Recent Posts

Review: Molecular regulators of nitrate response in plants (Curr. Biol.)

Nitrate is the major form of nitrogen used by plants in an aerobic crop cultivation scenario. Lamig et al. review recent additions to the already vast knowledge of nitrate signaling. A first line of regulation concerns nitrate uptake through post-transcriptional and post-translational regulation of nitrate…

ATTED-II v11: A plant gene coexpression database using a sample balancing technique by subagging of principal components (Plant Cell Physiol)

Genes are generally expressed in concert with one another with data often represented by gene co-expression networks. Gene co-expression data may be useful in identifying genes with unknown functions and are generally utilized in exploring molecular processes occurring during normal development as well…

Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization (Science)

In this seminal paper, Roszak et al. present a deeper understanding of the development of the protophloem cell lineage. The differentiation process from the phloem stem cell to the enucleated cell state spans approximately 19 cells. Using live imaging, FACS sorting and single-cell RNA sequencing, the…

Review: Convergent evolution of gene regulatory networks underlying plant adaptations (Plant Cell Environ.)

The transition from aquatic to terrestrial habitats exposed plants to low water availability, high light, radiation, and other environmental challenges. To overcome these challenges, plants developed morpho-physiological adaptations to tolerate dry environments and make photosynthesis more efficient.…

ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks (Plant Physiology)

ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks Gene regulatory networks (GFNs) are complex beasts, integrating multiple components of transcription factors (TFs), regulatory loci, and function -- not to mention the myriad datasets and methodologies…

Conserved gene regulatory network integrated with stress response factors in radish and Arabidopsis root cambium (Curr. Biol.)

The cambium is a layer of actively dividing cells between xylem and phloem tissues that is responsible for the thickening of primary or lateral roots and stems. Root crops are tightly associated with the cambium regulatory mechanism which is less characterized in root as compared to shoot development.…

Review: The bHLH network underlying plant shade-avoidance (Physiol. Plant.)

Shade avoidance is a complex phenomenon in which plants avoid shade by altering their developmental program in various ways including early flowering, hypocotyl elongation, and more. Many photoreceptors and transcription factors (TFs) are involved in regulating shade avoidance, including the bHLH (basic…

Integrated multi-omics framework of the plant response to jasmonic acid (Nature Plants)

Jasmonic acid (JA) is involved in fertility, seed emergence and defense. JA perception and signal transduction are well understood, but there is limited understanding of the JA responsive genome regulatory program since only one or a small number of components are usually studied at once. Zander et al.…

Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots (Plant Physiol.)

Iron (Fe) is an important micronutrient needed by plants for survival. Plants have evolved a range of morphological, physiological and molecular responses to Fe availability, including the transcriptional regulation of over one thousand genes in response to Fe deficiency (-Fe) in Arabidopsis. However,…