Recent Posts

Lateral root priming synergistically arises from root growth and auxin transport dynamics (bioRxiv)

Root system architecture is primarily determined by branching of the lateral roots. The position of a new lateral root is determined by oscillating auxin concentrations in the main root meristem. To understand the nature of auxin oscillations Van den Berg and ten Tusscher developed a multiscale root…

Bioinformatics core competencies for undergraduate life sciences education (PLOS One)

Undergraduate life science curricula need to incorporate training in bioinformatics. Wilson Sayres et al. surveyed 1260 faculty from across the US to identify their thoughts on what such training should involve. Not surprisingly, 95% of those surveyed agreed with the statement “I think bioinformatics…

Interview with Benjamin Firester, winner of the Regeneron Science Talent Search, 2018

From Facebook to disease control, starting in New York via the UK to the Volcani centre in Israel and back again, my interview with Benjy Firester, winner of the Regeneron Science Talent Search 2018, felt like a whistlestop global tour. This bright senior student at Hunter College High School in New…

Review. Use it or average it: Stochasticity in plant development (Curr. Opin. Plant Biol.)

In this interesting review, Roeder describes the importance of stochasticity in plant development. She starts off with an explanation: “A process that can be analyzed statistically but not predicted precisely is stochastic. Stochasticity does not imply the absence of regulation, just that the regulation…

Probing the stochastic property of endoreduplication in cell size determination of Arabidopsis thaliana leaf epidermal tissue

PLOS One. Endoreduplicated cells grow in size as their DNA content increases. The distribution of size was observed to be Poisson. This allowed the authors to create a mathematical model with a single parameter which describes the probability of exiting endoreduplication. The model recovers cell size…

A mathematical model of the interaction of abscisic acid, ethylene and methyl jasmonate on stomatal closure in plants

PLOS One. Plant stomatal opening is controlled by phytohormones, among other factors. This article models the phytohormone signaling response in guard cells using ordinary differential equations (ODEs). Sixteen components in this system were analyzed by constructing 16 different models and determining…

Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells

Proc. Natl. Acad. Sci. USA. GENIST (gene regulatory network inference from spatiotemporal data) is a new algorithm developed by de Luis Balaguer et al to predict new gene interactions and transcriptional regulators (available at https://github.com/madeluis/GENIST). The algorithm combines inference of…

A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loops

PLOS Biol. This article describes a stochastic mathematical model of the stomatal closure network responding to abscisic acid (ABA). The Boolean network is constructed from a comprehensive literature review of the components’ dependencies. The model’s predictions agree with experimental data 90%…

Adjustment of the Arabidopsis circadian oscillator by sugar signalling dictates the regulation of starch metabolism

Sci Reports. Both starch degradation and accumulating sucrose levels are related to the circadian cycle, although it is unknown which is the primary regulator. The authors created a mathematical model wherein the circadian oscillator responds to sucrose. The model predictions were experimentally validated…