Recent Posts

Addressing fundamental questions in plant science through synthetic biology

About this seminar In this seminar, we will examine the role that synthetic biology can play in answering fundamental questions in plant science. In studying plants for the past hundred years, we’ve learned a great deal about the mechanistic underpinnings of development and metabolism. However,…

MapMan4: A refined protein classification and annotation framework applicable to multi-omics data analysis (Mol Plant)

Revolutions in omics technologies have rapidly increased the number of plant genomes, transcriptomes and proteomes available. However, protein sequences need to be assigned a biological function to provide useful insights for comparative genomics and transcriptomics. Here, Schwacke et al present MapMan4,…

Designer pentatricopeptide repeat PPR protein as RNA affinity tag (Plant Cell)

Pentatricopeptide repeat (PPR) proteins bind RNA, using a code in which specific amino acid motifs recognize specific bases, similar to TAL effector proteins. In plants, PPR proteins localize almost exclusively to mitochondria and chloroplasts, with functions including RNA, stabilization, splicing and…

Application of TurboID-mediated proximity labeling for mapping a GSK3 Kinase signaling network in Arabidopsis (bioRxiv)

In this preprint Kim et al., have provided an optimized method for determining protein-protein interaction in plants using TurboID-mediated labelling.  TurboID is an engineered promiscuous biotin ligase that marks proteins it comes in contact with. Identification of interacting partners of a protein…

Drop-Seq for plants: High-throughput, single cell transcriptomics (Cell Reports)

Drop-Seq is an exciting high-throughput technology for single cell transcriptomics. Using microfluidics, single cells are encapsulated in drops with beads carrying “bar-coded” primers. The RNA from each individual cell is labeled with a unique primer code, then sequenced. Now, Shulse et al. have…

Data visualization: optimizing data exploration and illustrative storytelling

About this seminar The field of plant biology is undergoing a revolution due to the enormous amount of data that is being produced, either by high-throughput sequencing or non-destructive plant phenotyping platforms. Visualizing big-data is not an easy task but it helps with data interpretation, generation…

Structural and functional imaging of large and opaque plant specimen (J Exp Bot)

Even the simplest organisms are highly complex systems in which countless dynamic biochemical processes occur simultaneously. To fully understand the mechanical significance of such a complex molecular machine, the ability to accurately characterize dynamic processes at different scales is required.…

Review: Functional status of xylem through time ($) (Annu Rev Plant Biol)

If you haven’t been paying attention, you may have missed the great advances that have been taking place in xylem research recently. This excellent review by Brodersen et al. is your chance to catch up. Like all aspects of plant science, new tools and techniques have provided tremendous new insights…

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.…