MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.

Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.

Linking the key physiological functions of essential micronutrients to their deficiency symptoms in plants.

In this review, we untangle the physiological key functions of the essential micronutrients and link them to the deficiency responses in plants. Knowledge of these responses at the mechanistic level, and the resulting deficiency symptoms, have improved over the last decade and it appears timely to review recent insights for each of them. A proper understanding of the links between function and symptom is indispensable for an accurate and timely identification of nutritional disorders, thereby informing the design and development of sustainable fertilization strategies. Similarly, improved knowledge of the molecular and physiological functions of micronutrients will be important for breeding programmes aiming to develop new crop genotypes with improved nutrient-use efficiency and resilience in the face of changing soil and climate conditions.

Endodermal suberin restricts root leakage of cesium: a suitable tracer for potassium.

An urgent challenge within crop production is to maintain productivity in a world plagued by climate change and its associated plant stresses, such as heat, drought and salinity. A key factor in this endeavor is to understand the dynamics of root suberization, and its role in plant-water relations and nutrient transport. This study focuses on the hypothesis that endodermal suberin, acts as a physical barrier preventing radial potassium (K) movement out of the vascular tissues during translocation. Previous attempts to experimentally support this idea have produced inconsistent results. We developed a Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) method, allowing us to visualize the distribution of mineral elements and track K movement. Cesium (Cs), dosed in optimized concentrations, was found to be an ideal tracer for K, due to its low background and similar chemical/biological properties. In suberin mutants of Arabidopsis thaliana, we observed a positive correlation between suberin levels and K translocation efficiency, indicating that suberin enhances the plant's ability to retain K within the vascular tissues during translocation from root to shoot. In barley (Hordeum vulgare), fully suberized seminal roots maintained higher K concentrations in the stele compared to younger, less suberized root zones. This suggests that suberization increases with root maturity, enhancing the barrier against K leakage. In nodal roots, suberin was scattered towards the phloem in mature root zones. Despite this incomplete suberization, nodal roots still restrict outward K movement, demonstrating that even partial suberin barriers can significantly reduce K loss. Our findings provide evidence that suberin is a barrier to K leakage during root-to-shoot translocation. This understanding is crucial to maintain crop productivity in the face of climate change.

An 8-week Forced-rate Aerobic Cycling Program Improves Cardiorespiratory Fitness in Persons With Chronic Stroke: A Randomized Controlled Trial.

OBJECTIVE: To examine the cardiorespiratory effects of a forced-rate aerobic exercise (FE) intervention among individuals with chronic stroke compared with an upper extremity repetitive task practice (UE RTP) control group. DESIGN: Secondary analysis of data from a randomized controlled trial. SETTING: Research laboratory. PARTICIPANTS: Individuals with chronic stroke (N=60). INTERVENTIONS: Participants completed 24 sessions of FE followed by RTP (FE+RTP, N=30) or time matched RTP alone (N=30). The FE+RTP group was prescribed exercise at 60%-80% of heart rate reserve on a motorized stationary cycle ergometer for 45 minutes followed by 45 minutes of RTP. The control group completed 90 minutes of RTP. MAIN OUTCOME MEASURES: Metabolic exercise stress tests on a cycle ergometer were conducted at baseline and post-intervention. Outcomes included peak oxygen consumption (peak V̇o2) and anaerobic threshold (AT). RESULTS: Fifty participants completed the study intervention and pre/post stress tests. The FE+RTP group demonstrated significantly greater improvements in peak V̇o2 from 16.4±5.7 to 18.3±6.4 mL/min/kg compared with the RTP group (17.0±5.6 to 17.2±5.6 mL/min/kg, P=.020) and significantly greater improvements in AT from 10.3±2.8 to 11.5±3.6 mL/min/kg compared with the RTP group (10.8±3.9 to 10.4±3.2 mL/min/kg, P=.020). In analyzing predictors of post-intervention peak V̇o2, the multivariable linear regression model did not reveal a significant effect of age, sex, body mass index, or beta blocker usage. Similarly, bivariate linear regression models for the FE group only did not find any exercise variables (aerobic intensity, power, or cycling cadence) to be significant predictors of peak V̇o2. CONCLUSIONS: While the aerobic exercise intervention was integrated into rehabilitation to improve UE motor recovery, it was also effective in eliciting significant and meaningful improvements in cardiorespiratory fitness. This novel rehabilitation model may be an effective approach to improve motor and cardiorespiratory function in persons recovering from stroke.

Application of ZnO Nanoparticles Encapsulated in Mesoporous Silica on the Abaxial Side of a Solanum lycopersicum Leaf Enhances Zn Uptake and Translocation via the Phloem.

Foliar application of nutrient nanoparticles (NPs) is a promising strategy for improving fertilization efficiency in agriculture. Phloem translocation of NPs from leaves is required for efficient fertilization but is currently considered to be feasible only for NPs smaller than a cell wall pore size exclusion limit of <20 nm. Using mass spectrometry imaging, we provide here the first direct evidence for phloem localization and translocation of a larger (∼70 nm) fertilizer NP comprised of ZnO encapsulated in mesoporous SiO2 (ZnO@MSN) following foliar deposition. The Si content in the phloem tissue of the petiole connected to the dosed leaf was ∼10 times higher than in the xylem tissue, and ∼100 times higher than the phloem tissue of an untreated tomato plant petiole. Direct evidence of NPs in individual phloem cells has only previously been shown for smaller NPs introduced invasively in the plant. Furthermore, we show that uptake and translocation of the NPs can be enhanced by their application on the abaxial (lower) side of the leaf. Applying ZnO@MSN to the abaxial side of a single leaf resulted in a 56% higher uptake of Zn as well as higher translocation to the younger (upper) leaves and to the roots, than dosing the adaxial (top) side of a leaf. The higher abaxial uptake of NPs is in alignment with the higher stomatal density and lower density of mesophyll tissues on that side and has not been demonstrated before.

Visualising the ionome in resistant and susceptible plant-pathogen interactions.

At the morphological and anatomical levels, the ionome, or the elemental composition of an organism, is an understudied area of plant biology. In particular, the ionomic responses of plant-pathogen interactions are scarcely described, and there are no studies on immune reactions. In this study we explored two X-ray fluorescence (XRF)-based ionome visualisation methods (benchtop- and synchrotron-based micro-XRF [µXRF]), as well as the quantitative inductively coupled plasma optical emission spectroscopy (ICP-OES) method, to investigate the changes that occur in the ionome of compatible and incompatible plant-pathogen interactions. We utilised the agronomically important and comprehensively studied interaction between potato (Solanum tuberosum) and the late blight oomycete pathogen Phytophthora infestans as an example. We used one late blight-susceptible potato cultivar and two resistant transgenic plant lines (only differing from the susceptible cultivar in one or three resistance genes) both in control and P. infestans-inoculated conditions. In the lesions from the compatible interaction, we observed rearrangements of several elements, including a decrease of the mobile macronutrient potassium (K) and an increase in iron (Fe) and manganese (Mn), compared with the tissue outside the lesion. Interestingly, we observed distinctly different distribution patterns of accumulation at the site of inoculation in the resistant lines for calcium (Ca), magnesium (Mg), Mn and silicon (Si) compared to the susceptible cultivar. The results reveal different ionomes in diseased plants compared to resistant plants. Our results demonstrate a technical advance and pave the way for deeper studies of the plant-pathogen ionome in the future.

Modification of storage proteins in the barley grain increases endosperm zinc and iron under both normal and elevated atmospheric CO2.

Increasing atmospheric CO2 concentration is expected to enhance the grain yield of C3 cereal plants, while at the same time reducing the concentrations of minerals and proteins. This will lead to a lower nutritional quality and increase global problems associated with micronutrient malnutrition. Among the barley grain storage proteins, the C-hordein fraction has the lowest abundance of sulfur (S) containing amino acids and is poorest in binding of zinc (Zn). In the present study, C-hordein-suppressed barley lines with reduced C-hordein content, obtained by use of antisense or RNAi technology, were investigated under ambient and elevated atmospheric CO2 concentration. Grains of the C-hordein-suppressed lines showed 50% increase in the concentrations of Zn and iron (Fe) in the core endosperm relative to the wild-type under both ambient and elevated atmospheric CO2 . Element distribution images obtained using laser ablation-inductively coupled plasma-mass spectrometry confirmed the enrichment of Fe and Zn in the core endosperm of the lines with modified storage protein composition. We conclude that modification of grain storage proteins may improve the nutritional value of cereal grain with respect to Zn and Fe under both normal and future conditions of elevated atmospheric CO2 .

Foliar-applied manganese and phosphorus in deficient barley: Linking absorption pathways and leaf nutrient status.

Foliar fertilization delivers essential nutrients directly to plant tissues, reducing excessive soil fertilizer applications that can lead to eutrophication following nutrient leaching. Foliar nutrient absorption is a dynamic process affected by leaf surface structure and composition, plant nutrient status, and ion physicochemical properties. We applied multiple methods to study the foliar absorption behaviors of manganese (Mn) and phosphorus (P) in nutrient-deficient spring barley (Hordeum vulgare) at two growth stages. Nutrient-specific chlorophyll a fluorescence assays were used to visualize leaf nutrient status, while laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was used to visualize foliar absorption pathways for P and Mn ions. Rapid Mn absorption was facilitated by a relatively thin cuticle with a low abundance of waxes and a higher stomatal density in Mn-deficient plants. Following absorption, Mn accumulated in epidermal cells and in the photosynthetically active mesophyll, enabling a fast (6 h) restoration of Mn-dependent photosynthetic processes. Conversely, P-deficient plants developed thicker cuticles and epidermal cell walls, which reduced the penetration of P across the leaf surface. Foliar-applied P accumulated in trichomes and fiber cells above leaf veins without reaching the mesophyll and, as a consequence, no restoration of P-dependent photosynthetic processes was observed. This study reveals new links between leaf surface morphology, foliar-applied ion absorption pathways, and the restoration of affected physiological processes in nutrient-deficient leaves. Understanding that ions may have different absorption pathways across the leaf surface is critical for the future development of efficient fertilization strategies for crops in nutrient-limited soils.

Topical delivery of PD-1 inhibitors with laser-assisted passive diffusion and active intradermal injection: Investigation of cutaneous pharmacokinetics and biodistribution patterns.

BACKGROUND AND OBJECTIVES: Current cancer immunotherapeutic treatment with PD-1 inhibitors is administered systemically. However, a local treatment strategy may be advantageous as it could provide targeted drug delivery as well as attenuate side effects seen with systemic treatments. For keratinocyte cancers, where surgical excision is not always applicable, an alternate local treatment approach would be beneficial. This study aims to examine cutaneous pharmacokinetics and biodistribution of the PD-1 inhibitor nivolumab, locally delivered either by ablative fractional laser (AFL)-assisted passive diffusion or active intradermal injection, in vivo. MATERIALS AND METHODS: In vivo pig skin was either exposed to CO2 AFL (80 mJ/mb by two stacked pulses of 40 mJ/mb) at 5% or 15% density followed by topical application of nivolumab (1 mg/ml, 100 µl/10 × 10 mm) or intradermally injected with nivolumab (1 mg/ml, 100 µl). Cutaneous nivolumab delivery was evaluated at different timepoints (0, 1, 2, 4 hours and 2 days) at two tissue depths (100-800 and 900-1600 µm) by ELISA. Visualization of cutaneous biodistribution was shown in vertical tissue sections using HiLyte FluorTM 488 SE labeled nivolumab for fluorescence microscopy whereas nivolumab was DOTA-tagged with Dysprosium before the laser ablation-inductively coupled plasma-mass spectrometry analysis (LA-ICP-MS). RESULTS: Our in vivo study revealed different pharmacokinetic and biodistribution patterns for the AFL- and injection techniques. A superficial horizontal band-like uptake of nivolumab was provided with AFL-assisted passive diffusion whereas a deep focal deposition was seen with active intradermal injection, compared with controls showing remnant deposition on the skin surface. AFL-assisted nivolumab uptake in upper dermis peaked after 4 hours (p < 0.01). The cutaneous concentration of nivolumab achieved by intradermal injection was markedly higher than with AFL, the highest deposition with intradermal injection was detected at time 0 hours in both upper and deep dermis (p < 0.01) and decreased throughout the study period, although the concentration remained higher compared with saline control injections at all time points (0 hours -2 d) (p < 0.01). CONCLUSION: Local cutaneous delivery of nivolumab with either AFL or intradermal injection revealed two different pharmacokinetic and biodistribution patterns. Passive AFL-assisted diffusion of nivolumab resulted in enhanced uptake after 4 hours, while intradermal actively injected nivolumab showed immediate enhanced cutaneous deposition with retention up to 2 days after injection. The two local delivery techniques show potential for development of individualized treatment strategies depending on the clinical tumor appearance.

Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses.

X-rays are routinely used for structural studies through scattering, and femtosecond X-ray lasers can probe ultrafast dynamics. We aim to capture the femtosecond dynamics of liquid samples using simulations and deconstruct the interplay of ionization and atomic motion within the X-ray laser pulse. This deconstruction is resolution dependent, as ionization influences the low momentum transfers through changes in scattering form factors, while atomic motion has a greater effect at high momentum transfers through loss of coherence. Our methodology uses a combination of classical molecular dynamics and plasma simulation on a protic ionic liquid to quantify the contributions to the scattering signal and how these evolve with time during the X-ray laser pulse. Our method is relevant for studies of organic liquids, biomolecules in solution or any low-Z materials at liquid densities that quickly turn into a plasma while probed with X-rays.

The molecular-physiological functions of mineral macronutrients and their consequences for deficiency symptoms in plants.

The visual deficiency symptoms developing on plants constitute the ultimate manifestation of suboptimal nutrient supply. In classical plant nutrition, these symptoms have been extensively used as a tool to characterise the nutritional status of plants and to optimise fertilisation. Here we expand this concept by bridging the typical deficiency symptoms for each of the six essential macronutrients to their molecular and physiological functionalities in higher plants. We focus on the most recent insights obtained during the last decade, which now allow us to better understand the links between symptom and function for each element. A deep understanding of the mechanisms underlying the visual deficiency symptoms enables us to thoroughly understand how plants react to nutrient limitations and how these disturbances may affect the productivity and biodiversity of terrestrial ecosystems. A proper interpretation of visual deficiency symptoms will support the potential for sustainable crop intensification through the development of new technologies that facilitate automatised management practices based on imaging technologies, remote sensing and in-field sensors, thereby providing the basis for timely application of nutrients via smart and more efficient fertilisation.

Bioimaging Techniques Reveal Foliar Phosphate Uptake Pathways and Leaf Phosphorus Status.

Global demand for phosphorus (P) requires new agronomic practices to address sustainability challenges while increasing food production. Foliar P fertilization could increase P use efficiency; however, leaf entry pathways for inorganic phosphate ion (Pi) uptake remain unknown, and it is unclear whether foliar P applications can meet plant nutrient demands. We developed two techniques to trace foliar P uptake in P-deficient spring barley (Hordeum vulgare) and to monitor the effectiveness of the treatment on restoring P functionality. First, a whole-leaf P status assay was developed using an IMAGING PAM system; nonphotochemical quenching was a proxy for P status, as P-deficient barley developed nonphotochemical quenching at a faster rate than P-sufficient barley. The assay showed restoration of P functionality in P-deficient plants 24 h after foliar P application. Treated leaves reverted to P deficiency after 7 d, while newly emerging leaves exhibited partial restoration compared with untreated P-deficient plants, indicating Pi remobilization. Second, vanadate was tested as a possible foliar Pi tracer using high-resolution laser ablation-inductively coupled plasma-mass spectrometry elemental mapping. The strong colocalization of vanadium and P signal intensities demonstrated that vanadate was a sensitive and useful Pi tracer. Vanadate and Pi uptake predominantly occurred via fiber cells located above leaf veins, with pathways to the vascular tissue possibly facilitated by the bundle sheath extension. Minor indications of stomatal and cuticular Pi uptake were also observed. These techniques provided an approach to understand how Pi crosses the leaf surface and assimilates to meet plant nutrient demands.

Methods to Visualize Elements in Plants.

Understanding the distribution of elements in plants is important for researchers across a broad range of fields, including plant molecular biology, agronomy, plant physiology, plant nutrition, and ionomics. However, it is often challenging to evaluate the applicability of the wide range of techniques available, with each having its own strengths and limitations. Here, we compare scanning/transmission electron microscopy-based energy-dispersive x-ray spectroscopy, x-ray fluorescence microscopy, particle-induced x-ray emission, laser ablation inductively coupled plasma-mass spectrometry, nanoscale secondary ion mass spectroscopy, autoradiography, and confocal microscopy with fluorophores. For these various techniques, we compare their accessibility, their ability to analyze hydrated tissues (without sample preparation) and suitability for in vivo analyses, as well as examining their most important analytical merits, such as resolution, sensitivity, depth of analysis, and the range of elements that can be analyzed. We hope that this information will assist other researchers to select, access, and evaluate the approach that is most useful in their particular research program or application.

Topical Delivery of Nivolumab, a Therapeutic Antibody, by Fractional Laser and Pneumatic Injection.

BACKGROUND AND OBJECTIVES: PD-L1 is a tumor ligand that binds to the PD-1 receptor on immune cells, thereby inhibiting the antitumor immune response. The antibody nivolumab is a PD-1 inhibitor, Food and Drug Administration approved for systemic treatment of several aggressive cancer types. Topically applied nivolumab may hold potential as a future strategy to treat keratinocyte cancer, but its molecular properties preclude unassisted topical uptake. The aim of this study was to investigate uptake and biodistribution of topically delivered nivolumab, assisted by two physical enhancement techniques with different delivery kinetics; ablative fractional laser (AFL) and electronically controlled pneumatic injection (EPI). STUDY DESIGN/MATERIALS AND METHODS: In vitro porcine skin was exposed to CO2 AFL (20 mJ/mb, 5% density), followed by passive diffusion of nivolumab in a Franz cell (1 mg/ml, 18 hours, n = 6) or treated with EPI (4 bar) for immediate delivery of nivolumab (1 mg/ml, 10 minutes, n = 6). The resulting nivolumab skin concentrations were quantified by enzyme-linked immunosorbent assay (ELISA) at three skin depths (100, 500, and 1500 µm), comparing the uptake from assisted delivery with intact skin. Biodistribution of nivolumab in the skin for all interventions was visualized by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) and fluorescence microscopy. RESULTS: Delivery of nivolumab by AFL-assisted passive diffusion and immediate EPI both resulted in significantly enhanced uptake of nivolumab in all skin depths compared with intact skin (P < 0.05). With AFL, nivolumab concentrations reached 86.3 µg/cm3 (100 µm), 105.8 µg/cm3 (500 µm), and 19.3 µg/cm3 (1500 µm), corresponding to 2-10% of the applied concentration, with the highest deposition in the mid dermis. Immediate EPI delivered 429.4 µg/cm3 (100 µm), 584.9 µg/cm3 (500 µm), and 295.9 µg/cm3 (1500 µm) into the skin, corresponding to 29-58% of the applied nivolumab concentration. From qualitative visualization of the biodistribution, it appeared that nivolumab distributed in a horizontal and continuous homogenous band in the upper and mid dermis through AFL-exposed skin, whereas EPI-delivery showed a deep focal deposition extending into the deep dermis. CONCLUSIONS: AFL-assisted passive diffusion and immediate EPI-assisted delivery show the potential to deliver therapeutic antibodies locally. Future in vivo and pharmacokinetic studies would reveal the full potential for topical antibody delivery by energy-based devices. Lasers Surg. Med. © 2020 Wiley Periodicals LLC.

Efficacy and Safety of Laser-Assisted Combination Chemotherapy: An Explorative Imaging-Guided Treatment With 5-Fluorouracil and Cisplatin for Basal Cell Carcinoma.

BACKGROUND AND OBJECTIVES: Rising incidences of basal cell carcinoma (BCC) have increased the need for effective topical therapies. By enhancing cutaneous uptake of the chemotherapeutic agents, cisplatin and 5-fluorouracil (5-FU), laser-assisted delivery may provide a new combination treatment for BCC. Accordingly, this study aimed to evaluate tumor response, safety, and drug biodistribution in tumors and blood after topical laser-assisted 5-FU + CIS treatment in BCC patients. STUDY DESIGN/MATERIALS AND METHODS: This open-label, proof-of-concept trial investigated laser-assisted combination cisplatin + 5-FU treatment in 20 patients with histologically verified, low-risk superficial or nodular BCCs on the face (<20 mm) or trunk/extremities (<50 mm). After tumor demarcation guided by optical coherence tomography (OCT), BCCs were exposed to ablative fractional CO2 laser followed by 60 minutes topical cisplatin solution and 7-day exposure to 5% 5-FU cream under occlusion. After 30 days, treatment was repeated if any tumor residual was identified. Tumor response at day 30 and month 3 was assessed clinically as well as by OCT, reflectance confocal microscopy, and ultrasound, supplemented by histological verification at 3 months. Local skin reactions (LSRs) and side effects were evaluated on days 1, 3-5, 14, 30, and month 3. Drug detection in tumors and blood was performed in a subset of patients 1- and 24 hours after treatment. RESULTS: Nineteen patients completed the trial, with 32% (6/19) receiving a single treatment and 68% (13/19) treated twice. At 3 months, clinical clearance was seen in 18/19 patients with a corresponding 94% (17/18) achieving histological clearance. Baseline tumor thickness and subtype did not influence treatment number or clearance rate (P ≥ 0.61). LSRs were well-tolerated and consisted of erythema, edema, and erosion, followed by crusting by day 14. Erythema declined gradually by month 3, with 94% of patients and 79% of physicians rating cosmesis as "good" or "excellent." Scarring or hyperpigmentation was noted in 50% and 56%, respectively, while pain and infection were not observed during the follow-up period. Although chemotherapy uptake was visualized extending to deep skin layers, no systemic exposure to cisplatin or 5-FU was detected in patient blood. CONCLUSION: Laser-assisted cisplatin + 5-FU shows potential as an effective and tolerable treatment option for low-risk BCC, particularly in instances where self-application is not possible or where in-office, non-surgical therapy is preferred. Lasers Surg. Med. © 2020 Wiley Periodicals LLC.

The Intensity of Manganese Deficiency Strongly Affects Root Endodermal Suberization and Ion Homeostasis.

Manganese (Mn) deficiency affects various processes in plant shoots. However, the functions of Mn in roots and the processes involved in root adaptation to Mn deficiency are largely unresolved. Here, we show that the suberization of endodermal cells in barley (Hordeum vulgare) roots is altered in response to Mn deficiency, and that the intensity of Mn deficiency ultimately determines whether suberization increases or decreases. Mild Mn deficiency increased the length of the unsuberized zone close to the root tip, and increased the distance from the root tip at which the fully suberized zone developed. By contrast, strong Mn deficiency increased suberization closer to the root tip. Upon Mn resupply, suberization was identical to that seen on Mn-replete plants. Bioimaging and xylem sap analyses suggest that the reduced suberization in mildly Mn-deficient plants promotes radial Mn transport across the endodermis at a greater distance from the root tip. Less suberin also favors the inwards radial transport of calcium and sodium, but negatively affects the potassium concentration in the stele. During strong Mn deficiency, Mn uptake was directed toward the root tip. Enhanced suberization provides a mechanism to prevent absorbed Mn from leaking out of the stele. With more suberin, the inward radial transport of calcium and sodium decreases, whereas that of potassium increases. We conclude that changes in suberization in response to the intensity of Mn deficiency have a strong effect on root ion homeostasis and ion translocation.

The search for candidate genes associated with natural variation of grain Zn accumulation in barley.

Combating hidden hunger through molecular breeding of nutritionally enriched crops requires a better understanding of micronutrient accumulation. We studied natural variation in grain micronutrient accumulation in barley (Hordeum vulgare L.) and searched for candidate genes by assessing marker-trait associations (MTAs) and by analyzing transcriptional differences between low and high zinc (Zn) accumulating cultivars during grain filling. A collection of 180 barley lines was grown in three different environments. Our results show a pronounced variation in Zn accumulation, which was under strong genotype influence across different environments. Genome-wide association mapping revealed 13 shared MTAs. Across three environments, the most significantly associated marker was on chromosome 2H at 82.8 cM and in close vicinity to two yellow stripe like (YSL) genes. A subset of two pairs of lines with contrasting Zn accumulation was chosen for detailed analysis. Whole ears and flag leaves were analyzed 15 days after pollination to detect transcriptional differences associated with elevated Zn concentrations in the grain. A putative α-amylase/trypsin inhibitor CMb precursor was decidedly higher expressed in high Zn cultivars in whole ears in all comparisons. Additionally, a gene similar to barley metal tolerance protein 5 (MTP5) was found to be a potential candidate gene.

The iron-regulated transporter 1 plays an essential role in uptake, translocation and grain-loading of manganese, but not iron, in barley.

Transporters involved in manganese (Mn) uptake and intracellular Mn homeostasis in Arabidopsis and rice are well characterized, while much less is known for barley, which is particularly prone to Mn deficiency. In this study we have investigated the role of the iron-regulated transporter 1 (IRT1) for Mn uptake and translocation in barley plants. We employed an RNAi approach to reduce HvIRT1 expression to 5% of the wild-type level. This enabled characterization of the functional role of HvIRT1 by use of advanced imaging and phenotyping techniques applied to plants growing in hydroponics or soils with different Mn availability. Our results highlight the importance of HvIRT1 for the transport of Mn across the root endodermis into the stele. In the hvirt1-RNAi lines, a chlorotic phenotype with reduced shoot Mn concentration and impaired photosynthetic functionality was observed, especially under conditions with low Mn availability. We also document that HvIRT1 controlled the Mn distribution within the barley grain. Surprisingly, unlike other IRT1 orthologues, HvIRT1 played no significant role in iron uptake. We conclude that the barley IRT1 orthologue has a novel function with respect to ensuring sufficient shoot Mn concentrations. The preference of IRT1 for Mn instead of Fe is discussed in an evolutionary context.

Silicon affects seed development and leaf macrohair formation in Brachypodium distachyon.

Silicon (Si) has many beneficial effects in plants, especially for the survival from biotic and abiotic stresses. However, Si may negatively affect the quality of lignocellulosic biomass for bioenergy purposes. Despite many studies, the regulation of Si distribution and deposition in plants remains to be fully understood. Here, we have identified the Brachypodium distachyon mutant low-silicon 1 (Bdlsi1-1), with impaired channeling function of the Si influx transporter BdLSI1, resulting in a substantial reduction of Si in shoots. Bioimaging by laser ablation-inductively coupled plasma-mass spectrometry showed that the wild-type plants deposited Si mainly in the bracts, awns and leaf macrohairs. The Bdlsi1-1 mutants showed substantial (>90%) reduction of Si in the mature shoots. The Bdlsi1-1 leaves had fewer, shorter macrohairs, but the overall pattern of Si distribution in bracts and leaf tissues was similar to that in the wild-type. The Bdlsi1-1 plants supplied with Si had significantly lower seed weights, compared to the wild-type. In low-Si media, the seed weight of wild-type plants was similar to that of Bdlsi1-1 mutants supplied with Si, while the Bdlsi1-1 seed weight decreased further. We conclude that Si deficiency results in widespread alterations in leaf surface morphology and seed formation in Brachypodium, showing the importance of Si for successful development in grasses.

Multi-Element Bioimaging of Arabidopsis thaliana Roots.

Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventional protocols for microscopy, we observed that diffusible ions such as potassium and sodium were lost during sample dehydration. Thus, we developed a protocol that preserves ions in their native, cellular environment. Briefly, fresh roots are encapsulated in paraffin, cryo-sectioned, and freeze dried. Samples are finally analyzed by laser ablation-inductively coupled plasma-mass spectrometry, utilizing a specially designed internal standard procedure. The method can be further developed to maintain the native composition of proteins, enzymes, RNA, and DNA, making it attractive in combination with other omics techniques. To demonstrate the potential of the method, we analyzed a mutant of Arabidopsis unable to synthesize the metal chelator nicotianamine. The mutant accumulated substantially more zinc and manganese than the wild type in the tissues surrounding the vascular cylinder. For iron, the images looked completely different, with iron bound mainly in the epidermis of the wild-type plants but confined to the cortical cell walls of the mutant. The method offers the power of inductively coupled plasma-mass spectrometry to be fully employed, thereby providing a basis for detailed studies of ion transport in roots. Being applicable to Arabidopsis, the molecular and genetic approaches available in this system can now be fully exploited in order to gain a better mechanistic understanding of these processes.