Disruption of Dcp1 leads to a Dcp2-dependent aberrant ribosome profiles in Aspergillus nidulans.

There are multiple RNA degradation mechanisms in eukaryotes, key among these is mRNA decapping, which requires the Dcp1-Dcp2 complex. Decapping is involved in various processes including nonsense-mediated decay (NMD), a process by which aberrant transcripts with a premature termination codon are targeted for translational repression and rapid decay. NMD is ubiquitous throughout eukaryotes and the key factors involved are highly conserved, although many differences have evolved.

A modern pulse of ultrafast exhumation and diachronous crustal melting in the Nanga Parbat Massif.

We combine monazite petrochronology with thermal modeling to evaluate the relative roles of crustal melting, surface denudation, and tectonics in facilitating ultrafast exhumation of the Nanga Parbat Massif in the western Himalayan syntaxis. Our results reveal diachronous melting histories between samples and a pulse of ultrafast exhumation (9 to 13 mm/year) that began ~1 Ma and was preceded by several million years of slower, but still rapid, exhumation (2 to 5 mm/year). Recent studies show that an exhumation pulse of similar timing and magnitude occurred in the eastern Himalayan syntaxis.

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts.

Preferred orientations of garnet porphyroblasts reveal previously cryptic templating during nucleation.

Electron back scattered diffraction data of garnet crystals from the Nelson Aureole, British Columbia and the Mosher's Island formation, Nova Scotia, reveals that 22 garnet crystals are all oriented with one of three crystal directions parallel to the trace of the foliation plane in thin section. Structural models suggest that these relationships are due to preferential garnet nucleation onto muscovite, with the alignment of repeating rows of Al octahedra and Si tetrahedra in each leading to inheritance of garnet orientation from the muscovite. These results highlight that epitaxial nucleation may be a prevalent process by which porphyroblast minerals nucleate during metamorphism and carry implications for the role that non-classic nucleation pathways play in the crystallization of metamorphic minerals, the distribution of porphyroblasts in metamorphic rocks, and, in cases in which nucleation is the rate limiting step for crystallization, the energetics of metamorphic reactions.

Histone mRNA is subject to 3' uridylation and re-adenylation in Aspergillus nidulans.

The role of post-transcriptional RNA modification is of growing interest. One example is the addition of non-templated uridine residues to the 3' end of transcripts. In mammalian systems, uridylation is integral to cell cycle control of histone mRNA levels.

Growing a circular economy with fungal biotechnology: a white paper.

Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture and beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions.

High-Quality Draft Genome Sequence and Annotation of the Basidiomycete Yeast CBS10092, a Producer of Mannosylerythritol Lipids.

The basidiomycete (formally ) strain CBS10092 was originally isolated from an herbaceous plant in Russia. It is a known producer of mannosylerythritol lipids (MELs), the main component being MEL-C. Here, we present the 19.

Author Correction: Building a global alliance of biofoundries.

The original version of this Comment contained errors in the legend of Figure 2, in which the locations of the fifteenth and sixteenth GBA members were incorrectly given as '(15) Australian Genome Foundry, Macquarie University; (16) Australian Foundry for Advanced Biomanufacturing, University of Queensland.'. The correct version replaces this with '(15) Australian Foundry for Advanced Biomanufacturing (AusFAB), University of Queensland and (16) Australian Genome Foundry, Macquarie University'.

Similarity regression predicts evolution of transcription factor sequence specificity.

Transcription factor (TF) binding specificities (motifs) are essential for the analysis of gene regulation. Accurate prediction of TF motifs is critical, because it is infeasible to assay all TFs in all sequenced eukaryotic genomes. There is ongoing controversy regarding the degree of motif diversification among related species that is, in part, because of uncertainty in motif prediction methods.

The role of the GATA transcription factor AreB in regulation of nitrogen and carbon metabolism in Aspergillus nidulans.

In Aspergillus nidulans, nitrogen and carbon metabolism are under the control of wide-domain regulatory systems, including nitrogen metabolite repression, carbon catabolite repression and the nutrient starvation response. Transcriptomic analysis of the wild type strain grown under different combinations of carbon and nitrogen regimes was performed, to identify differentially regulated genes. Carbon metabolism predominates as the most important regulatory signal but for many genes, both carbon and nitrogen metabolisms coordinate regulation.

Sulphur and carbon cycling in the subduction zone mélange.

Subduction zones impose an important control on the geochemical cycling between the surficial and internal reservoirs of the Earth. Sulphur and carbon are transferred into Earth's mantle by subduction of pelagic sediments and altered oceanic lithosphere. Release of oxidizing sulphate- and carbonate-bearing fluids modifies the redox state of the mantle and the chemical budget of subduction zones.

Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper.

The EUROFUNG network is a virtual centre of multidisciplinary expertise in the field of fungal biotechnology. The first academic-industry Think Tank was hosted by EUROFUNG to summarise the state of the art and future challenges in fungal biology and biotechnology in the coming decade. Currently, fungal cell factories are important for bulk manufacturing of organic acids, proteins, enzymes, secondary metabolites and active pharmaceutical ingredients in white and red biotechnology.

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture.

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters.

Background: The filamentous fungus Aspergillus nidulans has been a tractable model organism for cell biology and genetics for over 60 years. It is among a large number of Aspergilli whose genomes have been sequenced since 2005, including medically and industrially important species. In order to advance our knowledge of its biology and increase its utility as a genetic model by improving gene annotation we sequenced the transcriptome of A.

RrmA regulates the stability of specific transcripts in response to both nitrogen source and oxidative stress.

Differential regulation of transcript stability is an effective means by which an organism can modulate gene expression. A well-characterized example is glutamine signalled degradation of specific transcripts in Aspergillus nidulans. In the case of areA, which encodes a wide-domain transcription factor mediating nitrogen metabolite repression, the signal is mediated through a highly conserved region of the 3' UTR.

Cytoplasmic mRNA 3' tagging in eukaryotes: does it spell the end?

Although functional RNA is generally protected against degradation, defects or irregularity during RNA biogenesis lead to rapid degradation. Cellular surveillance mechanisms therefore need to distinguish aberrant, erroneous, damaged or aging transcripts from normal RNAs in order to maintain fidelity and control of gene expression. The detection of defects seems to be primarily based on functionality or aberrant rates of a given step in RNA biogenesis, allowing efficient detection of many different errors without recognition of their specific nature.

mRNA 3' tagging is induced by nonsense-mediated decay and promotes ribosome dissociation.

For a range of eukaryote transcripts, the initiation of degradation is coincident with the addition of a short pyrimidine tag at the 3' end. Previously, cytoplasmic mRNA tagging has been observed for human and fungal transcripts. We now report that Arabidopsis thaliana mRNA is subject to 3' tagging with U and C nucleotides, as in Aspergillus nidulans.

The GATA factors AREA and AREB together with the co-repressor NMRA, negatively regulate arginine catabolism in Aspergillus nidulans in response to nitrogen and carbon source.

The filamentous fungus Aspergillus nidulans can utilize arginine both as a nitrogen and carbon source. Analysis of areA and areB single and double mutants has shown that the two GATA transcription factors AREA and AREB negatively regulate the expression of arginine catabolism genes agaA and otaA under nitrogen repressing conditions. AREA is necessary for the ammonium repression of agaA and otaA under carbon repressing conditions, while AREB is involved under carbon-limiting conditions.

Characterisation of AnBEST1, a functional anion channel in the plasma membrane of the filamentous fungus, Aspergillus nidulans.

Two distant homologues of the bestrophin gene family have been identified in the filamentous fungus, Aspergillus nidulans (anbest1 and anbest2). AnBEST1 was functionally characterised using the patch clamp technique and was shown to be an anion selective channel permeable to citrate. Furthermore, AnBEST1 restored the growth of the pdr12Δ yeast mutant on inhibitory concentrations of extracellular propionate, benzoate and sorbate, also consistent with carboxylated organic anion permeation of AnBEST1.

Melt migration in basalt columns driven by crystallization-induced pressure gradients.

The structure of columnar-jointed lava flows and intrusions has fascinated people for centuries and numerous hypotheses on the mechanisms of formation of columnar jointing have been proposed. In cross-section, weakly developed semicircular internal structures are a near ubiquitous feature of basalt columns. Here we propose a melt-migration model, driven by crystallization and a coeval specific volume decrease inside cooling and solidifying columns, which can explain the observed macroscopic features in columnar-jointed basalts.

The bZIP transcription factor MeaB mediates nitrogen metabolite repression at specific loci.

In Fusarium fujikuroi, bikaverin (BIK) biosynthesis is subject to repression by nitrogen. Unlike most genes subject to nitrogen metabolite repression, it has been shown that transcription of bik biosynthetic genes is not AreA dependent. Searching for additional transcription factors that may be involved in nitrogen regulation, we cloned and characterized the orthologue of Aspergillus nidulans meaB, which encodes a bZIP transcription factor.

Distinct roles for Caf1, Ccr4, Edc3 and CutA in the co-ordination of transcript deadenylation, decapping and P-body formation in Aspergillus nidulans.

Transcript degradation is a key step in gene regulation. In eukaryotes, mRNA decay is generally initiated by removal of the poly(A) tail mediated by the Ccr4-Caf1-Not complex. Deadenylated transcripts are then rapidly degraded, primarily via the decapping-dependent pathway.

CUCU modification of mRNA promotes decapping and transcript degradation in Aspergillus nidulans.

In eukaryotes, mRNA decay is generally initiated by the shortening of the poly(A) tail mediated by the major deadenylase complex Ccr4-Caf1-Not. The deadenylated transcript is then rapidly degraded, primarily via the decapping-dependent pathway. Here we report that in Aspergillus nidulans both the Caf1 and Ccr4 orthologues are functionally distinct deadenylases in vivo: Caf1 is required for the regulated degradation of specific transcripts, and Ccr4 is responsible for basal degradation.