Design, Synthesis, Electrochemical, and Biological Evaluation of Fluorescent Chlorido[N,N'-bis(methoxy/hydroxy)salicylidene-1,2-bis(4-methoxyphenyl)ethylenediamine]iron(III) Complexes as Anticancer Agents

The impact of methoxy and hydroxyl groups at the salicylidene moiety of chlorido[N,N'-bis(methoxy/hydroxy)salicylidene-1,2-bis(4-methoxyphenyl)ethylenediamine]iron(III) complexes was evaluated on human MDA-MB 231 breast cancer and HL-60 leukemia cells. Methoxylated complexes (C1-C3) inhibited proliferation, migration, and metabolic activity in a concentration-dependent manner following the rank order: C2 > C3 > C1. In particular, C2 was highly cytotoxic with an IC50 of 4.2 μM which was 6.6-fold lower than that of cisplatin (IC50 of 27.9 μM). In contrast, hydroxylated complexes C4-C6 were almost inactive up to the highest concentration tested due to lack of cellular uptake. C2 caused a dual mode of cell death, ferroptosis, and necroptosis, whereby at higher concentrations, ferroptosis was the preferred form. Ferroptotic morphology and the presence of ferrous iron and lipid reactive oxygen species proved the involvement of ferroptosis. C2 was identified as a promising lead compound for the design of drug candidates inducing ferroptosis.

Expanding the Utility of β-Diketiminate Ligands in Heavy Group VI Chemistry of Molybdenum and Tungsten

We report the synthesis of 17 molybdenum and tungsten complexes supported by the ubiquitous BDI ligand framework (BDI = β-diketiminate). The focal entry point is the synthesis of four molybdenum and tungsten(V) BDI complexes of the general formula [MO(BDI^R)Cl₂] [M = Mo, R = Dipp (1); M = W, R = Dipp (2); M = Mo, R = Mes (3); M = W, R = Mes (4)] synthesized by the reaction between MoOCl₃(THF)₂ or WOCl₃(THF)₂ and LiBDI^R. Reactivity studies show that the BDI^Dipp complexes are excellent precursors toward adduct formation, reacting smoothly with dimethylaminopyridine (DMAP) and triethylphosphine oxide (OPEt₃). No reaction with small phosphines has been observed, strongly contrasting the chemistry of previously reported rhenium(V) complexes. Additionally, the complexes 1 and 2 are good precursors for salt metathesis reactions. While 1 can be chemically reduced to the first stable example of a Mo(IV) BDI complex 15, reduction of 2 resulted in degradation of the BDI ligand via a nitrene transfer reaction, leading to MAD (4-((2,6-diisopropylphenyl)imino)pent-2-enide) supported tungsten(V) and tungsten(VI) complexes 16 and 17. All reported complexes have been thoroughly studied by VT-NMR and (heteronuclear) NMR spectroscopy, as well as UV-vis and EPR spectroscopy, IR spectroscopy, and X-ray diffraction analysis.

Curious Case of Cobaltocenium Carbaldehyde

Cobaltocenium carbaldehyde (formylcobaltocenium) hexafluoridophosphate, a long sought-after functionalized cobaltocenium salt, is accessible from cobaltocenium carboxylic acid by a three-step synthetic sequence involving (i) chlorination to the acid chloride, (ii) copper-borohydride reduction to the hydroxymethyl derivative, and (iii) Dess-Martin oxidation to the title compound. Due to the strongly electron-withdrawing cationic cobaltocenium moiety, no standard aldehyde reactivity is observed. Instead, nucleophilic addition followed by haloform-type cleavage prevails, thereby ruling out common useful aldehyde derivatization. One-electron reduction of cobaltocenium carbaldehyde hexafluoridophosphate affords the deep-blue, isolable cobaltocene carbaldehyde 19-valence-electron radical whose spin density is located fully at cobalt and not at the formyl carbon atom. ¹H/¹³C NMR, IR, EPR spectroscopy, high-resolution mass spectrometry, cyclic voltammetry, single crystal structure analysis (XRD), and density functional theory are applied to characterize these unusual formyl-cobaltocenium/cobaltocene compounds.

A mesoionic carbene complex of manganese in five oxidation states

Reaction between a carbazole-based mesoionic carbene ligand and manganese(II) iodide results in the formation of a rare air-stable manganese(IV) complex after aerobic workup. Cyclic voltammetry reveals the complex to be stable in five oxidation states. The electronic structure of all five oxidation states is elucidated chemically, spectroscopically (NMR, high-frequency EPR, UV-Vis, MCD), magnetically, and computationally (DFT, CASSCF).

Simulating Root Growth as a Function of Soil Strength and Yield With a Field-Scale Crop Model Coupled With a 3D Architectural Root Model

Accurate prediction of root growth and related resource uptake is crucial to accurately simulate crop growth especially under unfavorable environmental conditions. We coupled a 1D field-scale crop-soil model running in the SIMPLACE modeling framework with the 3D architectural root model CRootbox on a daily time step and implemented a stress function to simulate root elongation as a function of soil bulk density and matric potential. The model was tested with field data collected during two growing seasons of spring barley and winter wheat on Haplic Luvisol. In that experiment, mechanical strip-wise subsoil loosening (30-60 cm) (DL treatment) was tested, and effects on root and shoot growth at the melioration strip as well as in a control treatment were evaluated. At most soil depths, strip-wise deep loosening significantly enhanced observed root length densities (RLDs) of both crops as compared to the control. However, the enhanced root growth had a beneficial effect on crop productivity only in the very dry season in 2018 for spring barley where the observed grain yield at the strip was 18% higher as compared to the control. To understand the underlying processes that led to these yield effects, we simulated spring barley and winter wheat root and shoot growth using the described field data and the model. For comparison, we simulated the scenarios with the simpler 1D conceptual root model. The coupled model showed the ability to simulate the main effects of strip-wise subsoil loosening on root and shoot growth. It was able to simulate the adaptive plasticity of roots to local soil conditions (more and thinner roots in case of dry and loose soil). Additional scenario runs with varying weather conditions were simulated to evaluate the impact of deep loosening on yield under different conditions. The scenarios revealed that higher spring barley yields in DL than in the control occurred in about 50% of the growing seasons. This effect was more pronounced for spring barley than for winter wheat. Different virtual root phenotypes were tested to assess the potential of the coupled model to simulate the effect of varying root traits under different conditions.

Root System Scale Models Significantly Overestimate Root Water Uptake at Drying Soil Conditions

Soil hydraulic conductivity (k _soil ) drops significantly in dry soils, resulting in steep soil water potential gradients (ψ _s ) near plant roots during water uptake. Coarse soil grid resolutions in root system scale (RSS) models of root water uptake (RWU) generally do not spatially resolve this gradient in drying soils which can lead to a large overestimation of RWU. To quantify this, we consider a benchmark scenario of RWU from drying soil for which a numerical reference solution is available. We analyze this problem using a finite volume scheme and investigate the impact of grid size on the RSS model results. At dry conditions, the cumulative RWU was overestimated by up to 300% for the coarsest soil grid of 4.0 cm and by 30% for the finest soil grid of 0.2 cm, while the computational demand increased from 19 s to 21 h. As an accurate and computationally efficient alternative to the RSS model, we implemented a continuum multi-scale model where we keep a coarse grid resolution for the bulk soil, but in addition, we solve a 1-dimensional radially symmetric soil model at rhizosphere scale around individual root segments. The models at the two scales are coupled in a mass-conservative way. The multi-scale model compares best to the reference solution (-20%) at much lower computational costs of 4 min. Our results demonstrate the need to shift to improved RWU models when simulating dry soil conditions and highlight that results for dry conditions obtained with RSS models of RWU should be interpreted with caution.

Mesoionic Carbenes in Low- to High-Valent Vanadium Chemistry

We report the synthesis of vanadium(V) oxo complex 1 with a pincer-type dianionic mesoionic carbene (MIC) ligand L1 and the general formula [VOCl(L1)]. A comparison of the structural (SC-XRD), electronic (UV-vis), and electrochemical (cyclic voltammetry) properties of 1 with the benzimidazolinylidene congener 2 (general formula [VOCl(L2)]) shows that the MIC is a stronger donor also for early transition metals with low d-electron population. Since electrochemical studies revealed both complexes to be reversibly reduced, the stronger donor character of MICs was not only demonstrated for the vanadium(V) but also for the vanadium(IV) oxidation state by isolating the reduced vanadium(IV) complexes [Co(Cp*)2][1] and [Co(Cp*)2][2] ([Co(Cp*)2] = decamethylcobaltocenium). The electronic structures of the compounds were investigated by computational methods. Complex 1 was found to be a moderate precursor for salt metathesis reactions, showing selective reactivity toward phenolates or secondary amides, but not toward primary amides and phosphides, thiophenols, or aryls/alkyls donors. Deoxygenation with electron-rich phosphines failed to give the desired vanadium(III) complex. However, treatment of the deprotonated ligand precursor with vanadium(III) trichloride resulted in the clean formation of the corresponding MIC vanadium(III) complex 6, which undergoes a clean two-electron oxidation with organic azides yielding the corresponding imido complexes. The reaction with TMS-N3 did not afford a nitrido complex, but instead the imido complex 10. This study reveals that, contrary to popular belief, MICs are capable of supporting early transition-metal complexes in a variety of oxidation states, thus making them promising candidates for the activation of small molecules and redox catalysis.

Call for Participation: Collaborative Benchmarking of Functional-Structural Root Architecture Models. The Case of Root Water Uptake

Three-dimensional models of root growth, architecture and function are becoming important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common in many disciplines that use numerical models, such as natural and engineering sciences, functional-structural root architecture models have never been systematically compared. The following reasons might induce disagreement between the simulation results of different models: different representation of root growth, sink term of root water and solute uptake and representation of the rhizosphere. Presently, the extent of discrepancies is unknown, and a framework for quantitatively comparing functional-structural root architecture models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of complex models: root architecture, water flow in soil and water flow in roots. While the latter two will focus mainly on comparing numerical aspects, the root architectural models have to be compared at a conceptual level as they generally differ in process representation. Therefore, defining common inputs that allow recreating reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled problems are defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. This benchmarking will result in a better understanding of the different models and contribute toward improving them. Improved models will allow us to simulate various scenarios with greater confidence and avoid bugs, numerical errors or conceptual misunderstandings. This work will set a standard for future model development.

Mechanical and Hydric Stress Effects on Maize Root System Development at Different Soil Compaction Levels

Soil mechanical resistance, aeration, and water availability directly affect plant root growth. The objective of this work was to identify the contribution of mechanical and hydric stresses on maize root elongation, by modeling root growth while taking the dynamics of these stresses in an Oxisol into consideration. The maize crop was cultivated under four compaction levels (soil chiseling, no-tillage system, areas trafficked by a tractor, and trafficked by a harvester), and we present a new model, which allows to distinguish between mechanical and hydric stresses. Root length density profiles, soil bulk density, and soil water retention curves were determined for four compaction levels up to 50 cm in depth. Furthermore, grain yield and shoot biomass of maize were quantified. The new model described the mechanical and hydric stresses during maize growth with field data for the first time in maize crop. Simulations of root length density in 1D and 2D showed adequate agreement with the values measured under field conditions. Simulation makes it possible to identify the interaction between the soil physical conditions and maize root growth. Compared to the no-tillage system, grain yield was reduced due to compaction caused by harvester traffic and by soil chiseling. The root growth was reduced by the occurrence of mechanical and hydric stresses during the crop cycle, the principal stresses were mechanical in origin for areas with agricultural traffic, and water based in areas with soil chiseling. Including mechanical and hydric stresses in root growth models can help to predict future scenarios, and coupling soil biophysical models with weather, soil, and crop responses will help to improve agricultural management.

Connecting the dots between computational tools to analyse soil-root water relations

In recent years, many computational tools, such as image analysis, data management, process-based simulation, and upscaling tools, have been developed to help quantify and understand water flow in the soil-root system, at multiple scales (tissue, organ, plant, and population). Several of these tools work together or at least are compatible. However, for the uninformed researcher, they might seem disconnected, forming an unclear and disorganized succession of tools. In this article, we show how different studies can be further developed by connecting them to analyse soil-root water relations in a comprehensive and structured network. This 'explicit network of soil-root computational tools' informs readers about existing tools and helps them understand how their data (past and future) might fit within the network. We also demonstrate the novel possibilities of scale-consistent parameterizations made possible by the network with a set of case studies from the literature. Finally, we discuss existing gaps in the network and how we can move forward to fill them.

Hyperspectral imaging: a novel approach for plant root phenotyping

BACKGROUND

Root phenotyping aims to characterize root system architecture because of its functional role in resource acquisition. RGB imaging and analysis procedures measure root system traits via colour contrasts between roots and growth media or artificial backgrounds. In the case of plants grown in soil-filled rhizoboxes, where the colour contrast can be poor, it is hypothesized that root imaging based on spectral signatures improves segmentation and provides additional knowledge on physico-chemical root properties.

RESULTS

Root systems of Triticum durum grown in soil-filled rhizoboxes were scanned in a spectral range of 1000-1700 nm with 222 narrow bands and a spatial resolution of 0.1 mm. A data processing pipeline was developed for automatic root segmentation and analysis of spectral root signatures. Spectral- and RGB-based root segmentation did not significantly differ in accuracy even for a bright soil background. Best spectral segmentation was obtained from log-linearized and asymptotic least squares corrected images via fuzzy clustering and multilevel thresholding. Root axes revealed major spectral distinction between center and border regions. Root decay was captured by an exponential function of the difference spectra between water and structural carbon absorption regions.

CONCLUSIONS

Fundamentals for root phenotyping using hyperspectral imaging have been established by means of an image processing pipeline for automated segmentation of soil-grown plant roots at a high spatial resolution and for the exploration of spectral signatures encoding physico-chemical root zone properties.

CRootBox: a structural-functional modelling framework for root systems

Background and Aims

Root architecture development determines the sites in soil where roots provide input of carbon and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architecture models have been widely used and been further developed into functional-structural models that simulate the fate of water and solutes in the soil-root system. The root architecture model CRootBox presented here is a flexible framework to model root architecture and its interactions with static and dynamic soil environments.

Methods

CRootBox is a C++-based root architecture model with Python binding, so that CRootBox can be included via a shared library into any Python code. Output formats include VTP, DGF, RSML and a plain text file containing coordinates of root nodes. Furthermore, a database of published root architecture parameters was created. The capabilities of CRootBox for the unconfined growth of single root systems, as well as the different parameter sets, are highlighted in a freely available web application.

Key results

The capabilities of CRootBox are demonstrated through five different cases: (1) free growth of individual root systems; (2) growth of root systems in containers as a way to mimic experimental setups; (3) field-scale simulation; (4) root growth as affected by heterogeneous, static soil conditions; and (5) coupling CRootBox with code from the book Soil physics with Python to dynamically compute water flow in soil, root water uptake and water flow inside roots.

Conclusions

CRootBox is a fast and flexible functional-structural root model that is based on state-of-the-art computational science methods. Its aim is to facilitate modelling of root responses to environmental conditions as well as the impact of roots on soil. In the future, this approach will be extended to the above-ground part of the plant.

RGB and Spectral Root Imaging for Plant Phenotyping and Physiological Research: Experimental Setup and Imaging Protocols

Better understanding of plant root dynamics is essential to improve resource use efficiency of agricultural systems and increase the resistance of crop cultivars against environmental stresses. An experimental protocol is presented for RGB and hyperspectral imaging of root systems. The approach uses rhizoboxes where plants grow in natural soil over a longer time to observe fully developed root systems. Experimental settings are exemplified for assessing rhizobox plants under water stress and studying the role of roots. An RGB imaging setup is described for cheap and quick quantification of root development over time. Hyperspectral imaging improves root segmentation from the soil background compared to RGB color based thresholding. The particular strength of hyperspectral imaging is the acquisition of chemometric information on the root-soil system for functional understanding. This is demonstrated with high resolution water content mapping. Spectral imaging however is more complex in image acquisition, processing and analysis compared to the RGB approach. A combination of both methods can optimize a comprehensive assessment of the root system. Application examples integrating root and aboveground traits are given for the context of plant phenotyping and plant physiological research. Further improvement of root imaging can be obtained by optimizing RGB image quality with better illumination using different light sources and by extension of image analysis methods to infer on root zone properties from spectral data.

Root architecture simulation improves the inference from seedling root phenotyping towards mature root systems

Root phenotyping provides trait information for plant breeding. A shortcoming of high-throughput root phenotyping is the limitation to seedling plants and failure to make inferences on mature root systems. We suggest root system architecture (RSA) models to predict mature root traits and overcome the inference problem. Sixteen pea genotypes were phenotyped in (i) seedling (Petri dishes) and (ii) mature (sand-filled columns) root phenotyping platforms. The RSA model RootBox was parameterized with seedling traits to simulate the fully developed root systems. Measured and modelled root length, first-order lateral number, and root distribution were compared to determine key traits for model-based prediction. No direct relationship in root traits (tap, lateral length, interbranch distance) was evident between phenotyping systems. RootBox significantly improved the inference over phenotyping platforms. Seedling plant tap and lateral root elongation rates and interbranch distance were sufficient model parameters to predict genotype ranking in total root length with an RSpearman of 0.83. Parameterization including uneven lateral spacing via a scaling function substantially improved the prediction of architectures underlying the differently sized root systems. We conclude that RSA models can solve the inference problem of seedling root phenotyping. RSA models should be included in the phenotyping pipeline to provide reliable information on mature root systems to breeding research.

L-System model for the growth of arbuscular mycorrhizal fungi, both within and outside of their host roots

Development of arbuscular mycorrhizal fungal colonization of roots and the surrounding soil is the central process of mycorrhizal symbiosis, important for ecosystem functioning and commercial inoculum applications. To improve mechanistic understanding of this highly spatially and temporarily dynamic process, we developed a three-dimensional model taking into account growth of the roots and hyphae. It is for the first time that infection within the root system is simulated dynamically and in a spatially resolved way. Comparison between data measured in a calibration experiment and simulated results showed a good fit. Our simulations showed that the position of the fungal inoculum affects the sensitivity of hyphal growth parameters. Variation in speed of secondary infection and hyphal lifetime had a different effect on root infection and hyphal length, respectively, depending on whether the inoculum was concentrated or dispersed. For other parameters (branching rate, distance between entry points), the relative effect was the same independent of inoculum placement. The model also indicated that maximum root colonization levels well below 100%, often observed experimentally, may be a result of differential spread of roots and hyphae, besides intrinsic plant control, particularly upon localized placement of inoculum and slow secondary infection.

Can diversity in root architecture explain plant water use efficiency? A modeling study

Drought stress is a dominant constraint to crop production. Breeding crops with adapted root systems for effective uptake of water represents a novel strategy to increase crop drought resistance. Due to complex interaction between root traits and high diversity of hydrological conditions, modeling provides important information for trait based selection. In this work we use a root architecture model combined with a soil-hydrological model to analyze whether there is a root system ideotype of general adaptation to drought or water uptake efficiency of root systems is a function of specific hydrological conditions. This was done by modeling transpiration of 48 root architectures in 16 drought scenarios with distinct soil textures, rainfall distributions, and initial soil moisture availability. We find that the efficiency in water uptake of root architecture is strictly dependent on the hydrological scenario. Even dense and deep root systems are not superior in water uptake under all hydrological scenarios. Our results demonstrate that mere architectural description is insufficient to find root systems of optimum functionality. We find that in environments with sufficient rainfall before the growing season, root depth represents the key trait for the exploration of stored water, especially in fine soils. Root density, instead, especially near the soil surface, becomes the most relevant trait for exploiting soil moisture when plant water supply is mainly provided by rainfall events during the root system development. We therefore concluded that trait based root breeding has to consider root systems with specific adaptation to the hydrology of the target environment.

Root system markup language: toward a unified root architecture description language

The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow.

Coarse and fine root plants affect pore size distributions differently

AIMS

Small scale root-pore interactions require validation of their impact on effective hydraulic processes at the field scale. Our objective was to develop an interpretative framework linking root effects on macroscopic pore parameters with knowledge at the rhizosphere scale.

METHODS

A field experiment with twelve species from different families was conducted. Parameters of Kosugi's pore size distribution (PSD) model were determined inversely from tension infiltrometer data. Measured root traits were related to pore variables by regression analysis. A pore evolution model was used to analyze if observed pore dynamics followed a diffusion like process.

RESULTS

Roots essentially conditioned soil properties at the field scale. Rooting densities higher than 0.5 % of pore space stabilized soil structure against pore loss. Coarse root systems increased macroporosity by 30 %. Species with dense fine root systems induced heterogenization of the pore space and higher micropore volume. We suggested particle re-orientation and aggregate coalescence as main underlying processes. The diffusion type pore evolution model could only partially capture the observed PSD dynamics.

CONCLUSIONS

Root systems differing in axes morphology induced distinctive pore dynamics. Scaling between these effective hydraulic impacts and processes at the root-pore interface is essential for plant based management of soil structure.

Space-charge compensation measurements in electron cyclotron resonance ion source low energy beam transport lines with a retarding field analyzer

In this paper we describe the first systematic measurement of beam neutralization (space charge compensation) in the ECR low energy transport line with a retarding field analyzer, which can be used to measure the potential of the beam. Expected trends for the space charge compensation levels such as increase with residual gas pressure, beam current, and beam density could be observed. However, the overall levels of neutralization are consistently low (<60%). The results and the processes involved for neutralizing ion beams are discussed for conditions typical for ECR injector beam lines. The results are compared to a simple theoretical beam plasma model as well as simulations.

First charge breeding of a rare-isotope beam with the electron-beam ion trap of the ReA post-accelerator at the National Superconducting Cyclotron Laboratory

An electron-beam ion trap (EBIT) charge breeder is being brought into operation at the National Superconducting Cyclotron Laboratory at Michigan State University. The EBIT is part of the ReA post-accelerator for reacceleration of rare isotopes, which are thermalized in a gas "stopping" cell after being produced at high energy by projectile fragmentation. The ReA EBIT has a distinctive design; it is characterized by a high-current electron gun and a two-field superconducting magnet to optimize the capture and charge-breeding efficiency of continuously injected singly charged ion beams. Following a brief overview of the reaccelerator system and the ReA EBIT, this paper presents the latest commissioning results, particularly, charge breeding and reacceleration of the highly charged rare isotopes, (76)Ga(24 +, 25 +).

Root induced changes of effective 1D hydraulic properties in a soil column

AIMS

Roots are essential drivers of soil structure and pore formation. This study aimed at quantifying root induced changes of the pore size distribution (PSD). The focus was on the extent of clogging vs. formation of pores during active root growth.

METHODS

Parameters of Kosugi's lognormal PSD model were determined by inverse estimation in a column experiment with two cover crops (mustard, rye) and an unplanted control. Pore dynamics were described using a convection-dispersion like pore evolution model.

RESULTS

Rooted treatments showed a wider range of pore radii with increasing volumes of large macropores >500 μm and micropores <2.5 μm, while fine macropores, mesopores and larger micropores decreased. The non-rooted control showed narrowing of the PSD and reduced porosity over all radius classes. The pore evolution model accurately described root induced changes, while structure degradation in the non-rooted control was not captured properly. Our study demonstrated significant short term root effects with heterogenization of the pore system as dominant process of root induced structure formation.

CONCLUSIONS

Pore clogging is suggested as a partial cause for reduced pore volume. The important change in micro- and large macropores however indicates that multiple mechanic and biochemical processes are involved in root-pore interactions.

Recovering root system traits using image analysis exemplified by two-dimensional neutron radiography images of lupine

Root system traits are important in view of current challenges such as sustainable crop production with reduced fertilizer input or in resource-limited environments. We present a novel approach for recovering root architectural parameters based on image-analysis techniques. It is based on a graph representation of the segmented and skeletonized image of the root system, where individual roots are tracked in a fully automated way. Using a dynamic root architecture model for deciding whether a specific path in the graph is likely to represent a root helps to distinguish root overlaps from branches and favors the analysis of root development over a sequence of images. After the root tracking step, global traits such as topological characteristics as well as root architectural parameters are computed. Analysis of neutron radiographic root system images of lupine (Lupinus albus) grown in mesocosms filled with sandy soil results in a set of root architectural parameters. They are used to simulate the dynamic development of the root system and to compute the corresponding root length densities in the mesocosm. The graph representation of the root system provides global information about connectivity inside the graph. The underlying root growth model helps to determine which path inside the graph is most likely for a given root. This facilitates the systematic investigation of root architectural traits, in particular with respect to the parameterization of dynamic root architecture models.

A statistical approach to root system classification

Plant root systems have a key role in ecology and agronomy. In spite of fast increase in root studies, still there is no classification that allows distinguishing among distinctive characteristics within the diversity of rooting strategies. Our hypothesis is that a multivariate approach for "plant functional type" identification in ecology can be applied to the classification of root systems. The classification method presented is based on a data-defined statistical procedure without a priori decision on the classifiers. The study demonstrates that principal component based rooting types provide efficient and meaningful multi-trait classifiers. The classification method is exemplified with simulated root architectures and morphological field data. Simulated root architectures showed that morphological attributes with spatial distribution parameters capture most distinctive features within root system diversity. While developmental type (tap vs. shoot-borne systems) is a strong, but coarse classifier, topological traits provide the most detailed differentiation among distinctive groups. Adequacy of commonly available morphologic traits for classification is supported by field data. Rooting types emerging from measured data, mainly distinguished by diameter/weight and density dominated types. Similarity of root systems within distinctive groups was the joint result of phylogenetic relation and environmental as well as human selection pressure. We concluded that the data-define classification is appropriate for integration of knowledge obtained with different root measurement methods and at various scales. Currently root morphology is the most promising basis for classification due to widely used common measurement protocols. To capture details of root diversity efforts in architectural measurement techniques are essential.

HDR syndrome: a follow-up genotype-phenotype analysis of a de novo missense Thr272Ile mutation in exon 4 of GATA3

Hypoparathyroidism, sensorineural deafness and renal dysplasia (HDR) syndrome (MIM 146255) is a rare autosomal dominant disorder caused by mutations in the gene encoding GATA3, a dual zinc-finger transcription factor involved in vertebrate embryonic development. In this clinical case study we report on a follow-up of a phenotype associated with a GATA3 mutation. HDR syndrome was clinically diagnosed at age of 1.5 years in a boy with a de novo heterozygous missense (c.815C→T) mutation, Thr272Ile, in exon 4 of the GATA3 gene. Both parents were negative for Thr272Ile.At age of 17 months, the patient had a weight of 10.7, a body length of 78 cm, and a head circumference of 47.5 cm. By the age of 7 years, growth is age-appropriate, severe bilateral hearing loss (dB 60) was corrected by hearing aids. However, cognitive development (auditory sensory me-mory and language abilities) is at the lower ends of the test scores.In conclusion, a mildly impaired clinical course was achieved by the age of 7 years in a patient with HDR syndrome; this report adds to the body of data on genotype-phenotype analysis in HDR syndrome. ·

Low energy beam transport for facility for rare isotope beams driver linear particle accelerator

The driver linac for the facility for rare isotope beams (FRIB) will provide a wide range of primary ion beams for nuclear physics research. The linac will be capable of accelerating a uranium beam to an energy of up to 200 Mev∕u and delivering it to a fragmentation target with a maximum power of 400 kW. Stable ion beams will be produced by a high performance electron cyclotron resonance ion source operating at 28 GHz. The ion source will be located on a high voltage platform to reach an initial beam energy of 12 keV∕u. After extraction, the ion beam will be transported vertically down to the linac tunnel in a low energy beam transport (LEBT) system and injected into a radio frequency quadrupole (RFQ) operating at a frequency of 80.5 MHz. To meet the beam power requirements, simultaneous acceleration of two-charge states will be used for heavier ions (≥Xe). This paper presents the layout of the FRIB LEBT and the beam dynamics in the LEBT. In particular, simulation and design of the beam line section before charge state selection will be detailed. The need to use an achromatic design for the charge state selection system and the advantage of an ion beam collimation system to limit the emittance of the beam injected into the RFQ will be discussed in this paper.

Progress towards the development of a realistic electron cyclotron resonance ion source extraction model

In this paper, an ongoing effort to provide a simulation and design tool for electron cyclotron resonance ion source extraction and low energy beam transport is described and benchmarked against experimental results. Utilizing the particle-in-cell code WARP, a set of scripts has been developed: A semiempirical method of generating initial conditions, a 2D-3D hybrid method of plasma extraction and a simple beam transport deck. Measured emittances and beam profiles of uranium and helium beams are shown and the influence of the sextupole part of the plasma confinement field is investigated. The results are compared to simulations carried out using the methods described above. The results show that the simulation model (with some additional refinements) represents highly charged, well-confined ions well, but that the model is less applicable for less confined, singly charged ions.

Initial commissioning results with the NSCL Electron Beam Ion Trap

The ReA reaccelerator is being added to the National Superconducting Cyclotron Laboratory (NSCL) fragmentation facility in order to provide exotic rare-isotope beams, not available at the Isotope Separation On-Line facilities, in the several-MeV/u energy range. The first stage of the NSCL reaccelerator complex, consisting of an EBIT charge breeder, a room-temperature radiofrequency quadrupole (RFQ) accelerator, and superconducting linear accelerator modules, has been completed and is being put into operation. Commissioning of the EBIT has started by extracting charge-bred residual gas ions, ions created from a Ne gas jet directed across the EBIT's electron beam and ions captured from an external test ion source. Charge-bred ions from the Ne gas jet have been extracted as a pulse and accelerated through the RFQ and the two cryomodules.

DNA methylation studies on imprinted loci in a male monozygotic twin pair discordant for Beckwith-Wiedemann syndrome

Beckwith–Wiedemann syndrome (BWS) is one of the most prevalent congenital disorders predominantly caused by epigenetic alterations. Here we present an extensive case study of a monozygotic monochorionic male twin pair discordant for BWS. Our analysis allows to correlate BWS symptoms, like a protruding tongue, indented ears and transient neonatal hypoglycaemia, to an abnormal methylation at the KvDMR1. DNAs extracted from peripheral blood, skin fibroblasts, saliva and buccal swab of both twins, their sister and parents were analysed at 11 differentially methylated regions (DMRs) including all four relevant DMRs of the BWS region. The KvDMR1 was exclusively found to be hypomethylated in all cell types of the affected BWS twin, while the unaffected twin and the relatives showed normal methylation in fibroblasts, buccal swab and saliva DNA. Interestingly, the twins share a common blood-specific hypomethylation phenotype most probably caused by a feto-fetal transfusion between both twins. Because microsatellite analysis furthermore revealed a normal biparental karyotype for chromosome 11, our results point to an exclusive correlation of the observed BWS symptoms to locally restricted epimutations at the KvDMR1 of the maternal chromosome.

The effect of rf pulse pattern on bremsstrahlung and ion current time evolution of an ECRIS

Time-resolved helium ion production and bremsstrahlung emission from JYFL 14 GHz ECRIS is presented with different radio frequency pulse lengths. rf on times are varied from 5 to 50 ms and rf off times from 10 to 1000 ms between different measurement sets. It is observed that the plasma breakdown occurs a few milliseconds after launching the rf power into the plasma chamber, and in the beginning of the rf pulses a preglow transient is seen. During this transient the ion beam currents are increased by several factors compared to a steady state situation. By adjusting the rf pulse separation the maximum ion beam currents can be maintained during the so-called preglow regime while the amount of bremsstrahlung radiation is significantly decreased.

A dynamic model of nutrient uptake by root hairs

Root hairs are known to be important in the uptake of sparingly soluble nutrients by plants, but quantitative understanding of their role in this is weak. This limits, for example, the breeding of more nutrient-efficient crop genotypes. We developed a mathematical model of nutrient transport and uptake in the root hair zone of single roots growing in soil or solution culture. Accounting for root hair geometry explicitly, we derived effective equations for the cumulative effect of root hair surfaces on uptake using the method of homogenization. Analysis of the model shows that, depending on the morphological and physiological properties of the root hairs, one of three different effective models applies. They describe situations where: (1) a concentration gradient dynamically develops within the root hair zone; (2) the effect of root hair uptake is negligibly small; or (3) phosphate in the root hair zone is taken up instantaneously. Furthermore, we show that the influence of root hairs on rates of phosphate uptake is one order of magnitude greater in soil than solution culture. The model provides a basis for quantifying the importance of root hair morphological and physiological properties in overall uptake, in order to design and interpret experiments in different circumstances.

The third generation superconducting 28 GHz electron cyclotron resonance ion source VENUS (invited)

VENUS is a third generation electron cyclotron resonance (ECR) ion source, which incorporates a high field superconducting NbTi magnet structure, a 28 GHz gryotron microwave source and a state of the art closed cycle cryosystem. During the decade from initial concept to regular operation, it has demonstrated both the feasibility and the performance levels of this new generation of ECR ion sources and required innovation on magnet construction, plasma chamber design, and beam transport. In this paper, the development, performance, and major innovations are described as well as a look to the potential to construct a fourth generation ECR ion source.

Measurement of radial and axial high energy x-ray spectra in electron cyclotron resonance ion source plasmas

Radial and axial x-ray measurements of electron cyclotron resonance ion sources operating at microwave frequencies of 6.4 and 14 GHz are presented. Results indicate a greater detected photon energy in the radial direction than the axial direction for both the 6.4 GHz source and the 14 GHz source. It is also seen that the 14 GHz source produces x-rays with higher energies, when compared to the 6.4 GHz source, in both radial and axial directions.

Development of a pepper-pot device to determine the emittance of an ion beam generated by electron cyclotron resonance ion sources

This paper describes the recent development and commissioning of a pepper-pot emittance meter at the Lawrence Berkeley National Laboratory (LBNL). It is based on a potassium bromide (KBr) scintillator screen in combination with a charged coupled device camera. Pepper-pot scanners record the full four-dimensional transverse phase space emittances which are particularly interesting for electron cyclotron resonance ion sources. The strengths and limitations of evaluating emittances using optical pepper-pot scanners are described and systematic errors induced by the optical data acquisition system will be presented. Light yield tests of KBr exposed to different ion species and first emittance measurement data using ion beams extracted from the 6.4 GHz LBNL electron cyclotron resonance ion source are presented and discussed.

Nb3Sn superconducting magnets for electron cyclotron resonance ion sources

Electron cyclotron resonance (ECR) ion sources are an essential component of heavy-ion accelerators. Over the past few decades advances in magnet technology and an improved understanding of the ECR ion source plasma physics have led to remarkable performance improvements of ECR ion sources. Currently third generation high field superconducting ECR ion sources operating at frequencies around 28 GHz are the state of the art ion injectors and several devices are either under commissioning or under design around the world. At the same time, the demand for increased intensities of highly charged heavy ions continues to grow, which makes the development of even higher performance ECR ion sources a necessity. To extend ECR ion sources to frequencies well above 28 GHz, new magnet technology will be needed in order to operate at higher field and force levels. The superconducting magnet program at LBNL has been developing high field superconducting magnets for particle accelerators based on Nb(3)Sn superconducting technology for several years. At the moment, Nb(3)Sn is the only practical conductor capable of operating at the 15 T field level in the relevant configurations. Recent design studies have been focused on the possibility of using Nb(3)Sn in the next generation of ECR ion sources. In the past, LBNL has worked on the VENUS ECR, a 28 GHz source with solenoids and a sextupole made with NbTi operating at fields of 6-7 T. VENUS has now been operating since 2004. We present in this paper the design of a Nb(3)Sn ECR ion source optimized to operate at an rf frequency of 56 GHz with conductor peak fields of 13-15 T. Because of the brittleness and strain sensitivity of Nb(3)Sn, particular care is required in the design of the magnet support structure, which must be capable of providing support to the coils without overstressing the conductor. In this paper, we present the main features of the support structure, featuring an external aluminum shell pretensioned with water-pressurized bladders, and we analyze the expected coil stresses with a two-dimensional finite element mechanical model.

Measurement of the high energy component of the x-ray spectra in the VENUS electron cyclotron resonance ion source

High performance electron cyclotron resonance (ECR) ion sources, such as VENUS (Versatile ECR for NUclear Science), produce large amounts of x-rays. By studying their energy spectra, conclusions can be drawn about the electron heating process and the electron confinement. In addition, the bremsstrahlung from the plasma chamber is partly absorbed by the cold mass of the superconducting magnet, adding an extra heat load to the cryostat. Germanium or NaI detectors are generally used for x-ray measurements. Due to the high x-ray flux from the source, the experimental setup to measure bremsstrahlung spectra from ECR ion sources is somewhat different from that for the traditional nuclear physics measurements these detectors are generally used for. In particular, the collimation and background shielding can be problematic. In this paper, we will discuss the experimental setup for such a measurement, the energy calibration and background reduction, the shielding of the detector, and collimation of the x-ray flux. We will present x-ray energy spectra and cryostat heating rates depending on various ion source parameters, such as confinement fields, minimum B-field, rf power, and heating frequency.

Fourth generation electron cyclotron resonance ion sources

The concepts and technical challenges related to developing a fourth generation electron cyclotron resonance (ECR) ion source with a rf frequency greater than 40 GHz and magnetic confinement fields greater than twice B(ECR) will be explored in this article. Based on the semiempirical frequency scaling of ECR plasma density with the square of operating frequency, there should be significant gains in performance over current third generation ECR ion sources, which operate at rf frequencies between 20 and 30 GHz. While the third generation ECR ion sources use NbTi superconducting solenoid and sextupole coils, the new sources will need to use different superconducting materials, such as Nb(3)Sn, to reach the required magnetic confinement, which scales linearly with rf frequency. Additional technical challenges include increased bremsstrahlung production, which may increase faster than the plasma density, bremsstrahlung heating of the cold mass, and the availability of high power continuous wave microwave sources at these frequencies. With each generation of ECR ion sources, there are new challenges to be mastered, but the potential for higher performance and reduced cost of the associated accelerator continues to make this a promising avenue for development.

High intensity production of high and medium charge state uranium and other heavy ion beams with VENUS

The next generation, superconducting electron cyclotron resonance (ECR) ion source VENUS (versatile ECR ion source for nuclear science) started operation with 28 GHz microwave heating in 2004. Since then it has produced world record ion beam intensities. For example, 2850 e microA of O(6+), 200 e microA of U(33+) or U(34+), and in respect to high charge state ions, 1 e microA of Ar(18+), 270 e microA of Ar(16+), 28 e microA of Xe(35+), and 4.9 e microA of U(47+) have been produced. A brief overview of the latest developments leading to these record intensities is given and the production of high intensity uranium beams is discussed in more detail.

A novel HLA-DRB1*13 allele (DRB1*1357) identified by polymerase chain reaction with sequence-specific primers and direct sequencing

We describe the identification of a new DRB1*13 allele, DRB1*1357*, found in two Austrian Caucasian individuals. The novel allele was initially suspected because analysis with sequence-specific primers resulted in an unusual pattern of amplification. Thereafter, exon 2 was further characterized by sequence-based typing. The nucleotide sequence of DRB1*1357 is identical to DRB1*1319 except for a single substitution in codon 47 (TAC to TTC) leading to a change from phenylalanine to tyrosine.

Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

Serological and nucleotide sequence analysis of HLA-A*6812

We describe a novel HLA-A allele, HLA-A*6812. HLA-typing of a patient was performed by serology and by DNA-based analyses. Cloning and sequencing of exons 2 and 3 revealed that the genotype consisted of a common HLA-A*0101 allele and the novel HLA-A*6812 allele. HLA*6812 is identical to HLA-A*68012 except for a single non-synonymous nucleotide substitution leading to an exchange of a threonine to an isoleucine residue at position 142 of the HLA-class I alpha chain. The allele was also found in the patient's mother. The novel HLA-A68 molecule is recognised by some but not all of our HLA-A28-specific sera. These results confirm that position 142 is important for the serological properties of the HLA-A molecule.

Sequence-dependent stability of intramolecular DNA triple helices

A set of 21 oligodeoxynucleotides were designed to fold into intramolecular triple helices of the pyrimidine motif under appropriate conditions. UV melting experiments on the triplexes which only differ in the number and distribution of third strand cytosines reveal the influence of sequence and pH on triplex stability and can be summarized as follows: (1) increasing the cytosine content in the third strand results in a higher thermal stability of the triplex at acidic pH but lowers the triplex to duplex melting temperature at neutral pH; (2) cytosines at terminal positions destabilize the triple helical structure as compared to non-terminal positions; (3) contiguous cytosines lead to a pH dependent destabilization of the triplex, the destabilizing effect being more pronounced at higher pH. Analysis of these effects in terms of the various interactions within a triple helical complex indicate that the sequence-dependent stabilities are largely determined by the extent of protonation for individual third strand cytosines.

Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability

To investigate cytosine protonation and its influence on the sequence-dependent thermal stability of DNA triplexes in detail, we have employed homo- and heteronuclear NMR experiments on specifically (15)N-labeled oligodeoxynucleotides that were designed to fold into intramolecular triple helices of the pyrimidine motif under appropriate conditions. These experiments reveal that cytosines in central positions of the triplex are significantly protonated even at neutral pH. However, semiprotonation points for individual cytosine bases as determined from pH-dependent measurements show considerable differences depending on their position. Thus, protonation is disfavored for adjacent cytosines or for cytosines at the triplex termini, resulting in a smaller contribution to the overall free energy of the triple helical system. In contrast, protonation of the base upon substitution of 5-methylcytosine for cytosine in the triplex third strand is only affected to a minor extent, and triplex stabilization by the methyl substituent is shown to primarily arise from stacking energies and/or hydrophobic effects.

Structural heterogeneity in intramolecular DNA triple helices

Oligodeoxynucleotides designed to form intramolecular triple helices are widely used as model systems in thermodynamic and structural studies. We now report results from UV, Raman and NMR experiments demonstrating that the strand polarity, which also determines the orientation of the connecting loops, has a considerable impact on the formation and stability of pyr x pur x pyr triple helices. There are two types of monomolecular triplexes that can be defined by the location of their purine tract at either the 5'- or 3'-end of the sequence. We have examined four pairs of oligonucleotides with the same base composition but with reversed polarity that can fold into intramolecular triple helices with seven base triplets and two T4 loops under appropriate conditions. UV spectroscopic monitoring of thermal denaturation indicates a consistently higher thermal stability for the 5'-sequences at pH 5.0 in the absence of Mg2+ ions. Raman spectra provide evidence for the formation of triple helices at pH 5 for oligomers with purine tracts located at either the 5'- or 3'-end of the sequence. However, NMR measurements reveal considerable differences in the secondary structures formed by the two types of oligonucleotides. Thus, at acidic pH significant structural heterogeneity is observed for the 3'-sequences. Employing selectively 15N-labeled oligomers, NMR experiments indicate a folding pattern for the competing structures that at least partially changes both Hoogsteen and Watson-Crick base-base interactions.