A biofertilizing fungal endophyte of cranberry plants suppresses the plant pathogen .

Fungi colonizing plants are gaining attention because of their ability to promote plant growth and suppress pathogens. While most studies focus on endosymbionts from grasses and legumes, the large and diverse group of ericaceous plants has been much neglected. We recently described one of the very few fungal endophytes promoting the growth of the Ericaceae (American cranberry), notably the isolate EC4.

Magnetostriction-Driven Muon Localization in an Antiferromagnetic Oxide.

Magnetostriction results from the coupling between magnetic and elastic degrees of freedom. Though it is associated with a relatively small energy, we show that it plays an important role in determining the site of an implanted muon, so that the energetically favorable site can switch on crossing a magnetic phase transition. This surprising effect is demonstrated in the cubic rocksalt antiferromagnet MnO which undergoes a magnetostriction-driven rhombohedral distortion at the Néel temperature T_{N}=118  K.

Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction.

Compared to nuclear genomes, mitochondrial genomes (mitogenomes) are small and usually code for only a few dozen genes. Still, identifying genes and their structure can be challenging and time-consuming. Even automated tools for mitochondrial genome annotation often require manual analysis and curation by skilled experts.

Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes.

Background: Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.

Results: We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum.

Nuclear Genome Sequence and Gene Expression of an Intracellular Fungal Endophyte Stimulating the Growth of Cranberry Plants.

Ericaceae thrive in poor soil, which we postulate is facilitated by microbes living inside those plants. Here, we investigate the growth stimulation of the American cranberry () by one of its fungal endosymbionts, EC4. We show that the symbiont resides inside the epidermal root cells of the host but extends into the rhizosphere via its hyphae.

Chromosome-scale assemblies of genomes provide insights into infection-related chromatin reorganization.

The unicellular amoeba is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as and spp. Here we report complete, high-quality genome sequences for two extensively studied strains, Neff and C3.

Diploid-dominant life cycles characterize the early evolution of Fungi.

Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling.

Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies.

Fungi survive in diverse ecological niches by secreting proteins and other molecules into the environment to acquire food and interact with various biotic and abiotic stressors. Fungal secretome content is, therefore, believed to be tightly linked to fungal ecologies. We sampled 132 genomes from the early-diverging terrestrial fungal lineage zygomycetes (Mucoromycota and Zoopagomycota) and characterized their secretome composition.

Refining Mitochondrial Intron Classification With ERPIN: Identification Based on Conservation of Sequence Plus Secondary Structure Motifs.

Mitochondrial genomes-in particular those of fungi-often encode genes with a large number of Group I and Group II introns that are conserved at both the sequence and the RNA structure level. They provide a rich resource for the investigation of intron and gene structure, self- and protein-guided splicing mechanisms, and intron evolution. Yet, the degree of sequence conservation of introns is limited, and the primary sequence differs considerably among the distinct intron sub-groups.

Characterization of the mitogenome of Gongronella sp. w5 reveals substantial variation in Mucoromycota.

Gongronella is a genus of fungi in Mucorales (Mucoromycota). Some of its members have important biotechnological applications, but until now, not a single mitogenome has been characterized in Gongronella. Here, we present the complete mitogenome assembly of Gongronella sp.

Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system.

The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS).

Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii.

Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents.

An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome.

The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly accepted view assumes that M-mtRPs compensate for structural destabilization of mt-rRNA resulting from its evolutionary remodeling.

New Insights Into Sulfur Metabolism Through Coupled Gene Expression, Solution Chemistry, Microscopy, and Spectroscopy Analyses.

Here, we experimentally expand understanding of the reactions and enzymes involved in ATCC 19377 S and metabolism by developing models that integrate gene expression analyzed by RNA-Seq, solution sulfur speciation, electron microscopy and spectroscopy. The metabolism model involves the conversion of to , S and mediated by the sulfur oxidase complex (Sox), tetrathionate hydrolase (TetH), sulfide quinone reductase (Sqr), and heterodisulfate reductase (Hdr) proteins. These same proteins, with the addition of rhodanese (Rhd), were identified to convert S to , and polythionates in the S metabolism model.

The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome.

Background: Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required.

Exsolution of SrO during the Topochemical Conversion of LaSrCoRuO to the Oxyhydride LaSrCoRuOH.

 Reaction of the  = 1 Ruddlesden-Popper oxide LaSrCoRuO with CaH yields the oxyhydride phase LaSrCoRuOH via a topochemical anion exchange. Close inspection of the X-ray and neutron powder diffraction data in combination with HAADF-STEM images reveals that the nanoparticles of SrO are exsolved from the system during the reaction, with the change in cation stoichiometry accommodated by the inclusion of  > 1 (Co/Ru)OH "perovskite" layers into the Ruddlesden-Popper stacking sequence. This novel pseudotopochemical process offers a new route for the formation of > 1 Ruddlesden-Popper structured materials.

An updated phylogeny of the reveals that the parasitic and have independent origins.

The is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts.

Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus.

The yeast Magnusiomyces capitatus is an opportunistic human pathogen causing rare yet severe infections, especially in patients with hematological malignancies. Here, we report the 20.2 megabase genome sequence of an environmental strain of this species as well as the genome sequences of eight additional isolates from human and animal sources providing an insight into intraspecies variation.

LaSr NiRuO H : A 4d Transition-Metal Oxide-Hydride Containing Metal Hydride Sheets.

The synthesis of the first 4d transition metal oxide-hydride, LaSr NiRuO H , is prepared via topochemical anion exchange. Neutron diffraction data show that the hydride ions occupy the equatorial anion sites in the host lattice and as a result the Ru and Ni cations are located in a plane containing only hydride ligands, a unique structural feature with obvious parallels to the CuO sheets present in the superconducting cuprates. DFT calculations confirm the presence of S=1/2  Ni and S=0, Ru centers, but neutron diffraction and μSR data show no evidence for long-range magnetic order between the Ni centers down to 1.

CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.

Motivation: Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes.

Disseminated Histoplasmosis: A Challenging Differential Diagnostic Consideration for Suspected Malignant Lesions in the Digestive Tract.

Histoplasmosis is well characterized as an endemic fungal disease restricted to certain areas of the USA. In Middle Europe, most patients present with acute pulmonary symptoms after travelling to endemic areas. Here, we want to illustrate the case of a 67-year-old man who presented with persistent oral ulcers, hoarseness, dysphagia, diarrhea, and weight loss to our Department of Otorhinolaryngology in December 2014.

Genome Sequence of Spizellomyces punctatus.

Spizellomyces punctatus is a basally branching chytrid fungus that is found in the Chytridiomycota phylum. Spizellomyces species are common in soil and of importance in terrestrial ecosystems. Here, we report the genome sequence of S.

La2SrCr2O7: Controlling the Tilting Distortions of n = 2 Ruddlesden-Popper Phases through A-Site Cation Order.

Structural characterization by neutron diffraction, supported by magnetic, SHG, and μ(+)SR data, reveals that the n = 2 Ruddlesden-Popper phase La2SrCr2O7 adopts a highly unusual structural configuration in which the cooperative rotations of the CrO6 octahedra are out of phase in all three Cartesian directions (ΦΦΦz/ΦΦΦz; a(-)a(-)c(-)/a(-)a(-)c(-)) as described in space group A2/a. First-principles DFT calculations indicate that this unusual structural arrangement can be attributed to coupling between the La/Sr A-site distribution and the rotations of the CrO6 units, which combine to relieve the local deformations of the chromium-oxygen octahedra. This coupling suggests new chemical "handles" by which the rotational distortions or A-site cation order of Ruddlesden-Popper phases can be directed to optimize physical behavior.

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.

Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2].

La2SrCr2O7F2: A Ruddlesden-Popper Oxyfluoride Containing Octahedrally Coordinated Cr(4+) Centers.

The low-temperature fluorination of the n = 2 Ruddlesden-Popper phase La2SrCr2O7 yields La2SrCr2O7F2 via a topochemical fluorine insertion reaction. The structure-conserving nature of the fluorination reaction means that the chromium centers of the initial oxide phase retain an octahedral coordination environment in the fluorinated product, resulting in a material containing an extended array of apex-linked Cr(4+)O6 units. Typically materials containing networks of octahedrally coordinated Cr(4+) centers can only be prepared at high pressure; thus, the preparation of La2SrCr2O7F2 demonstrates that low-temperature topochemical reactions offer an alternative synthesis route to materials of this type.