Fungal network responses to grazing

Mycelial networks operate on scales from microscopic to many m² and naturally persist for extended periods. As fungi exhibit highly adaptive development, it is important to test behavioural responses on natural substrata with realistic nutrient levels across a range of spatial scales and extended time periods. Here we quantified network responses over 7.5 months in large (57 × 57 cm) microcosms to test whether grazing shifts the network to a more resilient architecture. Resource limitation constrained any ability to respond at all, with both grazed and ungrazed networks gradually thinning out over time. Added resources sustained further exploratory growth, but only transiently increased cross-connectivity and network resilience, when tested by simulated damage in silico. Grazed networks were initially weaker and emergence of new exploratory growth was curtailed. However, increased interstitial proliferation led to new cross-links, consolidating the existing mycelial network and increasing the resilience of the network to further attack.     

Overview of the matrisome--an inventory of extracellular matrix constituents and functions

Completion of genome sequences for many organisms allows a reasonably complete definition of the complement of extracellular matrix (ECM) proteins. In mammals this "core matrisome" comprises ～300 proteins. In addition there are large numbers of ECM-modifying enzymes, ECM-binding growth factors, and other ECM-associated proteins. These different categories of ECM and ECM-associated proteins cooperate to assemble and remodel extracellular matrices and bind to cells through ECM receptors. Together with receptors for ECM-bound growth factors, they provide multiple inputs into cells to control survival, proliferation, differentiation, shape, polarity, and motility of cells. The evolution of ECM proteins was key in the transition to multicellularity, the arrangement of cells into tissue layers, and the elaboration of novel structures during vertebrate evolution. This key role of ECM is reflected in the diversity of ECM proteins and the modular domain structures of ECM proteins both allow their multiple interactions and, during evolution, development of novel protein architectures.     

Cell-cell adhesion in fresh sugar-beet root parenchyma requires both pectin esters and calcium cross-links

Multicellular plants depend for their integrity on effective adhesion between their component cells. This adhesion depends upon various cross-links; ionic, covalent or weak interactions between the macromolecules of the adjacent cell walls. In sugar-beet ( Beta vulgaris L. Aztec) root parenchyma, cell-cell adhesion is disrupted by successive extractions with a calcium-chelating agent (imidazole) and a de-esterifying agent (sodium carbonate) but not by the calcium-chelating agent or the de-esterifying agent alone. Cell-cell adhesion in sugar-beet parenchyma thus depends upon both ester and Ca²⁺ cross-linked polymers. Pectic polysaccharides are removed by these treatments. Both parallel-electron energy-loss spectroscopy (PEELS) and Image-EELS show that calcium-binding sites are removed from the wall by imidazole. Using a monoclonal antibody that recognizes a relatively unesterified epitope of homogalacturonan, JIM 5, we show that a subset of JIM 5-reactive antigens remain in the middle lamella after Ca²⁺ chelation and that this subset is removed by cold (4° C) Na₂CO₃-induced breakage of ester bonds. Fourier transform infrared, nuclear magnetic resonance, and spectrophotometric assays show that methyl and feruloyl esters are removed from the wall by Na₂CO₃ but acetyl esters remain. Sodium carbonate extraction at 20° C removes cell wall autofluorescence and most of the feruloylated moieties from the wall. We propose that the chelator-resistant subset of ester-linked JIM 5-reactive pectins are important for cell-cell adhesion.     

Organic-rich bimineralic ooids record biological processes in Shark Bay,Western Australia

Marine ooids have formed in microbially colonized environments for billions of years, but the microbial contributions to mineral formation in ooids continue to be debated. Here we provide evidence of these contributions in ooids from Carbla Beach, Shark Bay, Western Australia. Dark 100–240 μm diameter ooids from Carbla Beach contain two different carbonate minerals. These ooids have 50–100 μm-diameter dark nuclei that contain aragonite, amorphous iron sulfide, detrital aluminosilicate grains and organic matter, and 10–20 μm-thick layers of high-Mg calcite that separate nuclei from aragonitic outer cortices. Raman spectroscopy indicates organic enrichments in the nuclei and high-Mg calcite layers. Synchrotron-based microfocused X-ray fluorescence mapping reveals high-Mg calcite layers and the presence of iron sulfides and detrital grains in the peloidal nuclei. Iron sulfide grains within the nuclei indicate past sulfate reduction in the presence of iron. The preservation of organic signals in and around high-Mg calcite layers and the absence of iron sulfide suggest that organics stabilized high-Mg calcite under less sulfidic conditions. Aragonitic cortices that surround the nuclei and Mg-calcite layers do not preserve microporosity, iron sulfide minerals nor organic enrichments, indicating growth under more oxidizing conditions. These morphological, compositional, and mineralogical signals of microbial processes in dark ooids from Shark Bay, Western Australia, record the formation of ooid nuclei and the accretion of magnesium-rich cortical layers in benthic, reducing, microbially colonized areas.     

Leveraging GWAS data to identify metabolic pathways and networks involved in maize lipid biosynthesis

Maize (Zea mays mays) oil is a rich source of polyunsaturated fatty acids (FAs) and energy, making it a valuable resource for human food, animal feed, and bio‐energy. Although this trait has been studied via conventional genome‐wide association study (GWAS), the single nucleotide polymorphism (SNP)‐trait associations generated by GWAS may miss the underlying associations when traits are based on many genes, each with small effects that can be overshadowed by genetic background and environmental variation. Detecting these SNPs statistically is also limited by the levels set for false discovery rate. A complementary pathways analysis that emphasizes the cumulative aspects of SNP‐trait associations, rather than just the significance of single SNPs, was performed to understand the balance of lipid metabolism, conversion, and catabolism in this study. This pathway analysis indicated that acyl‐lipid pathways, including biosynthesis of wax esters, sphingolipids, phospholipids and flavonoids, along with FA and triacylglycerol (TAG) biosynthesis, were important for increasing oil and FA content. The allelic variation found among the genes involved in many degradation pathways, and many biosynthesis pathways leading from FAs and carbon partitioning pathways, was critical for determining final FA content, changing FA ratios and, ultimately, to final oil content. The pathways and pathway networks identified in this study, and especially the acyl‐lipid associated pathways identified beyond what had been found with GWAS alone, provide a real opportunity to precisely and efficiently manipulate high‐oil maize genetic improvement.     

The trail of chromium(III) in vivo from the blood to the urine: the roles of transferrin and chromodulin

The chromium-binding oligopeptide chromodulin (also known as low-molecular-weight chromium-binding substance) has been shown to activate the tyrosine kinase activity of the insulin receptor in response to insulin and has been proposed to be part of a novel autoamplification mechanism for insulin signaling. The model requires that Cr3+ be moved from the blood to insulin-sensitive tissues in response to insulin and subsequently be lost in the urine as chromodulin; however, the model has not been tested by in vivo studies. In vivo studies with rats have shown that the iron transport protein transferrin serves as the major chromic ion transport agent and that this transport is stimulated by insulin. The ion is transported to a variety of tissues, while liver and kidneys are the major target. In hepatocytes, chromodulin occurs in appreciable levels in the cytosol and in the nucleus. Apochromodulin levels appear to be maintained under homeostatic control, although the only detectable form of urinary chromium is probably chromodulin. Increases in urinary chromium loss in response to insulin are reflected by increases in chromodulin, establishing a direct link between carbohydrate metabolism and the oligopeptide.     

Monolysocardiolipins accumulate in Barth syndrome but do not lead to enhanced apoptosis

Barth syndrome (BTHS) is an X-linked recessive disorder that is biochemically characterized by low cellular levels of the mitochondrial phospholipid cardiolipin (CL). Previously, we discovered that the yeast disruptant of the TAZ ortholog in Saccharomyces cerevisiae not only displays CL deficiency but also accumulates monolysocardiolipins (MLCLs), which are intermediates in CL remodeling. Therefore, we set out to investigate whether MLCL accumulation also occurs in BTHS. Indeed, we observed MLCL accumulation in heart, muscle, lymphocytes, and cultured lymphoblasts of BTHS patients; however, only very low levels of these lysophospholipids were found in platelets and fibroblasts of these patients. Although the fatty acid composition of the MLCLs was different depending on the tissue source, it did parallel the fatty acid composition of the (remaining) CLs. The possible implications of these findings for the two reported CL remodeling mechanisms, transacylation and deacylation/reacylation, are discussed. Because MLCLs have been proposed to be involved in the initiation of apoptosome-mediated cell death by the sequestration of the proapoptotic protein (t)BH3-interacting domain death agonist (Bid) to the mitochondrial membrane, we used control and BTHS lymphoblasts to investigate whether the accumulation of MLCLs results in higher levels of apoptosis. We found no differences in susceptibility to death receptor-mediated apoptosis or in cellular distribution of Bid, cytochrome c, and other parameters, implying that MLCL accumulation does not lead to enhanced apoptosis in cultured BTHS lymphoblasts.     

The genes gmdA, encoding an amidase, and bzuA, encoding a cytochrome P450, are required for benzamide utilization in Aspergillus nidulans

Two unlinked loci, gmdA and bzuA, have previously been identified as being required for the utilization of benzamide as the sole nitrogen source by Aspergillus nidulans. We have cloned each of these genes via direct complementation. The gmdA gene encodes a predicted product belonging to the amidase signature sequence family that displays similarity to AmdS from A. nidulans. However, identity is significantly higher to the amdS gene from Aspergillus niger. The bzuA gene encodes a protein belonging to the cytochrome P450 superfamily and is orthologous to the benzoate para-hydroxylase-encoding gene bphA of A. niger. The bzuA1 mutation prevents the use of benzoate as a carbon source and intracellular accumulation of benzoate results in growth inhibition on benzamide. Northern blot analysis has shown that gmdA expression is subject solely to AreA-dependent nitrogen metabolite repression while bzuA is strongly benzoate inducible and subject to CreA-mediated carbon catabolite repression and a probable inactivation of benzoate induction by glucose. Fluorescence microscopy of a fusion of the N-terminal end of BzuA to green fluorescent protein revealed that this protein localizes to the endoplasmic reticulum.     

UniEuk: Time to Speak a Common Language in Protistology!

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.