Recent Posts

Optimizing PollenCounter for high throughput phenotyping of pollen quality in tomatoes (MethodsX)

PollenCounter is an open source, ImageJ based macro that splits RGB images of stained pollen grains into the primary channels. The program estimates pollen viability in plants through analyzing red (total number of pollen grains) and green (only viable pollen grains) images, after which the particles…

An inducible genome editing system for plants (Nature Plants)

To understand gene function, it is necessary to study loss-of-function phenotypes. However, knockouts of some genes are lethal, which makes it impossible to study their loss-of-function phenotype. Although here are inducible overexpression systems and inducible knockdown systems, as yet there has been…

An optogenetic tool for plants grown in ambient light (Nature Methods)

Optogenetics has revolutionized mammalian biology by its ability to fine-tune gene expression in individual cells by pulses of light. However, its application in plants has been challenging because the white light required for plant growth misfires the system. Ochoa-Fernandez et al. solved this problem…

Vacuolar channel CLCa is involved in guard cell pH homeostasis (PNAS)

In plants, stomata are involved in a host of responses, controlled by ion homeostasis in guard cells. In an attempt to understand the function of a plant chloride channel (CLC), CLCa, which transports chloride (Cl-) and nitrate (NO3-) in guard cells, Demes and colleagues sought to establish a relationship…

Review Single-cell genomics and epigenomics: Technologies and applications in plants ($) (Trends Plant Sci)

Plants (embryophytes) are by definition multicellular, but we seek to understand them as the sum of the activities of individual cells. Much of this knowledge rests on information obtained through grinding up tissues  made up from several cell types. This review by Luo et al. describes methods for plant…

Dual-sensing genetically encoded fluorescent indicators, ABA and second messenger dynamics (Plant Cell)

Responses to a changing environment require an interplay between primary and secondary messengers. Hormones like abscisic acid (ABA), auxin etc. act as a primary messengers, whereas molecules like Ca2+, reactive oxygen species (ROS), other cations and anions act as a secondary messenger. In this paper,…

A FRET sensor reports kinase activity in planta (eLIFE)

Abscisic acid (ABA) is a phytohormone involved in imparting tolerance to a variety of stress conditions. Importantly, ABA is involved in stomatal closure, mediated by the sucrose non-fermenting1-related protein kinase 2 (SnRK2) family of proteins. To report SnRK2 activity in vivo, Zhang and co-workers…

Robotic Assay for Drought (RoAD): An automated phenotyping system for brassinosteroid and drought response (bioRxiv)

  Developing drought tolerant plants is an important challenge in agriculture. Drought responses and plant growth are regulated by several signaling pathways, one of which is activated by brassinosteroids (BRs), a group of plant steroid hormones. In order to better understand the crosstalk…

Measuring both microbial load and diversity with a single amplicon sequencing library (bioRxiv)

Amplicon sequencing of microbial DNA is a gold standard for analyzing the relative abundance of microbes in host-associated microbiomes. To gain more accurate insights into microbiome changes, it is crucial to know the absolute abundance of microbes, which can be analyzed by integrating relative abundance…