A different look at the spin state of Co3+^{3+} ions in CoO5_{5} pyramidal coordination

Using soft-x-ray absorption spectroscopy at the Co-$L_{2,3}$ and O-$K$ edges, we demonstrate that the Co$^{3+}$ ions with the CoO$_{5}$ pyramidal coordination in the layered Sr$_2$CoO$_3$Cl compound are unambiguously in the high spin state. Our result questions the reliability of the spin state assignments made so far for the recently synthesized layered cobalt perovskites, and calls for a re-examination of the modeling for the complex and fascinating properties of these new materials.Comment: 5 pages 3 figure

Magnetic Structures of High Temperature Phases of TbBaCo2O5.5

Neutron diffraction studies have been carried out on a single crystal of oxygen-deficient perovskite TbBaCo2O5.5 in the temperature range of 7-370 K. There have been observed several magnetic or structural transitions. Among these, the existence of the transitions to the insulating phase from the metallic one at ~340 K, to the one with the ferromagnetic moment at ~280 K and possibly to the antiferromagnetic one at ~260 K, with decreasing temperature T correspond to those reported in former works. We have studied the magnetic structures at 270 K and 250 K and found that all Co3+ ions of the CoO6 octahedra are in the low spin state and those of the CoO5 pyramids carry spins which are possibly in the intermediate spin state. Non-collinear magnetic structures are proposed at these temperatures. Two other transitions have also been observed at the temperatures, ~100 K and ~250 K.Comment: 9 pages, 2 tables, 10 figure

Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy

BACKGROUND: Fungal conidia are usually dormant unless the extracellular conditions are right for germination. Despite the importance of dormancy, little is known about the molecular mechanism underlying entry to, maintenance of, and exit from dormancy. To gain comprehensive and inter-species insights, transcriptome analyses were conducted across Aspergillus fumigatus, Aspergillus niger, and Aspergillus oryzae. RESULTS: We found transcripts of 687, 694, and 812 genes were enriched in the resting conidia compared with hyphae in A. fumigatus, A. niger, and A. oryzae, respectively (conidia-associated genes). Similarly, transcripts of 766, 1,241, and 749 genes were increased in the 1 h-cultured conidia compared with the resting conidia (germination-associated genes). Among the three Aspergillus species, we identified orthologous 6,172 genes, 91 and 391 of which are common conidia- and germination-associated genes, respectively. A variety of stress-related genes, including the catalase genes, were found in the common conidia-associated gene set, and ribosome-related genes were significantly enriched among the germination-associated genes. Among the germination-associated genes, we found that calA-family genes encoding a thaumatin-like protein were extraordinary expressed in early germination stage in all Aspergillus species tested here. In A. fumigatus 63 % of the common conidia-associated genes were expressed in a bZIP-type transcriptional regulator AtfA-dependent manner, indicating that AtfA plays a pivotal role in the maintenance of resting conidial physiology. Unexpectedly, the precocious expression of the germination-associated calA and an abnormal metabolic activity were detected in the resting conidia of the atfA mutant, suggesting that AtfA was involved in the retention of conidial dormancy. CONCLUSIONS: A comparison among transcriptomes of hyphae, resting conidia, and 1 h-grown conidia in the three Aspergillus species revealed likely common factors involved in conidial dormancy. AtfA positively regulates conidial stress-related genes and negatively mediates the gene expressions related to germination, suggesting a major role for AtfA in Aspergillus conidial dormancy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2689-z) contains supplementary material, which is available to authorized users

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

Anomalous Hall Resistivity of TbBaCo2O5.53 with Non-trivial Magnetic Structure

To investigate the Hall resistivity rH of systems with non-trivial spin structures, transport and magnetic properties of the oxygen deficient perovskite system TbBaCo2O5.53 with non-trivial magnetic structures have been adopted. As has been already known, the system exhibits, with decreasing temperature T, a transition to a ferromagnetic (FM) phase with non-collinear magnetic structure at TC 280 K in zero magnetic field and with further decreasing T, the spontaneous magnetization begins to decrease at T1~260 K and becomes zero at TN 245 K, where an antiferromagnetic (AFM) phase with non-collinear magnetic structure is realized. The metamagnetic behavior is induced by the relatively small magnetic field H (< 5 T) in the T region between ~200 K and T1. In this T region, unusual H dependence of rH has been observed. By analyzing the observed rH and magnetization M, the H dependence of the anomalous Hall coefficients Rs has been obtained at various fixed temperatures. Based on the magnetic structure reported previously by our group, the possible relevance of the non-trivial magnetic structure to the observed unusual behavior of rH is pointed out.Comment: 6 pages, 11 figures, submitted to J. Phys. Soc. Jp

Transcription activation by the siderophore sensor Btr is mediated by ligand-dependent stimulation of promoter clearance

Bacterial transcription factors often function as DNA-binding proteins that selectively activate or repress promoters, although the biochemical mechanisms vary. In most well-understood examples, activators function by either increasing the affinity of RNA polymerase (RNAP) for the target promoter, or by increasing the isomerization of the initial closed complex to the open complex. We report that Bacillus subtilis Btr, a member of the AraC family of activators, functions principally as a ligand-dependent activator of promoter clearance. In the presence of its co-activator, the siderophore bacillibactin (BB), the Btr:BB complex enhances productive transcription, while having only modest effects on either RNAP promoter association or the production of abortive transcripts. Btr binds to two direct repeat sequences adjacent to the −35 region; recognition of the downstream motif is most important for establishing a productive interaction between the Btr:BB complex and RNAP. The resulting Btr:BB dependent increase in transcription enables the production of the ferric-BB importer to be activated by the presence of its cognate substrate