ClearDepth: a simple, robust, and low-cost method to assess root depth in soil.

Root depth is a major determinant of plant performance during drought and a key trait for strategies to improve soil carbon sequestration to mitigate climate change. While the model Arabidopsis thaliana offers numerous advantages for studies of root system architecture and root depth, its small and fragile roots severely limit the use of the methods and techniques currently available for such studies in soils. To overcome this, we have developed ClearDepth, a conceptually simple, non-destructive, sensitive, and low-cost method to estimate the root depth of Arabidopsis in relatively small pots that are amenable to mid- and large-scale studies.

Natural variation of TBR confers plant zinc toxicity tolerance through root cell wall pectin methylesterification.

Zinc (Zn) is an essential micronutrient but can be cytotoxic when present in excess. Plants have evolved mechanisms to tolerate Zn toxicity. To identify genetic loci responsible for natural variation of plant tolerance to Zn toxicity, we conduct genome-wide association studies for root growth responses to high Zn and identify 21 significant associated loci.

transcriptome responses to low water potential using high-throughput plate assays.

Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant . Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol, and salt (NaCl) treatments to reduce the water potential of agar media, and thus induce drought conditions in the laboratory. However, while these types of stress can create phenotypes that resemble those of water deficit experienced by soil-grown plants, it remains unclear how these treatments compare at the transcriptional level.

Nutrient levels control root growth responses to high ambient temperature in plants.

Global warming will lead to significantly increased temperatures on earth. Plants respond to high ambient temperature with altered developmental and growth programs, termed thermomorphogenesis. Here we show that thermomorphogenesis is conserved in Arabidopsis, soybean, and rice and that it is linked to a decrease in the levels of the two macronutrients nitrogen and phosphorus.

Fast and Efficient Root Phenotyping via Pose Estimation.

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train) and error-prone (derived geometric features are sensitive to instance mask integrity).

Assessing Temperature Responses in Roots.

Due to global warming, it is important to understand how plants respond to high ambient temperature. Plant growth responses to high ambient temperature are termed thermomophogenesis and have been explored for more than a decade. However, this was mostly focused on the above-ground part of plants, the shoot.

PAT (Periderm Assessment Toolkit): A Quantitative and Large-Scale Screening Method for Periderm Measurements.

The periderm is a vital protective tissue found in the roots, stems, and woody elements of diverse plant species. It plays an important function in these plants by assuming the role of the epidermis as the outermost layer. Despite its critical role for protecting plants from environmental stresses and pathogens, research on root periderm development has been limited due to its late formation during root development, its presence only in mature root regions, and its impermeability.

Identification of mebendazole as an ethylene signaling activator reveals a role of ethylene signaling in the regulation of lateral root angles.

The lateral root angle or gravitropic set-point angle (GSA) is an important trait for root system architecture (RSA) that determines the radial expansion of the root system. The GSA therefore plays a crucial role for the ability of plants to access nutrients and water in the soil. Only a few regulatory pathways and mechanisms that determine GSA are known.

GLK transcription factors accompany ELONGATED HYPOCOTYL5 to orchestrate light-induced seedling development in Arabidopsis.

Light-induced de-etiolation is an important aspect of seedling photomorphogenesis. GOLDEN2 LIKE (GLK) transcriptional regulators are involved in chloroplast development, but to what extent they participate in photomorphogenesis is not clear. Here, we show that ELONGATED HYPOCOTYL5 (HY5) binds to GLK promoters to activate their expression, and also interacts with GLK proteins in Arabidopsis (Arabidopsis thaliana).

Fast and efficient root phenotyping via pose estimation.

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train), and error-prone (derived geometric features are sensitive to instance mask integrity).

Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution.

Plants are sessile organisms that constantly adapt to their changing environment. The root is exposed to numerous environmental signals ranging from nutrients and water to microbial molecular patterns. These signals can trigger distinct responses including the rapid increase or decrease of root growth.

A lignin-derived material improves plant nutrient bioavailability and growth through its metal chelating capacity.

The lignocellulosic biorefinery industry can be an important contributor to achieving global carbon net zero goals. However, low valorization of the waste lignin severely limits the sustainability of biorefineries. Using a hydrothermal reaction, we have converted sulfuric acid lignin (SAL) into a water-soluble hydrothermal SAL (HSAL).

The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in Arabidopsis thaliana.

The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFB auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified.

Plasmodesmata mediate cell-to-cell transport of brassinosteroid hormones.

Brassinosteroids (BRs) are steroidal phytohormones that are essential for plant growth, development and adaptation to environmental stresses. BRs act in a dose-dependent manner and do not travel over long distances; hence, BR homeostasis maintenance is critical for their function. Biosynthesis of bioactive BRs relies on the cell-to-cell movement of hormone precursors.

The Perpendicular Extraction - Visionary Concept with the Prospect of Generating the Perfect Extraction of Teeth, or a Misguided Vision that had to Fail Due to Anatomical Circumstances?

From the second half of the 18th century to the last third of the 19th century, a period of about 100 years, perpendicular (vertical) extraction, became an ideal for many authors, since molars were the most difficult teeth to remove. However, extraction instruments available at that time, caused pronounced damage to the alveolar bone and gingiva. For many authors and clinicians, vertical extraction was the only way to meet this challenge.

The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in .

The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFBs auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified.

Climate change challenges, plant science solutions.

Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g.

Removing systemic barriers to equity, diversity, and inclusion: Report of the 2019 Plant Science Research Network workshop "Inclusivity in the Plant Sciences".

A future in which scientific discoveries are valued and trusted by the general public cannot be achieved without greater inclusion and participation of diverse communities. To envision a path towards this future, in January 2019 a diverse group of researchers, educators, students, and administrators gathered to hear and share personal perspectives on equity, diversity, and inclusion (EDI) in the plant sciences. From these broad perspectives, the group developed strategies and identified tactics to facilitate and support EDI within and beyond the plant science community.

The receptor kinase SRF3 coordinates iron-level and flagellin dependent defense and growth responses in plants.

Iron is critical for host-pathogen interactions. While pathogens seek to scavenge iron to spread, the host aims at decreasing iron availability to reduce pathogen virulence. Thus, iron sensing and homeostasis are of particular importance to prevent host infection and part of nutritional immunity.

A Multiplexed, Time-Resolved Assay of Root Gravitropic Bending on Agar Plates.

The ability of roots to orient their growth relative to the vector of gravity, root gravitropism (positive gravitropism), is observed in root systems of higher plants and is an essential part of plant growth and development. While there are various methods for quantifying root gravitropism, many methods that can efficiently measure gravitropism at a reasonable throughput do not yield temporal resolution of the process, while methods that allow for high-temporal resolution are often not suitable for an efficient measurement of multiple roots. Here, we describe a method to analyze the root gravitropism activity at an increased throughput with a fine time-resolution using Arabidopsis thaliana plants.

A genome-wide association study reveals cytokinin as a major component in the root defense responses against Ralstonia solanacearum.

Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host's root upon infection, which remain mostly unknown.

Using natural variation to understand plant responses to iron availability.

Iron bioavailability varies dramatically between soil types across the globe. This has given rise to high levels of natural variation in plant iron responses, allowing members of even a single species to thrive across a wide range of soil types. In recent years we have seen the use of genome-wide association analysis to identify natural variants underlying plant responses to changes in iron availability in both Arabidopsis and important crop species.