Biology subjects

Watt, M.

Publications and source records attributed to Watt, M..

10 recordsLinked to original sources

bioRxiv2025

Systems-level Plant Responses Reveal Pseudomonas-Mediated Growth Promotion in Brachypodium Under Nitrogen Limitation

Plant molecular adaptation to plant growth promoting bacteria (PGPB) under nutrient stress remains unclear, yet is essential for advancing PGPB use in agriculture. The model grass Brachypodium dystachion was studied together with Pseudomonas koreeensis (Pk) at two nitrogen (N) conditions. Non-invasive shoot phenotyping showed an immediate response to low-N, while beneficial effects of Pk became quantifiable after day 19. Increased N content in inoculated plants, along with Pks ability to grow on N-free media, suggests bacterial N contribution at deficient N. In low-N conditions, Pk-inoculated plants showed 33.2% more N than uninoculated controls and biomass comparable to high-N plants. Pk had no effect under sufficient N. Proteomics and lipidomics revealed that lipid profiles were primarily shaped by N availability, while protein abundance responded to both Pk and N status. Inoculated low-N plants displayed protein profiles resembling those of high-N controls, with some distinct exceptions. The plant-microbe interaction is dynamic and developed over 3 weeks, leading to increased biomass and N content. Root proteins strongly induced by Pk under low-N included lipid degradation enzymes, N transporters, and regulatory proteins, suggesting a coordinated remodelling of energy metabolism supporting whole-plant biomass and increased abundance of N uptake proteins.

plant biology↗

bioRxiv2025

Amyloid-beta pathology increases synaptic engulfment by glia in feline cognitive dysfunction syndrome: A naturally occurring model of Alzheimer's disease

Feline cognitive dysfunction syndrome (CDS) is an age-related neurodegenerative disorder, comparable to dementia in people, characterised by behavioural changes such as increased vocalisation, altered social interactions, sleep-wake cycle, disorientation and house-soiling. Although the underlying mechanisms remain poorly understood, pathologies similar to those observed in Alzheimers disease (AD), have been identified in the brains of aged or CDS-affected cats, including brain atrophy, neuronal loss, amyloid-beta plaques, tau pathology, and cerebral amyloid angiopathy. Neuroinflammation and synapse loss, other important hallmarks of AD, may also play important roles in feline ageing and CDS, but these are yet to be explored. Several mechanisms of synapse loss have been described in human AD and mouse models of amyloidopathy, including synaptic accumulation of amyloid-beta, and the aberrant induction of synaptic engulfment by microglia and astrocytes. In this study, immunohistochemistry and confocal microscopy were used to examine the parietal cortex of young (n=7), aged (n=10), and CDS-affected (n=8) cats. Linear mixed effect modelling revealed that amyloid-beta accumulates within synapses in the aged and CDS-affected brain. Additionally, in the aged and CDS groups there was microgliosis, astrogliosis and increased synaptic engulfment by microglia and astrocytes in regions with A{beta} plaques. Further, microglia and astrocytes show increased internalisation of amyloid-beta-containing synapses near plaques. These findings suggest that amyloid-beta exerts a pathogenic effect in the feline brain, with mechanisms mirroring those seen in human AD.

neuroscience↗

bioRxiv2024

Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

microbiology↗

bioRxiv2023

Disrupting the interaction between AMBRA1 and DLC1 is a promising therapeutic strategy for neurodegeneration that prevents apoptosis while enhancing autophagy and mitophagy

Activating molecule in Beclin1-regulated autophagy (AMBRA1) has critical roles in autophagy, mitophagy, cell cycle regulation, neurogenesis and apoptosis. Dysregulation of these processes are hallmarks of various neurodegenerative diseases and therefore AMBRA1 represents a potential therapeutic target. The flexibility of its intrinsically disordered regions allows AMBRA1 to undergo conformational changes and thus perform its function as an adaptor protein for various different complexes. Understanding the relevance of these multiple protein-protein interactions will allow us to gain information about which to target pharmacologically. To compare potential AMBRA1 activation strategies we have designed and validated several mutant constructs (ACTA, TAT, WD40 and S1014) in addition to characterising their effects on proliferation, apoptosis, autophagy and mitophagy in SHSY5Y cells. AMBRA1TAT, which is a mutant form of AMBRA1 that cant interact with dynein light chain (DLC)1 at the microtubules, produced the most promising results. Indeed, overexpression of this mutant protected cells against apoptosis and induced autophagy and mitophagy in SHSY5Y cells in addition to enhancing the switch from quiescence to proliferation in mouse neural stem cells. Future studies should focus on designing compounds that inhibit the protein-protein interaction between AMBRA1 and DLC1 and thus have potential to be used as a drug strategy to treat neurodegeneration.

cell biology↗

bioRxiv2022

pGG-PIP: A GreenGate (GG) entry vector collection with Plant Immune system Promoters (PIP)

The regulatory sequences controlling the expression of a gene (i.e., the promoter) are essential to properly understand a genes function. From their use in mutant complementation assays, to studying their responsiveness to different stimuli via transcriptional reporter lines or using them as proxy for the activation of certain pathways, assays using promoter sequences are valuable tools for insight into the genetic architecture underlying plant life. The GreenGate (GG) system is a plant-specific variant of the Golden Gate assembly method, a modular cloning system that allows the hierarchical assembly of individual donor DNA fragments into one expression clone via a single reaction step. Here, we present a collection of 75 GG entry vectors carrying putative regulatory sequences for Arabidopsis thaliana genes involved in many different pathways of the plant immune system, designated Plant Immune system Promoters (PIP). This pGG-PIP entry vector set enables the rapid assembly of expression vectors to be used for transcriptional reporters of plant immune system components, mutant complementation assays when coupled with coding sequences, mis-expression experiments for genes of interest, or the targeted use of CRISPR/Cas9 genome editing. We used pGG-PIP vectors to create fluorescent transcriptional reporters in A. thaliana and demonstrated the potential of these reporters to image the responsiveness of specific plant immunity genes to infection and colonization by the fungal pathogen Fusarium oxysporum. Using the PLANT ELICITOR PEPTIDE (PEP) pathway as an example, we show that several components of this pathway are locally activated in response to colonization by the fungus.

plant biology↗

bioRxiv2022

Spatially distinct phytohormone responses of individual Arabidopsis thaliana root cells to infection and colonization by Fusarium oxysporum

Jasmonic acid (JA), ethylene (ET) and salicylic acid (SA) are the three major phytohormones coordinating a plants defense response to pathogenic attack. While JA and ET are assumed to primarily control the defense against necrotrophic pathogens, SA-induced defense responses target mainly biotrophic microbes, and can include drastic measures such as programmed cell death as part of the plants hypersensitive response (HR). Fusarium oxysporum is a hemibiotrophic fungal pathogen of several plant species, including many important food crops, and the model plant species Arabidopsis thaliana. Colonization of the plants root vascular tissue by the fungus eventually results in wilting and plant death. A general role for JA, ET and SA in combating infection and colonization of the plant by F. oxysporum has been demonstrated, but their distinct roles and modes of action have so far not been described. Here, using high resolution microscopy with fluorescent marker lines of A. thaliana roots infected with F. oxysporum we show that SA acts spatially separate from JA, in a distinct set of root cells immediately neighboring the fungal colonization site. There, SA induces HR to stop the spread of colonization. JA acts in a different, but also clearly defined set of cells, slightly removed from the colonization site, where it initiates a defense response to actively resist the invader. ET is activated in a stretch of cells that covers both, the cells with activated SA and JA signaling, and may be involved in creating these two distinct zones. These results show how the three phytohormones act together, but spatially and functionally separate from each other, to fight this hemibiotrophic pathogen. Such a high-resolution analysis to resolve the plants immune response to pathogenic infection on an individual cell level and in intact tissue has so far been lacking. Graphical AbstractO_LIColonization of the A. thaliana root tip by F. oxysporum strain Fo5176 leads to immediate cell death of the colonized and surrounding tissue. C_LIO_LIAs the colonization front progresses through the vasculature, the cell death front moves along with it through not only the vasculature, but also the surrounding tissues. C_LIO_LIWRKY70 positively regulates salicylic acid (SA) biosynthesis in cells immediately adjacent to the colonized tissue, inducing a hypersensitive response (HR), thereby killing off the cells deemed lost to the intruder, establishing the cell death front. C_LIO_LISlightly further removed from the HR zone, WRKY11 induces jasmonate (JA) biosynthesis in cells of the vasculature to launch a defense response aimed at actively repelling the fungus. C_LI O_FIG O_LINKSMALLFIG WIDTH=122 HEIGHT=200 SRC="FIGDIR/small/521292v2_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1bd280forg.highwire.dtl.DTLVardef@191052aorg.highwire.dtl.DTLVardef@1ea43acorg.highwire.dtl.DTLVardef@100ecdb_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2021

Variation in root system architecture among the founder parents of two 8-way MAGIC wheat populations for selection in breeding

Root system architecture (RSA) is a target for breeding because of the interest to develop crops with roots that use nutrients and water more effectively. Breeding for RSA requires phenotypic diversity in populations amenable to QTL identification to provide markers for large breeding programs. This study examined the variation for root traits across the parents of two multi-parent advanced generation inter-cross (MAGIC) wheat populations from NIAB and CSIRO for 16 days in an upgraded version of the non-invasive, germination paper-based phenotyping platform, GrowScreen-PaGe. Across all parents, total root length varied up to 1.90 fold, root biomass 2.25 fold and seminal root angle 1.16 fold. The CSIRO parents grew faster, exhibited slightly wider seminal root angle and produced larger root systems compared to NIAB parents. Lateral root lengths, leaf lengths and biomass contrasted most between fastest (Robigus - NIAB and AC Barrie - CSIRO) and slowest growing parents (Rialto - NIAB and G204 Xiaoyan54 - CSIRO). Lengths of lateral and total root, and leaf number and length had moderate to high heritability (0.30-0.67) and repeatability. Lengths of lateral roots and leaves are good targets for enhancing wheat crop establishment, a critical stage for crop productivity.

plant biology↗

bioRxiv2020

Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply

The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with 67Zn isotope revealed whole plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1893 zinc-responsive genes. Multiple ZIP transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.

plant biology↗

bioRxiv2019

Resolution of the proteome, transcript and ionome dynamics upon Zn re-supply in Zn-deficient Arabidopsis

O_LIRegulation of plant Zn acquisition is poorly understood, while Zn deficiency affects over 2 billion people worldwide. We therefore dissected the dynamic response to changes in Zn supply in Arabidopsis. C_LIO_LIHydroponically-grown Zn starved plants were re-supplied with Zn. Subsequent time-resolved sampling strategy allowed concomitant quantification of the dynamics of Zn uptake, microsomal and soluble proteins, and specific transcripts, in space (roots and shoots) and time. C_LIO_LIZn accumulates in roots within 10min, but 8h are needed before shoot Zn increases. By 8h, root Zn concentration was ~60% of non-starved plants. Overexpressed root Zn transporters further peaked in 10-30min post re-supply, before reaching a minimum in 120min and 200 ppm Zn. Zn-responding signaling/regulatory molecules include receptor and MAP kinases, calcium signaling proteins, phosphoinositides, G-proteins, COP9 signalosome members, as well as multiple transcription factors. C_LIO_LIZn acquisition is a highly controlled dynamic process. Our study identifies novel players in Zn homeostasis and points to cross-talk with other nutrients. It paves the way for directed investigation of so far omitted candidates which dynamically respond to sudden changes in Zn supply but are expressed at similar levels at steady-state Zn deficiency and sufficiency. C_LI

plant biology↗

bioRxiv2018

Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

O_LIThere is a dynamic reciprocity between plants and their environment: On one hand, the physiochemical properties of soil influence plant morphology and metabolism, while on the other, root morphology and exudates shape the environment surrounding roots. Here, we investigate both of these aspects as well as the reproducibility of these responses across laboratories.\nC_LIO_LIThe model grass Brachypodium distachyon was grown in phosphate-sufficient and phosphate-deficient mineral media, as well as in sterile soil extract, within fabricated ecosystem (EcoFAB) devices across four laboratories.\nC_LIO_LITissue weight and phosphate content, total root length, root tissue and exudate metabolic profiles were found to be consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct in all laboratories, with root hairs four times longer compared to other growth conditions. Further, plants depleted half of the investigated metabolites from the soil extract.\nC_LIO_LITo interact with their environment, plants not only adapt morphology and release complex metabolite mixtures; they also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high inter-laboratory reproducibility, demonstrating that their value in standardized investigations of plant traits.\nC_LI

plant biology↗