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Understanding the flow of water in natural watercourses has become increasingly important as climate change increases the incidence of extreme rainfall events which cause flooding. Vegetation in rivers and streams reduce water conveyance and natural vegetation plays a critical role in flood events which needs to be understood more fully. A funded project at Loughborough University is therefore examining the influence of vegetation upon water flow, requiring measurement of both the 3-D water surface and flow velocities. Experimental work therefore requires the measurement of water surface morphology and velocity (i.e. speed and direction) in a controlled laboratory environment using a flume but also needs to be adaptable to work in a real river. Measuring the 3D topographic characteristics and velocity field of a flowing water surface is difficult and the purpose of this paper is to describe recent experimental work to achieve this. After reviewing past work in this area, the use of close range digital photogrammetry for capturing both the 3D water surface and surface velocity is described. The selected approach uses either two or three synchronised digital SLR cameras in combination with PhotoModeler for data processing, a commercial close range photogrammetric package. One critical aspect is the selection and distribution of appropriate floating marker points, which are critical if automated and appropriate measurement methods are to be used. Two distinct targeting approaches are available: either large and distinct specific floating markers or some fine material capable of providing appropriate texture. Initial work described in this paper uses specific marker points, which also provide the potential measuring surface velocity. The paper demonstrates that a high degree of measurement and marking automation is possible in a flume environment, where lighting influences can be highly controlled. When applied to a real river it is apparent that only lower degrees of automation are practicable. The study has demonstrated that although some automation is possible for point measurement, point matching needs to be manually guided in a natural environment where lighting cannot be controlled.

To acclimate to hypoxic waterlogged conditions, the roots of wetland plants form a radial oxygen loss (ROL) barrier that can promote oxygen diffusion to the root tips. We hypothesized that the low-nitrate concentrations that occur after molecular oxygen is consumed in waterlogged soils are an environmental trigger for ROL barrier formation in rice (Oryza sativa). We previously identified 128 tissue-specific up/downregulated genes during rice ROL barrier formation. The RiceXPro database showed that many of these genes were differentially regulated in response to nitrogen deficiency. Therefore, we assessed changes in the concentrations of ionic species of nitrogen under stagnant conditions, i.e. in a nutrient solution that mimics waterlogged soil conditions, and examined the effects of an increase or decrease of nitrate in the nutrient solution on ROL barrier formation and exodermal suberization. Preventing nitrate deficiency in the stagnant nutrient solution suppressed the formation of an ROL barrier. Conversely, a decrease in nitrate strongly induced ROL barrier formation, even under aerated conditions. In parallel with ROL barrier formation, suberin lamellae formed at the exodermis. Nitrate deficiency also promoted aerenchyma formation and the enlargement of root diameters. These findings suggest that the severe decline of nitrates under waterlogged conditions is an environmental cue for exodermal suberization to form an ROL barrier in rice roots., Competing Interests: Conflict of interest. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Background and Aims: Internal root aeration is essential for root growth in waterlogged conditions. Aerenchyma provides a path for oxygen to diffuse to the roots. In most wetland species, including rice, a barrier to radial oxygen loss (ROL) allows more of the oxygen to diffuse to the root tip, enabling root growth into anoxic soil. Most dryland crops, including barley, do not form a root ROL barrier. We previously found that abscisic acid (ABA) signalling is involved in the induction of ROL barrier formation in rice during waterlogging. Although rice typically does not form a tight ROL barrier in roots in aerated conditions, an ROL barrier with suberized exodermis was induced by application of exogenous ABA. Therefore, we hypothesized that ABA application could also trigger root ROL barrier formation with hypodermal suberization in barley., Methods: Formation of an ROL barrier was examined in roots in different exogenous ABA concentrations and at different time points using cylindrical electrodes and Methylene Blue staining. Additionally, we evaluated root porosity and observed suberin and lignin modification. Suberin, lignin and Casparian strips in the cell walls were observed by histochemical staining. We also evaluated the permeability of the apoplast to a tracer., Key Results: Application of ABA induced suberization and ROL barrier formation in the adventitious roots of barley. The hypodermis also formed lignin-containing Casparian strips and a barrier to the infiltration of an apoplastic tracer (periodic acid). However, ABA application did not affect root porosity., Conclusions: Our results show that in artificial conditions, barley can induce the formation of ROL and apoplastic barriers in the outer part of roots if ABA is applied exogenously. The difference in ROL barrier inducibility between barley (an upland species) and rice (a wetland species) might be attributable to differences in ABA signalling in roots in response to waterlogging conditions., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Submergence during germination impedes aerobic metabolisms and limits the growth of most higher plants. However, some wetland plants including rice can germinate under submerged conditions. It has long been hypothesized that the first elongating shoot tissue, the coleoptile, acts as a snorkel to acquire atmospheric oxygen (O 2 ) to initiate the first leaf elongation and seminal root emergence. Here, we obtained direct evidence for this hypothesis by visualizing the spatiotemporal O 2 dynamics during submerged germination in rice using a planar O 2 optode system. In parallel with the O 2 imaging, we tracked the anatomical development of shoot and root tissues in real-time using an automated flatbed scanner. Three hours after the coleoptile tip reached the water surface, O 2 levels around the embryo transiently increased. At this time, the activity of alcohol dehydrogenase (ADH), an enzyme critical for anaerobic metabolism, was significantly reduced, and the coleorhiza covering the seminal roots in the embryo was broken. Approximately 10 h after the transient burst in O 2 , seminal roots emerged. A transient O 2 burst around the embryo was shown to be essential for seminal root emergence during submerged rice germination. The parallel application of a planar O 2 optode system and automated scanning system can be a powerful tool for examining how environmental conditions affect germination in rice and other plants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Shiono, Koshide, Iwasaki, Oguri, Fukao, Larsen and Glud.)

To acclimate to waterlogged conditions, wetland plants form a barrier to radial oxygen loss (ROL) that can enhance oxygen transport to the root apex. We hypothesized that one or more hormones are involved in the induction of the barrier and searched for such hormones in rice. We previously identified 98 genes that were tissue-specifically upregulated during ROL barrier formation in rice. The RiceXPro database showed that most of these genes were highly enhanced by exogenous abscisic acid (ABA). We then examined the effect of ABA on ROL barrier formation by using an ABA biosynthesis inhibitor (fluridone, FLU), by applying exogenous ABA and by examining a mutant with a defective ABA biosynthesis gene (osaba1). FLU suppressed barrier formation in a stagnant solution that mimics waterlogged soil. Under aerobic conditions, rice does not naturally form a barrier, but 24 h of ABA treatment induced barrier formation. osaba1 did not form a barrier under stagnant conditions, but the application of ABA rescued the barrier. In parallel with ROL barrier formation, suberin lamellae formed in the exodermis. These findings strongly suggest that ABA is an inducer of suberin lamellae formation in the exodermis, resulting in an ROL barrier formation in rice., (© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation.)

Plant hormones can act in synergistic and antagonistic ways in response to biotic and abiotic stresses and during plant growth and development. Thus, a technique is needed to simultaneously determine the distribution and concentration of several plant hormones. A relatively new technology, mass spectrometry imaging (MSI), enables the direct mapping and imaging of biomolecules on tissue sections. MSI permits simultaneous detection of multiple analytes on a single section of plant tissue, even in the absence of target-specific markers such as antibodies. Recently, MSI has been used to localize multiple, small molecule (m/z < 500) plant hormones by the nanoparticle-assisted laser desorption/ionization (Nano-PALDI) mass spectrometry (MS) method. Here, we illustrate a technology for multiple-hormone imaging using Nano-PALDI MSI and discuss its potential in investigating the role of hormone signaling in plant development and stress responses., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: Detailed datasets containing root system and its architecture in soil are required to improve understanding of resource capture by roots. However, most of the root study methods have paid little attention to make and preserve whole root specimens. This study introduces root system sampling equipment that makes the entire root specimen with minimum impairment and without displacement of the spatial arrangement of the root system in root boxes. The objectives are to assess: whether the equipment can rapidly sample the entire root system; whether root surface area is measurable from a scanned digital image of the root specimen; and whether staining of the entire root specimens would provide multidimensional visual information on the interaction between soil and physiological function of root system architecture (RSA). For validation, we examined the root response of two soybean cultivars to arbuscular mycorrhizal (AM) inoculation and the effect of waterlogging stress on the physiological activity of buckwheat RSA., Results: The root boxes allowed soybean and buckwheat plants to grow uniformly across the replications. Both species showed significant differences between cultivars and/or among treatments in shoot and root traits. The equipment enabled to sample the whole-root specimens of soybean and buckwheat, where the tips of the fine roots were alive (diameter < 0.2 mm). Also, the whole root specimens of soybean were made in about 7 min. The root surface area calculated from the scanned soybean specimens showed a significant correlation with that calculated from the roots spread out in water (a common method). Staining of the soybean root specimens enabled us to observe the localized root proliferation induced by AM colonization. Moreover, staining of the buckwheat root specimens made it possible to examine the respiratory activity of each root at different depths., Conclusions: The present method realized: fast and accurate production of the whole root specimen and precise calculation of the specimens' root surface area. Moreover, staining of the root specimens enabled analyzing the interaction between soil and physiological function of RSA. The evaluation of root traits, using our methods, will contribute to developing agronomic management and breeding program for sustainable food production., (© 2021. The Author(s).)

A simple and rapid analytical method was developed for determination of four biogenic amines [histamine (Him), cadaverine (Cad), tyramine (Tym), 2-phenylethylamine (Pea)] in fish and fish products. This method uses a new derivatization reagent, 2,4,6-triethyl-3,5-dimethyl pyrylium trifluoromethanesulfonate (Py-Tag). The four biogenic amines in the samples were extracted with trichloroacetic acid. The diluted extract was derivatized with Py-Tag (15 min at 50°C) and then subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). The limits of quantification for the method were 2 mg/kg for Him, Tym, and Pea and 10 mg/kg for Cad. The matrix effects derived from the tested fish and fish products were negligible in the LC-MS/MS analysis. The impact of the sample matrices on the Py-Tag derivatization was also negligible. The trueness and repeatability of the method were assessed by performing replicate analyses (n = 5) of five samples of fish and fish products, each spiked with the four biogenic amines at three different concentration levels. Analysis of the samples found 87%-104% of the spiked concentrations and the relative standard deviations were <6.1%. A reference sample and quality control canned fish samples were analyzed by the method, and the concentrations of the Him were within acceptable limits. The developed method was successfully used to determine concentrations of the four biogenic amines in 48 fish and fish products on the Japanese market. The developed method does not require cleanup using a solid-phase extraction column or similar, and the derivatization reaction time was only 15 min. The results suggested that the present method is reliable and suitable for rapid analysis of the four biogenic amines in fish and fish products., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier B.V.)

Protein-protein interactions (PPIs) intimately govern various biological processes and disease states and therefore have been identified as attractive therapeutic targets for small-molecule drug discovery. However, the development of highly potent inhibitors for PPIs has proven to be extremely challenging with limited clinical success stories. Herein, we report irreversible inhibitors of the human double minute 2 (HDM2)/p53 PPI, which employ a reactive N -acyl- N -alkyl sulfonamide (NASA) group as a warhead. Mass-based analysis successfully revealed the kinetics of covalent inhibition and the modification sites on HDM2 to be the N-terminal α-amine and Tyr67, both rarely seen in traditional covalent inhibitors. Finally, we demonstrated prolonged p53-pathway activation and more effective induction of the p53-mediated cell death in comparison to a noncovalent inhibitor. This study highlights the potential of the NASA warhead as a versatile electrophile for the covalent inhibition of PPIs and opens new avenues for the rational design of potent covalent PPI inhibitors.

Internal aeration is crucial for root growth under waterlogged conditions. Many wetland plants have a structural barrier that impedes oxygen leakage from the basal part of roots called a radial oxygen loss (ROL) barrier. ROL barriers reduce the loss of oxygen transported via the aerenchyma to the root tips, enabling long-distance oxygen transport for cell respiration at the root tip. Because the root tip does not have an ROL barrier, some of the transferred oxygen is released into the waterlogged soil, where it oxidizes and detoxifies toxic substances (e.g., sulfate and Fe 2+ ) around the root tip. ROL barriers are located at the outer part of roots (OPRs). Their main component is thought to be suberin. Suberin deposits may block the entry of potentially toxic compounds in highly reduced soils. The amount of ROL from the roots depends on the strength of the ROL barrier, the length of the roots, and environmental conditions, which causes spatiotemporal changes in the root system's oxidization pattern. We summarize recent achievements in understanding how ROL barrier formation is regulated and discuss opportunities for breeding waterlogging-tolerant crops., (Copyright © 2021 by JAPANESE SOCIETY OF BREEDING.)

This study focused on the physicochemical interactions between acidic and basic drugs in aqueous solutions. Their ion pair interactions were evaluated in an in vitro study. The model non-steroid anti-inflammatory drugs (NSAIDs), indomethacin (INM) and diclofenac (DIC), were used as acidic and hydrophobic drugs, whereas cimetidine (CIM), famotidine (FAM), and imidazole (IMD) were used as basic additives with heterocyclic moieties. The drug mixtures were evaluated by thermal analysis, dissolution test, nuclear magnetic resonance (NMR) spectroscopy, and mass spectroscopy. The fusion enthalpy of DIC-CIM, INM-CIM, and INM-arginine (ARG) sample was calculated based on melting temperature transformation. The DIC mixture with CIM, IMD, antipyrine (ANT), and ARG showed enhanced solubility, whereas the DIC-FAM mixture sample showed a decreased solubility. Electrospray ionization mass spectroscopy was carried out to detect binary mixtures. The interactions in DIC-FAM mixture sample were found between the carboxyl group of DIC and the amine groups of FAM by NMR. These findings were suggested that DIC-FAM mixture samples construct ion pair complexes based on the theory of Bjerrum. Moreover, the acid model drug and basic model drug also can be constructed 1:1 complexes that affects their solubility in the solvent of water type., (Copyright © 2020. Published by Elsevier B.V.)

A barrier to radial oxygen loss (ROL), which reduces the loss of oxygen transported via the aerenchyma to the root tips, enables the roots of wetland plants to grow into anoxic/hypoxic waterlogged soil. However, little is known about its genetic regulation. Quantitative trait loci (QTLs) mapping can help to understand the factors that regulate barrier formation. Rice ( Oryza sativa ) inducibly forms an ROL barrier under stagnant conditions, while a few wetland plants constitutively form one under aerated conditions. Here, we evaluated the formation of a constitutive ROL barrier in a total of four accessions from two wild rice species. Three of the accessions were wetland accessions of O. glumaepatula , and the fourth was a non-wetland species of O. rufipogon . These species have an AA type genome, which allows them to be crossed with cultivated rice. The three O. glumaepatula accessions (W2165, W2149, and W1183) formed an ROL barrier under aerated conditions. The O. rufipogon accession (W1962) did not form a constitutive ROL barrier, but it formed an inducible ROL barrier under stagnant conditions. The three O. glumaepatula accessions should be useful for QTL mapping to understand how a constitutive ROL barrier forms. The constitutive barrier of W2165 was closely associated with suberization and resistance to penetration by an apoplastic tracer (periodic acid) at the exodermis but did not include lignin at the sclerenchyma.

Plant hormones can act in synergistic and antagonistic ways in response to biotic and abiotic stresses and in plant growth and development. Thus, a technique is needed to simultaneously determine the distributions and concentrations of several plant hormones. Previously, we reported that localizations of two plant hormones [cytokinin (CK) and abscisic acid (ABA)] can be simultaneously visualized in a plant tissue using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). In MALDI-MS, however, self-ionization of an organic matrix occasionally interferes with ionizations of small molecules (<500 m / z ) including most plant hormones. Another technique, nanoparticle-assisted laser desorption/ionization (Nano-PALDI), can avoid matrix self-ionization using nanoparticles to assist the ionization of analytes. Here, we compared the ionization efficiencies of common plant hormones by MALDI-MS and Nano-PALDI-MS. For the comparison, we prepared a standard mix of seven plant hormones [ABA, auxin (IAA), brassinosteroid (Br), two CKs ( trans -zeatin, t Z, and 6-(γ,γ-dimethylallylamino) purine, iP), jasmonic acid, and salicylic acid (SA)], an ethylene precursor (1-aminocyclopropane-1-carboxylic acid, ACC), and a heavy hydrogen-labeled ABA (D 6 -ABA). Basic MALDI-MS detected all compounds except IAA, Br, and D 6 -ABA, while Nano-PALDI-MS detected all nine compounds. By Nano-PALDI-MS imaging (MSI), each of the abovementioned hormones and ACC were also detected in root cross sections of rice which were incubated in the hormone mix for 2 h. In the elongation zone of untreated roots, Nano-PALDI-MSI revealed high levels of ABA and CKs in the outer part of roots and much lower levels in the stele, but Br, SA, and ACC were broadly distributed in the cross section. IAA seemed to be distributed in the epidermis, cortex, and stele. Multiple-hormone imaging using Nano-PALDI-MS has great potential for investigating the roles of hormone signaling in crop development and stress responses.

Analytical method was developed for determining the total residue of ethofumesate (ET) herbicide using GC-MS/MS. The ET residues were analyzed as a sum of ET, 2-keto-ethofumesate (KET), and open-ring-2-keto-ethofumesate (OKET) and its conjugate. The extracted samples were partitioned with hexane and NaOH solution. For ET analysis, the hexane layer was cleaned up by a silica gel cartridge prior to GC-MS/MS analysis. For the analyses of the metabolites, the aqueous layer was heated with HCl to hydrolyze the conjugates, thereafter, heated in acetic anhydride to convert OKET to KET, and cleaned up by a silica gel cartridge prior to GC-MS/MS analysis. The method was validated for ET, KET, and OKET in garlic, onion, and sugar beet at 0.3 and 0.01 mg/kg. The recoveries were 94-113%, with relative standard deviations of <6%. The limits of detection were 0.0005 mg/kg for all analytes. The proposed method is suitable for regulatory analysis., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Passage cells are frequently found in the exodermis and the endodermis of the roots. Because passage cells lack an apoplastic diffusion barrier, they are thought to provide pathways for the transport of nutrients and the entrance of endomycorrhizal fungi. Exodermal passage cells possess Casparian strips but not suberin lamellae. So far, exodermal passage cells have not been associated with a particular internal structure. In some wetland plants, the outer part of the root (i.e., epidermis, exodermis, and sclerenchyma) of emerging lateral root primordia has an oxygen leaky zone called a window. The exodermis at the window site also lacks suberin lamellae, but it remains unclear whether the exodermis at the window site also lacks Casparian strips. Here, we report that several of the exodermal cells in the window of Echinochloa crus-galli grown under aerated or deoxygenated stagnant agar nutrient solution also lack lignin, which is a major constituent of Casparian strips. The sclerenchyma cells that form part of the window also lacked lignin deposits. Sites at which lateral root primordia developed were highly permeable to an apoplastic tracer (periodic acid). These observations indicate that windows consist of a novel type of passage cell at the exodermis that lacks lignin as well as suberin lamellae.

Internal aeration is crucial for root growth under waterlogged conditions. Some wetland plants have a structural barrier that impedes oxygen leakage from the basal part of roots called a radial oxygen loss (ROL) barrier. The ROL barrier reduces loss of oxygen transported via the aerenchyma to the root tips, enabling root growth into anoxic soil. The roots of some plants develop an ROL barrier under waterlogged conditions, while they remain leaky to oxygen under well-drained or aerated conditions. The main components of the inducible ROL barrier are thought to be suberin and lignin deposited at the outer cellular space (apoplast) in the outer part of roots. On the other hand, a few wetland plants including a species of Echinochloa form a constitutive ROL barrier, i.e., it is formed even in the absence of waterlogging. However, little is known about the components of constitutive ROL barriers. An ROL barrier is considered to be a characteristic of wetland species because it has not been found in any non-wetland species so far. Here, we examined whether Echinochloa species from non-waterlogged fields also form an inducible or constitutive ROL barrier. We found that three species of Echinochloa from non-waterlogged fields constitutively developed an ROL barrier under aerated conditions. Over 85% of their root exodermis cells were covered with suberin lamellae and had well-developed Casparian strips. These substances inhibited the infiltration of an apoplastic tracer (periodic acid), suggesting that the ROL barrier can also prevent the entry of phytotoxic compounds from the soil. Unlike the other Echinochloa species, E. oryzicola , which mainly inhabits rice paddies, was found to lack a constitutive ROL barrier under aerated conditions. Although close to 90% of its sclerenchyma was well lignified, it leaked oxygen from the basal part of roots. A high percentage (55%) of the root exodermis cells were not fortified with suberin lamellae. These results suggest that suberin is an important component of constitutive ROL barriers.

A reliable liquid chromatography-tandem mass spectrometry method was developed to determine total florfenicol residues in bovine tissues and eel. Florfenicol and its metabolites (florfenicol amine, monochloroflorfenicol, florfenicol oxamic acid, and florfenicol alcohol) were analyzed as the marker residue, florfenicol amine, as defined by several regulatory agencies. After hydrolysis with hydrochloric acid, samples were defatted and subjected to solid-supported liquid extraction and Oasis MCX-cartridge cleanup before analysis. The method was validated for florfenicol and its metabolites at two levels in eel and bovine muscle, fat, and liver. Excellent recoveries were obtained (93-104%), with relative standard deviations of <6% for all compounds. Negligible matrix effects and minimal analyte loss during sample preparation enabled accurate quantification by external calibration using solvent standards. No interfering peaks were observed around the retention time of florfenicol amine, indicating the high selectivity of the method. Retention times in the spiked samples corresponding to that of the calibration standard in solvent did not exceed ±0.1 min. Ion ratios from the spiked sample were within ±10% (relative) of the calibration standards. Calibration curves were linear in the range of 0.5 to 100 ng/mL, with coefficients of determination higher than 0.998. The limits of quantification and limits of detection of the proposed method were estimated to be 0.01 mg/kg and 0.0005 mg/kg, respectively, in all food samples. Thus, the developed method is considered reliable and suitable for regulatory use., (Copyright © 2019 Elsevier B.V. All rights reserved.)