weighted edges in the network representation. These networks are then analyzed using the InfoMap community detection algorithm to identify structural communities, ultimately allowing visualization and comparison of protein isoform structures through interactive network displays and alluvial diagrams. The method is applicable to protein isoforms from any biological system, providing comprehensive analysis of alternative splicing consequences at the protein level by examining structural domains as integrated units. This holistic approach enables users to evaluate potential functional differences between isoforms based on their structural organization. C_FIG

bioinformatics↗

bioRxiv2023

Pseudomonas syringae infectivity correlates to altered transcript and metabolite levels of Arabidopsis Mediator mutants

Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16, med18, med25 and cdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in med16 and cdk8, but increased in med25, which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin Camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that MED16, MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infections. HIGHLIGHTPlants need to defend themselves against different types of infections. We show that subunits of the Mediator transcriptional coactivator coordinate metabolic responses of Arabidopsis thaliana to infections by Pseudomonas syringae.

plant biology↗

bioRxiv2022

Arabidopsis mutants representing each of the four Mediator modules reveal unique functions in the transcriptional response to salt stress

Changes in growth environment trigger stress responses in most organisms. The mechanisms mediating these responses are only partly understood and involve signaling pathways and transcription factors. Mediator is a conserved co-regulator complex required for transcriptional regulation of all eukaryotic protein-encoding genes. However, its function in abiotic stress responses is elusive. We here describe global gene expression changes triggered by salt stress in Arabidopsis. To explore the involvement of Mediator in salt stress response we characterized med9, med16, med18, and cdk8 mutants representing each of the four modules of Mediator. Our transcriptome data revealed enrichment of shared and specific cis-elements corresponding to unique transcription factors in promoters of mis-regulated genes for each mutant. We show that individual Mediator subunits interact with specific transcription factors to generate a transcriptional stress response and that the mutant phenotypes support the transcriptome data. med16 and med18, and to some extent cdk8, display defects in abscisic acid and anthocyanin metabolism and we identify signal molecules, transcription factors and target genes involved in these pathways as dysregulated in the Mediator mutants. Our results reveal how signals from different stress response pathways are dependent on and integrated by Mediator subunits to coordinate a functional response to salt stress.

genomics↗

bioRxiv2019

A comparison of humans and baboons suggests germline mutation rates do not track cell divisions

In humans, most germline mutations are inherited from the father. This observation is widely interpreted as resulting from the replication errors that accrue during spermatogenesis. If so, the male bias in mutation should be substantially lower in a closely related species with similar rates of spermatogonial stem cell divisions but a shorter mean age of reproduction. To test this hypothesis, we resequenced two 3-4 generation nuclear families (totaling 29 individuals) of olive baboons (Papio anubis), who reproduce at ~10 years of age on average. We inferred sex-specific mutation rates by analyzing the data in parallel with three three-generation human pedigrees (26 individuals). The mutation rate per generation in baboons is 0.55x10-8 per base pair, approximately half that of humans. Strikingly, however, the degree of male mutation bias is approximately 3:1, similar to that of humans; in fact, a similar male bias is seen across mammals that reproduce months, years or decades after birth. These results echo findings in humans that the male bias is stable with parental ages and cast further doubt on the assumption that germline mutations track cell divisions. Our mutation rate estimates for baboons raise a further puzzle in suggesting a divergence time between apes and Old World Monkeys of 67 My, too old to be consistent with the fossil record; reconciling them now requires not only a slowdown of the mutation rate per generation in humans but also in baboons.

evolutionary biology↗

bioRxiv2016

THE IDENTIFICATION OF SOURCE AND VECTOR OF A PROLIFIC MARINE INVADER

The source and vector of an introduced species inform its ecological and evolutionary history and may guide management that seeks to prevent future introductions. Surprisingly, few studies have successfully used genetic tools to independently inform the specific source and pathway of biological invasions. The ecological history of many introduced species, including their origins and vectors, is often based on suppositions or educated guesses. Here, we used mitochondrial and microsatellite genotyping to trace the invasion of the Asian seaweed Gracilaria vermiculophylla (Rhodophyta) along the three coastlines of the Northern Hemisphere to which it has been introduced: the western coast of North America, eastern coast of the United States and the coasts of Europe and northwest Africa. Analyzing 37 native and 53 introduced sites, we identified the Pacific coastline of northeastern Japan as the ultimate source of the Northern Hemisphere invasion. Coincidentally, most exports of the oyster Crassostrea gigas historically originated from this region and both species often grow in close proximity. Based on genetic signatures, each of the three coastlines likely received thalli directly from Japan, as well as material from another introduced coastline (i.e., a secondary invasion). Our ability to document a source region, which was enabled by a robust sampling of locations and loci that previous studies lacked, reflected strong phylogeographic structure along native coastlines. We suggest Gracilaria vermiculophylla is an important representative example of many species likely exported out of Japan by the oyster trade and its genetic signatures that may be a hallmark of oyster introduction legacies.

evolutionary biology↗