Recent Posts

From plasmodesma geometry to effective symplasmic permeability through biophysical modelling (eLIFE)

Plasmodesmata are tiny regulated channels that connect adjacent plant cells through which nutrients, signaling molecules and viruses can move. To try to resolve discrepancies between functional and structural studies, Deinum et al. have developed a model for plasmodesmatal permeability that predicts…

Machine learning enables high-throughput phenotyping for analyses of the genetic architecture of bulliform cell patterning in maize (G3)

Bulliform cells lie in rows along the upper (adaxial) surface of the maize leaf, and through changes in volume contribute to leaf-rolling, which is a response to water deficit. Several mutants have been identified that affect bulliform cell formation and function, but as yet their occurance in natural…

A virtual nodule environment (ViNE) of metabolic integration during symbiotic nitrogen fixation (bioRxiv)

Genetic and molecular studies have revealed a complex exchange of signals and metabolites accompanying the development and process of symbiotic nitrogen fixation. Clearly, the photosynthesis-capable plant provides fixed carbon to the bacterial symbiont, which uses some of this energy for its core metabolism…

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…

Predicting metabolism during growth by osmotic cell expansion (bioRxiv)

Growth is driven by cell expansion, which is driven by both synthesis of metabolites and osmotically-driven expansion. This latter contribution is typically overlooked in metabolic flux analysis. To remedy this, Shameer et al. have developed a model, GrOE-FBA (Growth by Osmotic Expansion- Flux Balance…

Review: Formal description of plant morphogenesis (J Exp Bot) ($)

In recent years, a number of tools have been developed to describe and model plant morphogenesis, and these approaches have greatly informed our understanding of the molecular processes that underpin the control of growth. This excellent review by Pałubicki et al. is “an attempt to bring together…

Chromatin signature and transcription factor binding provide a predictive basis for understanding plant gene expression (Plant Cell Physiol)

Machine learning is a booming research field, also in Plant Science. Here, Wu et al. use chromatin modifications and transcription factors to predict transcription levels in Arabidopsis and rice. This is not only important for prediction but also to understand the mechanisms underlying epigenetic regulation.…

Modeling crop yield changes due to increased photosynthetic capabilities ($) (Nature Plants)

With the need to feed the growing population and the threat of global climate change, there is an imminent need to increase crop yields. One commonly accepted method of accomplishing this is by enhancing the photosynthetic capability of major crop plants, which may result in an increased yield. A recent…

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,…