Strongly Localized Magnetization Modes in Permalloy Antidot Lattices

Antidot lattices (ADLs) patterned into soft magnetic thin films exhibit rich ferromagnetic resonance (FMR) spectra corresponding to many different magnetization modes. One of the predicted modes is highly localized at the edges of the antidots; this mode is difficult to detect experimentally. Here we present FMR data for a permalloy thin film patterned into a square array of square antidots. Comparison of these data with micromagnetic simulations permits identification of several edge modes. Our simulations also reveal the effect of the antidot shape on the mode dispersion

The effect of water potential on accumulation of some essential elements in sugarbeet leaves, Beta vulgaris ssp. vulgaris

An investigation has been conducted on the effect of reduced water potential in nutrient solution on the accumulation of some essential macro- and micro nutrients in the aboveground pails of young sugarbeet plants. Plants of 8 different sugarbeet genotypes were exposed for 21 days to a nutrient solution whose water potential of 0.1 MPa was regulated by PEG. Contents of N, P, K Ca, Mg, Fe, Mn, Cu and Zn declined in all genotypes under water deficiency but the intensity of reduction varied among the genotypes. The results indicated that some harmful effects of water deficiency could be attributed to disturbances in plant mineral nutrition, especially the lack of N, P, and Mg, as well as to impaired ratios between the contents of particular elements, especially K/Ca

Quantum Engineering With Hybrid Magnonic Systems and Materials (Invited Paper)

Quantum technology has made tremendous strides over the past two decades with remarkable advances in materials engineering, circuit design, and dynamic operation. In particular, the integration of different quantum modules has benefited from hybrid quantum systems, which provide an important pathway for harnessing different natural advantages of complementary quantum systems and for engineering new functionalities. This review article focuses on the current frontiers with respect to utilizing magnons for novel quantum functionalities. Magnons are the fundamental excitations of magnetically ordered solid-state materials and provide great tunability and flexibility for interacting with various quantum modules for integration in diverse quantum systems. The concomitant-rich variety of physics and material selection enable exploration of novel quantum phenomena in materials science and engineering. In addition, the ease of generating strong coupling with other excitations makes hybrid magnonics a unique platform for quantum engineering. We start our discussion with circuit-based hybrid magnonic systems, which are coupled with microwave photons and acoustic phonons. Subsequently, we focus on the recent progress of magnon–magnon coupling within confined magnetic systems. Next, we highlight new opportunities for understanding the interactions between magnons and nitrogen-vacancy centers for quantum sensing and implementing quantum interconnects. Lastly, we focus on the spin excitations and magnon spectra of novel quantum materials investigated with advanced optical characterization

Heterologous expression screens in Nicotiana benthamiana identify a candidate effector of the wheat Yellow Rust Pathogen that associates with processing bodies

Rust fungal pathogens of wheat (Triticum spp.) affect crop yields worldwide. The molecular mechanisms underlying the virulence of these pathogens remain elusive, due to the limited availability of suitable molecular genetic research tools. Notably, the inability to perform high-throughput analyses of candidate virulence proteins (also known as effectors) impairs progress. We previously established a pipeline for the fast-forward screens of rust fungal candidate effectors in the model plant Nicotiana benthamiana. This pipeline involves selecting candidate effectors in silico and performing cell biology and protein-protein interaction assays in planta to gain insight into the putative functions of candidate effectors. In this study, we used this pipeline to identify and characterize sixteen candidate effectors from the wheat yellow rust fungal pathogen Puccinia striiformis f sp tritici. Nine candidate effectors targeted a specific plant subcellular compartment or protein complex, providing valuable information on their putative functions in plant cells. One candidate effector, PST02549, accumulated in processing bodies (P-bodies), protein complexes involved in mRNA decapping, degradation, and storage. PST02549 also associates with the P-body-resident ENHANCER OF mRNA DECAPPING PROTEIN 4 (EDC4) from N. benthamiana and wheat. We propose that P-bodies are a novel plant cell compartment targeted by pathogen effectors

Reducing the number of accepted species in Aspergillus series Nigri

The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy.The Czech Ministry of Health, the Charles University Research Centre program, the Czech Academy of Sciences Long-term Research Development Project, the project of Charles University Grant Agency, JST SPRING, the Foundational Biodiversity Information Programme (FBIP) of the National Research Foundation of South Africa, the Japan Society for the Promotion of Science - Postdoctoral Fellowships for Research in Japan and Grant-in-aid for a JSPS research fellow.https://www.journals.elsevier.com/studies-in-mycologyam2023BiochemistryGeneticsMicrobiology and Plant Patholog

A monograph of Aspergillus section Candidi

Aspergillus section Candidi encompasses white- or yellow-sporulating species mostly isolated from indoor and cave environments, food, feed, clinical material, soil and dung. Their identification is non-trivial due to largely uniform morphology. This study aims to re-evaluate the species boundaries in the section Candidi and present an overview of all existing species along with information on their ecology. For the analyses, we assembled a set of 113 strains with diverse origin. For the molecular analyses, we used DNA sequences of three house-keeping genes (benA, CaM and RPB2) and employed species delimitation methods based on a multispecies coalescent model. Classical phylogenetic methods and genealogical concordance phylogenetic species recognition (GCPSR) approaches were used for comparison. Phenotypic studies involved comparisons of macromorphology on four cultivation media, seven micromorphological characters and growth at temperatures ranging from 10 to 45 °C. Based on the integrative approach comprising four criteria (phylogenetic and phenotypic), all currently accepted species gained support, while two new species are proposed (A. magnus and A. tenebricus). In addition, we proposed the new name A. neotritici to replace an invalidly described A. tritici. The revised section Candidi now encompasses nine species, some of which manifest a high level of intraspecific genetic and/or phenotypic variability (e.g., A. subalbidus and A. campestris) while others are more uniform (e.g., A. candidus or A. pragensis). The growth rates on different media and at different temperatures, colony colours, production of soluble pigments, stipe dimensions and vesicle diameters contributed the most to the phenotypic species differentiation.Czech Ministry of Health, the Charles University Research Centre program no. 204069, Czech Academy of Sciences Long-term Research Development Project, the project of Charles University Grant Agency, the Japan Society for the Promotion of Science Postdoctoral Fellowships for Research in Japan, the Grant-in-aid for JSPS research fellow and the Future Leaders - African Independent Research fellowship programme.https://www.journals.elsevier.com/studies-in-mycologyam2023BiochemistryGeneticsMicrobiology and Plant Patholog

Taxonomy of Aspergillus series Versicolores : species reduction and lessons learned about intraspecific variability

Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera.The project of Charles University Grant Agency, the project of Charles University Grant Agency, the Charles University Research Centre program, Czech Academy of Sciences Long-term Research Development Project, the Japan Society for the Promotion of Science Postdoctoral Fellowships for Research in Japan, the Grant-inaid for JSPS research fellows, the Future Leaders - African Independent Research fellowship programme funded by the UK Government’s Global Challenges Research Fund.https://www.journals.elsevier.com/studies-in-mycologyam2023BiochemistryGeneticsMicrobiology and Plant Patholog

Signal enhancement in protein NMR using the spin-noise tuning optimum

We have assessed the potential of an alternative probe tuning strategy based on the spin-noise response for application in common high-resolution multi-dimensional biomolecular NMR experiments with water signal suppression on aqueous and salty samples. The method requires the adjustment of the optimal tuning condition, which may be offset by several 100 kHz from the conventional tuning settings using the noise response of the water protons as an indicator. Although the radio frequency-pulse durations are typically longer under such conditions, signal-to-noise gains of up to 22% were achieved. At salt concentrations up to 100 mM a substantial sensitivity gain was observed

String Phase in an Artificial Spin Ice

One-dimensional strings of local excitations are a fascinating feature of the physical behavior of strongly correlated topological quantum matter. Here we study strings of local excitations in a classical system of interacting nanomagnets, the Santa Fe Ice geometry of artificial spin ice. We measured the moment configuration of the nanomagnets, both after annealing near the ferromagnetic Curie point and in a thermally dynamic state. While the Santa Fe Ice lattice structure is complex, we demonstrate that its disordered magnetic state is naturally described within a framework of emergent strings. We show experimentally that the string length follows a simple Boltzmann distribution with an energy scale that is associated with the system's magnetic interactions and is consistent with theoretical predictions. The results demonstrate that string descriptions and associated topological characteristics are not unique to quantum models but can also provide a simplifying description of complex classical systems with non-trivial frustration

Entropy-driven order in an array of nanomagnets

Long-range ordering is typically associated with a decrease in entropy. Yet, it can also be driven by increasing entropy in certain special cases. Here we demonstrate that artificial spin-ice arrays of single-domain nanomagnets can be designed to produce such entropy-driven order. We focus on the tetris artificial spin-ice structure, a highly frustrated array geometry with a zero-point Pauling entropy, which is formed by selectively creating regular vacancies on the canonical square ice lattice. We probe thermally active tetris artificial spin ice both experimentally and through simulations, measuring the magnetic moments of the individual nanomagnets. We find two-dimensional magnetic ordering in one subset of these moments, which we demonstrate to be induced by disorder (that is, increased entropy) in another subset of the moments. In contrast with other entropy-driven systems, the discrete degrees of freedom in tetris artificial spin ice are binary and are both designable and directly observable at the microscale, and the entropy of the system is precisely calculable in simulations. This example, in which the system’s interactions and ground-state entropy are well defined, expands the experimental landscape for the study of entropy-driven ordering