The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.This work was funded by a grant from the CSIRO Transformational Biology Capability Platform to Adnane Nemri. Claire Anderson was supported by an ARC Discovery Grant (DP120104044) awarded to David A. Jones and Peter N. Dodds

Thermodynamic stability and contributions to the Gibbs free energy of nanocrystalline Ni₃Fe

The heat capacities of nanocrystalline Ni₃Fe and control materials with larger crystallites were measured from 0.4–300 K. The heat capacities were integrated to obtain the enthalpy, entropy, and Gibbs free energy and to quantify how these thermodynamic functions are altered by nanocrystallinity. From the phonon density of states (DOS) measured by inelastic neutron scattering, we find that the Gibbs free energy is dominated by phonons and that the larger heat capacity of the nanomaterial below 100 K is attributable to its enhanced phonon DOS at low energies. Besides electronic and magnetic contributions, the nanocrystalline material has an additional contribution at higher temperatures, consistent with phonon anharmonicity. The nanocrystalline material shows a stronger increase with temperature of both the enthalpy and entropy compared to the bulk sample. Its entropy exceeds that of the bulk material by 0.4 k_B/atom at 300 K. This is insufficient to overcome the enthalpy of grain boundaries and defects in the nanocrystalline material, making it thermodynamically unstable with respect to the bulk control material

Precise implications for real-space pair distribution function modeling of effects intrinsic to modern time-of-flight neutron diffractometers

Total scattering and pair distribution function (PDF) methods allow for detailed study of local atomic order and disorder, including materials for which Rietveld refinements are not traditionally possible (amorphous materials, liquids, glasses and nanoparticles). With the advent of modern neutron time-of-flight (TOF) instrumentation, total scattering studies are capable of producing PDFs with ranges upwards of 100–200 Å, covering the correlation length scales of interest for many materials under study. Despite this, the refinement and subsequent analysis of data are often limited by confounding factors that are not rigorously accounted for in conventional analysis programs. While many of these artifacts are known and recognized by experts in the field, their effects and any associated mitigation strategies largely exist as passed-down `tribal' knowledge in the community, and have not been concisely demonstrated and compared in a unified presentation. This article aims to explicitly demonstrate, through reviews of previous literature, simulated analysis and real-world case studies, the effects of resolution, binning, bounds, peak shape, peak asymmetry, inconsistent conversion of TOF to d spacing and merging of multiple banks in neutron TOF data as they directly relate to real-space PDF analysis. Suggestions for best practice in analysis of data from modern neutron TOF total scattering instruments when using conventional analysis programs are made, as well as recommendations for improved analysis methods and future instrument design

Precise implications for real-space pair distribution function modeling of effects intrinsic to modern time-of-flight neutron diffractometers

Total scattering and pair distribution function (PDF) methods allow for detailed study of local atomic order and disorder, including materials for which Rietveld refinements are not traditionally possible (amorphous materials, liquids, glasses and nanoparticles). With the advent of modern neutron time-of-flight (TOF) instrumentation, total scattering studies are capable of producing PDFs with ranges upwards of 100–200 Å, covering the correlation length scales of interest for many materials under study. Despite this, the refinement and subsequent analysis of data are often limited by confounding factors that are not rigorously accounted for in conventional analysis programs. While many of these artifacts are known and recognized by experts in the field, their effects and any associated mitigation strategies largely exist as passed-down `tribal' knowledge in the community, and have not been concisely demonstrated and compared in a unified presentation. This article aims to explicitly demonstrate, through reviews of previous literature, simulated analysis and real-world case studies, the effects of resolution, binning, bounds, peak shape, peak asymmetry, inconsistent conversion of TOF to d spacing and merging of multiple banks in neutron TOF data as they directly relate to real-space PDF analysis. Suggestions for best practice in analysis of data from modern neutron TOF total scattering instruments when using conventional analysis programs are made, as well as recommendations for improved analysis methods and future instrument design

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21, 130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16, 271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts

The Ubiquitin Proteasome System Is a Key Regulator of Pluripotent Stem Cell Survival and Motor Neuron Differentiation

The ubiquitin proteasome system (UPS) plays an important role in regulating numerous cellular processes, and a dysfunctional UPS is thought to contribute to motor neuron disease. Consequently, we sought to map the changing ubiquitome in human iPSCs during their pluripotent stage and following differentiation to motor neurons. Ubiquitinomics analysis identified that spliceosomal and ribosomal proteins were more ubiquitylated in pluripotent stem cells, whilst proteins involved in fatty acid metabolism and the cytoskeleton were specifically ubiquitylated in the motor neurons. The UPS regulator, ubiquitin-like modifier activating enzyme 1 (UBA1), was increased 36-fold in the ubiquitome of motor neurons compared to pluripotent stem cells. Thus, we further investigated the functional consequences of inhibiting the UPS and UBA1 on motor neurons. The proteasome inhibitor MG132, or the UBA1-specific inhibitor PYR41, significantly decreased the viability of motor neurons. Consistent with a role of the UPS in maintaining the cytoskeleton and regulating motor neuron differentiation, UBA1 inhibition also reduced neurite length. Pluripotent stem cells were extremely sensitive to MG132, showing toxicity at nanomolar concentrations. The motor neurons were more resilient to MG132 than pluripotent stem cells but demonstrated higher sensitivity than fibroblasts. Together, this data highlights the important regulatory role of the UPS in pluripotent stem cell survival and motor neuron differentiation

A comparison of the content of memory rehabilitation groups for patients with neurological disabilities

The aim of the study was to compare the fidelity of manualised group memory rehabilitation programmes for participants with neurological disabilities. A sample of 11 neurological patients with memory problems, enrolled in a ran¬domised controlled trial comparing compensation, restitution and self-help treatments, were observed during group sessions. Time-sampling was used to record the activity of the participants and the content of the discussion at one minute intervals. There was a significant difference between groups in the amount of time the group leader and participants spent talking (p < .001). Par¬ticipants in the compensation and restitution groups spent significantly more time in memory rehabilitation discussion than participants in the self-help group (p < .001). There was also a significant difference between the amount of time spent discussing internal and external memory aids in the com¬pensation and restitution groups (p < .001). These results support the fidelity of the interventions provided. This study also highlights the usefulness of time-sampling as a method to record the content and activity in rehabilitation groups

Lung Megakaryocytes are Immune Modulatory Cells that Present Antigen to CD4+ T cells.

Although platelets are the cellular mediators of thrombosis, they are also immune cells. Platelets interact both directly and indirectly with immune cells, impacting their activation and differentiation, as well as all phases of the immune response. Megakaryocytes (Mks) are the cell source of circulating platelets, and until recently Mks were typically only considered bone marrow–resident (BM-resident) cells. However, platelet-producing Mks also reside in the lung, and lung Mks express greater levels of immune molecules compared with BM Mks. We therefore sought to define the immune functions of lung Mks. Using single-cell RNA sequencing of BM and lung myeloid-enriched cells, we found that lung Mks, which we term MkL, had gene expression patterns that are similar to antigen-presenting cells. This was confirmed using imaging and conventional flow cytometry. The immune phenotype of Mks was plastic and driven by the tissue immune environment, as evidenced by BM Mks having an MkL-like phenotype under the influence of pathogen receptor challenge and lung-associated immune molecules, such as IL-33. Our in vitro and in vivo assays demonstrated that MkL internalized and processed both antigenic proteins and bacterial pathogens. Furthermore, MkL induced CD4+ T cell activation in an MHC II–dependent manner both in vitro and in vivo. These data indicated that MkL had key immune regulatory roles dictated in part by the tissue environment.pre-print236 K

GBA mutations are associated with Rapid eye movement sleep behavior disorder

Rapid eye movement sleep behavior disorder and GBA mutations are both associated with Parkinson’s disease. The GBA gene was sequenced in idiopathic rapid eye movement sleep behavior disorder patients (n = 265), and compared to controls (n = 2240). Rapid eye movement sleep behavior disorder questionnaire was performed in an independent Parkinson’s disease cohort (n = 120). GBA mutations carriers had an OR of 6.24 (10.2% in patients vs. 1.8% in controls, P < 0.0001) for rapid eye movement sleep behavior disorder, and among Parkinson’s disease patients, the OR for mutation carriers to have probable rapid eye movement sleep behavior disorder was 3.13 (P = 0.039). These results demonstrate that rapid eye movement sleep behavior disorder is associated with GBA mutations, and that combining genetic and prodromal data may assist in identifying individuals susceptible to Parkinson’s disease