Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence

The recent release of the genome sequences of a number of crop and model plant species has made it possible to define the genome organisation and functional characteristics of specific genes and gene families of agronomic importance. For instance, Sorghum bicolor, maize (Zea mays) and Brachypodium distachyon genome sequences along with the model grass species rice (Oryza sativa) enable the comparative analysis of genes involved in plant defence. Germin-like proteins (GLPs) are a small, functionally and taxonomically diverse class of cupin-domain containing proteins that have recently been shown to cluster in an area of rice chromosome 8. The genomic location of this gene cluster overlaps with a disease resistance QTL that provides defence against two rice fungal pathogens (Magnaporthe oryzae and Rhizoctonia solani). Studies showing the involvement of GLPs in basal host resistance against powdery mildew (Blumeria graminis ssp.) have also been reported in barley and wheat. In this mini-review, we compare the close proximity of GLPs in publicly available cereal crop genomes and discuss the contribution that these proteins, and their genome sequence organisation, play in plant defenc

On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation

Volumetric crystal structure indexing and orientation mapping are key data processing steps for virtually any quantitative study of spatial correlations between the local chemistry and the microstructure of a material. For electron and X-ray diffraction methods it is possible to develop indexing tools which compare measured and analytically computed patterns to decode the structure and relative orientation within local regions of interest. Consequently, a number of numerically efficient and automated software tools exist to solve the above characterisation tasks. For atom probe tomography (APT) experiments, however, the strategy of making comparisons between measured and analytically computed patterns is less robust because many APT datasets may contain substantial noise. Given that general enough predictive models for such noise remain elusive, crystallography tools for APT face several limitations: Their robustness to noise, and therefore, their capability to identify and distinguish different crystal structures and orientation is limited. In addition, the tools are sequential and demand substantial manual interaction. In combination, this makes robust uncertainty quantifying with automated high-throughput studies of the latent crystallographic information a difficult task with APT data. To improve the situation, we review the existent methods and discuss how they link to those in the diffraction communities. With this we modify some of the APT methods to yield more robust descriptors of the atomic arrangement. We report how this enables the development of an open-source software tool for strong-scaling and automated identifying of crystal structure and mapping crystal orientation in nanocrystalline APT datasets with multiple phases.Comment: 36 pages, 19 figures, preprin

Digital news report: Australia 2015

This report gives a clear picture of how the Australian news consumer compares to eleven other countries surveyed in 2015: Denmark, Finland, France, Germany, Ireland, Italy, Japan, Spain, UK, USA and urban Brazil. The Digital News Report: Australia is part of a global survey by the Reuters Institute for the Study of Journalism at the University of Oxford. Further in-depth analysis of Australian digital news consumption has been conducted and published by the News & Media Research Centre at the University of Canberra

Comparison of regional gene expression differences in the brains of the domestic dog and human

Comparison of the expression profiles of 2,721 genes in the cerebellum, cortex and pituitary gland of three American Staffordshire terriers, one beagle and one fox hound revealed regional expression differences in the brain but failed to reveal marked differences among breeds, or even individual dogs. Approximately 85 per cent (42 of 49 orthologue comparisons) of the regional differences in the dog are similar to those that differentiate the analogous human brain regions. A smaller percentage of human differences were replicated in the dog, particularly in the cortex, which may generally be evolving more rapidly than other brain regions in mammals. This study lays the foundation for detailed analysis of the population structure of transcriptional variation as it relates to cognitive and neurological phenotypes in the domestic dog

The Jacobi orientation and the two-variable elliptic genus

We explain the relationship between the sigma orientation and Witten genus on the one hand and the two-variable elliptic genus on the other. We show that if E is an elliptic spectrum, then the Theorem of the Cube implies the existence of canonical SU-orientation of the associated spectrum of Jacobi forms. In the case of the elliptic spectrum associated to the Tate curve, this gives the two-variable elliptic genus. We also show that the two-variable genus arises as an instance of the circle-equivariant sigma orientation.Comment: Revised to better exhibit complex orientation of MSU^(CP^\infty_{-infty}

Cancer Patient and clinician acceptability and feasibility of a supportive care screening and referral process

Background: Incorporating supportive care into routine cancer care is an increasing priority for the multi-disciplinary team with growing evidence of its importance to patient-centred care. How to design and deliver a process which is appropriate for patients, clinicians and health services in rural areas needs further investigation. Objective: To (i) examine the patient and clinician acceptability and feasibility of incorporating a supportive care screening and referral process into routine cancer care in a rural setting, and (ii) explore any potential influences of patient variables on the acceptability of the process. Methods: A total of 154 cancer patients and 36 cancer clinicians across two rural areas of Victoria, Australia participated. During treatment visits, patients and clinicians participated in a supportive care process involving screening, discussion of problems, and provision of information and referrals. Structured questionnaires with open and closed questions were used to measure patient and clinician acceptability and feasibility. Results: Patients and clinicians found the supportive care process highly acceptable. Screening identified relevant patient problems (90%) and problems that may not have otherwise been identified (83%). The patient-clinician discussion helped patients realize help was available (87%) and enhanced clinician-patient rapport (72%). Patients received useful referrals to services (76%). Feasibility issues included timing of screening for newly diagnosed patients, privacy in discussing problems, clinician time and availability of referral options. No patient demographic or disease factors influenced acceptability or feasibility. Conclusions: Patients and clinicians reported high acceptability for the supportive care process, although mechanisms for incorporating the process into health care need to be further developed

Detection of BRAF Mutation in Urine DNA as a Molecular Diagnostic for Canine Urothelial and Prostatic Carcinoma

Urothelial carcinoma (UC) of the lower urinary tract and prostatic carcinoma (PC) are aggressive genitourinary cancers in dogs, characterized by invasion to surrounding tissues and high metastatic potential. Current diagnosis of canine UC and PC requires histopathological examination of a biopsy. Such specimens require specialized medical equipment and are invasive procedures, limiting the availability of diagnosis by histopathology for many canine patients. Access to a non-invasive means to confirm diagnosis is currently an unmet need. Recently, the canine BRAF V595E mutation was detected in ~80% of canine UCs and PCs. In this study, we developed a droplet digital PCR (ddPCR) assay for detection of the canine BRAF V595E mutation in canine urogenital tumors. The assay was evaluated in DNA samples prepared from biopsy specimens of UC (n = 48) and PC (n = 27), as well and non-neoplastic bladder epithelium (n = 38). In addition the assay was assessed for use with DNA isolated from free catch urine samples derived from canine patients with UC (n = 23), PC (n = 3), as well as from dogs with cystitis and healthy controls (n = 37). In all cases the sensitivity to detect the mutant allele was compared with conventional Sanger sequencing. ddPCR had superior sensitivity for detection of the V595E mutation: 75% of UC, 85% of PC, and 0% of control samples were mutation positive, respectively, and the V595E mutation was detected at a level as low as just 1 in 10,000 alleles (~0.01%). Furthermore, the ddPCR assay identified the mutation in free catch urine samples from 83% of canine UC and PC patients, demonstrating its utility as a non-invasive means of diagnosis. We have shown that ddPCR is a sensitive molecular technique with the potential to facilitate accurate and non-invasive means of canine UC and PC diagnosis

Assessing the contributions of childhood maltreatment subtypes and depression case-control status on telomere length reveals a specific role of physical neglect

Background: Studies have provided evidence that both childhood maltreatment and depressive disorders are associated with shortened telomere lengths. However, as childhood maltreatment is a risk factor for depression, it remains unclear whether this may be driving shortened telomere lengths observed amongst depressed patients. Furthermore, it's unclear if the effects of maltreatment on telomere length shortening are more pervasive amongst depressed patients relative to controls, and consequently whether biological ageing may contribute to depression's pathophysiology. The current study assesses the effects of childhood maltreatment, depression case/control status, and the interactive effect of both childhood maltreatment and depression case/control status on relative telomere length (RTL). Method: DNA samples from 80 depressed subjects and 100 control subjects were utilized from a U.K. sample (ages 20-84), with childhood trauma questionnaire data available for all participants. RTL was quantified using quantitative polymerase chain reactions. Univariate linear regression analyses were used to assess the effects of depression status, childhood maltreatment and depression by childhood maltreatment interactions on RTL. The false discovery rate (q 50 years old). There were no significant depression case/control status by childhood maltreatment interactions. Limitations: A relatively small sample limited our power to detect interaction effects, and we were unable to consider depression chronicity or recurrence. Conclusion: Shortened RTL was specifically associated with childhood physical neglect, but not the other subtypes of maltreatment or depression case/control status. Our results suggest that the telomere-eroding effects of physical neglect may represent a biological mechanism important in increasing risk for ageing-related disorders. As physical neglect is more frequent amongst depressed cases generally, it may also represent a confounding factor driving previous associations between shorter RTL and depression case status.Peer reviewe

Elastomeric pump infusion failures caused by inadequate Luer lock connector engagement to needleless connectors

Needleless connectors are used widely across all types of vascular access devices and provide safe, needleless administration of intravenous fluids and medications. An analysis of patients from an outpatient parenteral antimicrobial therapy program is presented in which elastomeric pumps had failed to flow due to incomplete tightening of Luer lock needleless connections. An alert was issued to community nursing staff responsible for daily elastomeric pump changes to ensure that needleless connectors were properly checked for full tightening. The frequency of failure of flow events before and after the alert was reviewed. Force and torque profiles required to activate the internal mechanism of connectors were measured in the 4 most frequently used needleless connectors in the outpatient parenteral antimicrobial therapy program. The degree of torque and force required to activate the different needleless connectors varied and was identified as a factor contributing to inadequate connection with the elastomeric pump and consequent failure of flow. Repeated feedback to nursing staff over the study period about the force and torque required for needleless connector flow activation resulted in a highly significant decrease in the rate of failure of flow events per elastomeric pump from a rate of 0.0147 events per elastomeric pump per year in the last 3 months of 2018 to 0.0003 in the first 6 months of 2020 (difference = 0.0144 [CI, 0.0097-0.02]; P < .0001)