Biology subjects

Gaudinier, A.

Publications and source records attributed to Gaudinier, A..

6 recordsLinked to original sources

bioRxiv2026

SeedMeasure: an efficient approach and open-source program to quantify seed size

PremiseSeed size and morphology are critical traits in agriculture, ecology, and genetics, but high-throughput quantification of these traits is often limited by labor-intensive manual measurements or expensive, platform-specific imaging software. Methods and ResultsWe developed SeedMeasure, a lightweight, open-source, and cross-platform command-line tool written in Python that automates the measurement of seed area, length, and width from images. Using a simple imaging setup, the program processes images by correcting for perspective skew, filtering debris, and exports quantitative data alongside quality-check images. We validated SeedMeasure across nine diverse species, ranging from small Arabidopsis thaliana seeds to large Zea mays kernels. The tool quickly handles images using multithreading and demonstrates high reproducibility, yielding low coefficients of variation across repeated runs. ConclusionsCompared to existing software, SeedMeasure is free, offers faster processing through parallel computing, and provides standalone executables that require no programming dependencies. SeedMeasure offers an accessible, cost-effective, and high-throughput approach for rapid phenotypic profiling, making advanced seed morphological analysis available to researchers without specialized laboratory hardware.

Plant Biology↗

bioRxiv2026

Quenching corrinoid-based interactions in a model bacterial coculture.

Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents one attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite quenching strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti, a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid and show that BtuG specifically blocks corrinoid-dependent growth. We use this tool to calculate the amount of cobalamin released by S. meliloti cells and find that the cobalamin release rate is dependent on the growth phase of the producer, increasing to a maximum of approximately 40 cobalamin molecules per minute per cell in late exponential phase. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity molecular sponges to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and empower precision microbiome manipulation strategies.

microbiology↗

bioRxiv2023

Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation

Nitrogen (N) is an essential macronutrient and its bioavailability plays a major role in how plant development is tuned to environmental nutrient status. To find novel factors in early root system architecture responses to N conditions, we performed Arabidopsis thaliana root transcriptome profiling of a short-term time course in limiting and sufficient N conditions. Using this data, we inferred transcriptional regulatory networks in each condition, which revealed the N-condition specific responses of jasmonate regulation; transcriptional factor (TF) ERF107 plays a more generalized role in lateral root development while TF LBD13 is specific to N-limiting conditions. Further, we used a single cell LR cell-type specific transcriptome dataset to model and analyze the roles of TFs LBD13, ERF107, and PDF2 in early stages of LR development. Linking the N time course transcriptomics, LR mutant phenotypes, and cell-type specific single cell profiling, these approaches provide multiple lines of evidence to find and test the roles of TFs that are involved in early root patterning responses to N conditions.

plant biology↗

bioRxiv2023

Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits

Nitrogen is an essential element for all life processes in plants. As such, plant roots dynamically respond to nitrogen availability below-ground by executing a signaling and transcriptional cascade resulting in altered plant growth, optimized for nutrient uptake. The NIN-LIKE PROTEIN 7 (NLP7) transcription factor senses nitrogen and along with its closely related paralog NLP6, partially coordinates these transcriptional responses. While post-translational regulation of NLP6/7 is well established, its upstream transcriptional regulation remains understudied in Arabidopsis and other plant species. Here, we dissect a previously identified sub-circuit upstream of NLP6/7 in Arabidopsis and which was predicted to contain multiple multi-node feedforward loops suggestive of an optimized design principle of nitrogen transcriptional regulation. This sub-circuit comprises AUXIN RESPONSE FACTOR 18 (ARF18), ARF9, DEHYDRATION RESPONSE ELEMENT BINDING-PROTEIN 26 (DREB26), A NAC-DOMAIN CONTAINING PROTEIN 32 (ANAC032), NLP6 and NLP7 and their regulation of NITRITE REDUCTASE 1 (NIR1). Conservation and divergence of this circuit and their influence on N-dependent root system architecture are similarly assessed in Solanum lycopersicum. The specific binding sites of these factors within their respective promoters and their putative cis-regulatory architecture are identified. The direct or indirect nature of these interactions are validated in planta. The resulting models were genetically validated in varying concentrations of available nitrate by measuring the transcriptional output of the network revealing rewiring of nitrogen regulation across distinct plant lineages. Significance StatementNitrogen is a critical nutrient for plant growth and yield. While external N has facilitated modern agriculture, over-application of N-containing fertilizers has drastic ecological and environmental consequences. Here, we experimentally validate a six gene regulatory circuit with extensive feedforward loops identified to act upstream of the critical NIN-LIKE PROTEIN 6/7 transcription factors which regulates a nitrogen metabolic enzyme. Our results indicate conservation and divergence in these circuits between Arabidopsis and tomato despite the similar role of NLP7 in N-dependent changes in root system architecture. The resulting network models complement existing knowledge of NLP7 regulation by providing a framework for targeted transcriptional engineering to increase plant nitrogen use efficiency.

plant biology↗

bioRxiv2021

A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism

In single-celled microbes, transcriptional regulation by single transcription factors is sufficient to shift primary metabolism. Corresponding genome-level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Relative to individual microbes, plant metabolism is more complex. Primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber and medicine, we set out to develop a genome-scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein-DNA interactions between Arabidopsis thaliana transcription factors and promoters of primary metabolism and specialized metabolism were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the TCA cycle. The resulting network suggests that plant metabolic design principles are distinct from that of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental- and stress-conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants.

systems biology↗

bioRxiv2018

A single cis-element that controls cell-type specific expression in Arabidopsis

C4 photosynthesis evolved repeatedly from the ancestral C3 state, improving photosynthetic efficiency by ∼50%. In most C4 lineages photosynthesis is compartmented between mesophyll and bundle sheath cells but how gene expression is restricted to these cell types is poorly understood. Using the C3 model Arabidopsis thaliana we identified cis-elements and transcription factors driving expression in bundle sheath strands. Upstream of the bundle sheath preferentially expressed MYB76 gene we identified a region necessary and sufficient for expression containing two cis-elements associated with the MYC and MYB families of transcription factors. MYB76 expression is reduced in mutant alleles for each. Moreover, down-regulated genes shared by both mutants are preferentially expressed in the bundle sheath. Our findings are broadly relevant for understanding the spatial patterning of gene expression, provide specific insights into mechanisms associated with evolution of C4 photosynthesis and identify a short tuneable sequence for manipulating gene expression in the bundle sheath.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗