Recent Posts

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

/
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…

More Than Just a FAD(5): Unsaturated Fatty Acids in Chloroplasts Elicit Protective Autoimmunity

Arabidopsis (Arabidopsis thaliana) chloroplast-division mutants that have abnormally large chloroplasts have been around for quite some time, not only because they can be identified relatively easily through screening (Pyke & Leech 1991) and because their spectacular morphology sparks intrigue, but…

The rhythm of the light: how light and the clock drive cycling of transcript levels in barley

Circadian rhythms are ubiquitous among living things. A core set of so-called clock genes and their products assemble an oscillatory network that provides a rhythm to anticipate dawn and dusk (Hsu and Harmer, 2014). The circadian clock regulates the day/night rhythms of plants and light itself has many…

In the Transcripts: Long-read Transcriptomics Enables a Novel Type of Transposable Element Annotation in Plants

Transposable Elements (TEs) are mobile genetic elements and major constituents of eukaryotic chromosomes. TEs promote genetic and epigenetic variation within genomes and are a major source of evolutionary novelty and adaptation (Lisch, 2013). In plants, TEs represent from 20% of the genomic content in…

NLR-Annotator: a tool for de novo annotation of intracellular immune receptor repertoire

Wei Zhang ORCID: 0000-0002-5092-643X Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS, 66506, USA weizhang17@ksu.edu Nucleotide-binding domain leucine-rich repeat (NLR) proteins serve as intracellular immune receptors in plants to…

Comparative profiling examines roles of DNA regulatory sequences and accessible chromatin during cold stress response in grasses

Physical access to regulatory DNA, including cis-regulatory sequences found within proximal promoters and distal enhancer elements, is a vital property of chromatin.  In turn, their access is determined by nucleosome occupancy and post-translational modification of histone proteins. A continuum of chromatin…

Predicting Gene Regulatory Networks

Zhou et al. develop and test potential gene regulatory networks in maize. Plant Cell https://doi.org/10.1105/tpc.20.00080 By Peng Zhou and Nathan Springer Background: Transcription factors (TFs) play critical roles in regulating the expression of genes. A single TF can control the expression of…

Arabidopsis bioinformatics resources: Current state, challenges, and priorities for the future (Plant Direct)

Future research success demands that data are reliable, accessible and shareable. This means that as types and magnitudes of data change, best practices for how data are collected and stored must be regularly updated. Following a focused workshop, the International Arabidopsis Informatics Consortium…

Tomato Genome Goes Nano

Schmidt et al. demonstrate that nanopore technology can be applied to plant genomes https://doi.org/10.1105/tpc.17.00521 By Schmidt, M. H.-W., Vogel, A., Denton, A. K., Bolger, A. M., Bolger, M. E., and Usadel, B. Background: An organism’s genome contains all the necessary information for its…