Recent Posts

Nanoscale movements of cellulose microfibrils in primary cell walls ($)

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Cell walls are complex mixtures of cellulose microfibrils, proteins and other materials. Their mechanical properties can be measured and modeled, but it is not always simple to translate these measurements to changes at the molecular level. Zhang et al. used atomic force microscopy to provide an unprecedented…

Nutrient dose-responsive transcriptome changes driven by Michaelis–Menten kinetics underlie plant growth rates (PNAS)

Plants can increase their growth and biomass proportionately to an increase in nutrient dose and, conversely, their growth is limited by limiting nutrients. In this study, Swift et al. explored the molecular underpinnings of the nutrient dose-response phenomenon. The authors first show that nitrogen-dose…

Review: Plant networks as traits and hypotheses: Moving beyond description ($) (TIPS)

In Star Wars Episode 2, Obi Wan identifies the location of a missing planet by walking through a 3D projection of the galaxy. I’ve always hoped that if we obtain enough data and figure out how to display it properly, we’ll “see” what parts are out of place or missing. But getting from simple…

Review: Combinatorial nutrient stresses reveal emergent properties ($) (TIPS)

Plants require at least 14 mineral nutrients to complete their life cycle. These mineral nutrients are unevenly distributed within the soil, and plants have evolved physiological adaptations (changes in root growth, exudation, symbiotic relationships with soil organisms, etc.). to address these nutrient…

Systems Biology of Deetiolation

Upon exposure to light, many leaf and stem cells acquire photosynthetic competence by converting pale etioplasts into green chloroplasts. Deetiolation involves the concerted and synchronized activity of a highly complex biogenesis program. Thylakoid membranes must develop from disassembling prolamellar…

Network paths for nitrogen response in Arabidopsis (Nature Comms)

A goal of systems biology is to study how transcription factors participate in gene regulatory networks (GRN) underlying biological processes. In a recent report, Brooks et al. used network science to uncover how transcription factors mediate the early response to nitrogen (N). Authors identified the…

Review. Multicellular systems biology: Applying network science to plant organ patterning and function (Mol Plant)

I really enjoyed this review article, which very successfully introduces the reader to the why and how of how to apply network science to plant science. Bassel never veers off into abstraction or “math-speak”, but instead roots his explanations in familiar biological or ordinary terms. As an example,…

Global plant–symbiont organization and emergence of biogeochemical cycles resolved by evolution-based trait modelling (Nature Ecol Evol)

Most plants depend on microbial partners (symbionts) to help them take up nutrients from the soil. Lu and Hedin set out to identify how these plant-symbiont partnerships contribute to plant distributions and biogeochemical cycles, using an evolution-based modelling approach. The model takes into account…

Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato

Potato is susceptible to many pathogens. To facilitate breeding programs, Ramšak et al. combined transcriptomic data from potato/virus interactions with a defense network model developed mainly from Arabidopsis. Their model revealed a previously undescribed interaction between ethylene and salicylate…

Review: The spring of systems biology-driven breeding ($) (TIPS)

In this excellent review, Lavarenne et al. provide an accessible introduction to the tools and objectives of gene regulatory network (GRN) analysis. They include a glossary, show diagrams displaying different stages of GRN analysis, and provide links to key papers in which different methods have been…