The value of research data to the nation

Executive Director’s report Ross Wilkinson, ANDS How can Australia address the challenge of living in bushfire prone city fringes? How can Australia most effectively farm and preserve our precious soil? How can Australia understand the Great Barrier Reef? No single discipline can answer these questions, but to address these challenges data is needed from a range of sources and disciplines. Research data that is well organised and available allows research to make substantial contributions vital to Australia’s future. For example, by drawing upon data that is able to be used by soil scientists, geneticists, plant scientists, climate analysts, and others, it is possible to conduct the multidisciplinary investigations necessary to tackle truly difficult and important challenges. The data might be provided by a Terrestrial Ecosystems Research Network OzFluz tower, insect observations recorded by a citizen through the Atlas of Living Australia, genetic sequencing of insects through a Bioplatforms Australia facility, weather observations by the Bureau of Meteorology, or historical data generated by CSIRO over many decades. Each will provide a part of the jigsaw, but the pieces must be able to be put together. This requires careful collection and organisation, which together deliver enormous value to the country. However, nationally significant problems are often tackled by international cooperation, so Australia’s data assets enable Australian researchers to work with the best in the world, solving problems of both national and international significance. Australia’s data assets and research data infrastructure provide Australian researchers with an excellent platform for international collaboration. Australia has world-leading research data infrastructure: our ability to store, compute, discover, explore, analyse and publish is the best in the world. The ability to capture data through a wide range of capabilities, from the Australian Synchrotron to Integrated Marine Observation System [IMOS: imos.org.au] ocean gliders, the combination of national storage and computation through RDSI, NCI and Pawsey initiatives, the ability to publish and discover data through ANDS, the ability to analyse and explore data through Nectar, and state and local eResearch capabilities, highlights just some of the capabilities that Australian researchers are able to access. Importantly, their international partners are able to work with them using many of these resources. As well, Australian research organisations are assembling many resources to support their research. These include policies, procedures, practical infrastructure, and very importantly – people! The eResearch team and the data librarians are always keen to help. This issue of Share highlights how the data resources of Australia are providing a very substantial national benefit, and how that benefit is being realised

The mechanisms responsible for 2-dimensional pattern formation in bacterial macrofiber populations grown on solid surfaces: fiber joining and the creation of exclusion zones

BACKGROUND: When Bacillus subtilis is cultured in a complex fluid medium under conditions where cell separation is suppressed, populations of multicellular macrofibers arise that mature into ball-like structures. The final sedentary forms are found distributed in patterns on the floor of the growth chamber although individual cells have no flagellar-driven motility. The nature of the patterns and their mode of formation are described in this communication. RESULTS: Time-lapse video films reveal that fiber-fiber contact in high density populations of macrofibers resulted in their joining either by entwining or supercoiling. Joining led to the production of aggregate structures that eventually contained all of the fibers located in an initial area. Fibers were brought into contact by convection currents and motions associated with macrofiber self-assembly such as walking, pivoting and supercoiling. Large sedentary aggregate structures cleared surrounding areas of other structures by dragging them into the aggregate using supercoiling of extended fibers to power dragging. The spatial distribution of aggregate structures in 6 mature patterns containing a total of 637 structures was compared to that expected in random theoretical populations of the same size distributed in the same surface area. Observed and expected patterns differ significantly. The distances separating all nearest neighbors from one another in observed populations were also measured. The average distance obtained from 1451 measurements involving 519 structures was 0.73 cm. These spacings were achieved without the use of flagella or other conventional bacterial motility mechanisms. A simple mathematical model based upon joining of all structures within an area defined by the minimum observed distance between structures in populations explains the observed distributions very well. CONCLUSIONS: Bacterial macrofibers are capable of colonizing a solid surface by forming large multicellular aggregate structures that are distributed in unique two-dimensional patterns. Cell growth geometry governs in an hierarchical way the formation of these patterns using forces associated with twisting and supercoiling to drive motions and the joining of structures together. Joining by entwining, supercoiling or dragging all require cell growth in a multicellular form, and all result in tightly fused aggregate structures

The dynamic behavior of bacterial macrofibers growing with one end prevented from rotating: variation in shaft rotation along the fiber's length, and supercoil movement on a solid surface toward the constrained end

BACKGROUND: Bacterial macrofibers twist as they grow, writhe, supercoil and wind up into plectonemic structures (helical forms the individual filaments of which cannot be taken apart without unwinding) that eventually carry loops at both of their ends. Terminal loops rotate about the axis of a fiber's shaft in contrary directions at increasing rate as the shaft elongates. Theory suggests that rotation rates should vary linearly along the length of a fiber ranging from maxima at the loop ends to zero at an intermediate point. Blocking rotation at one end of a fiber should lead to a single gradient: zero at the blocked end to maximum at the free end. We tested this conclusion by measuring directly the rotation at various distances along fiber length from the blocked end. The movement of supercoils over a solid surface was also measured in tethered macrofibers. RESULTS: Macrofibers that hung down from a floating wire inserted through a terminal loop grew vertically and produced small plectonemic structures by supercoiling along their length. Using these as markers for shaft rotation we observed a uniform gradient of initial rotation rates with slopes of 25.6°/min. mm. and 36.2°/min. mm. in two different fibers. Measurements of the distal tip rotation in a third fiber as a function of length showed increases proportional to increases in length with constant of proportionality 79.2 rad/mm. Another fiber tethered to the floor grew horizontally with a length-doubling time of 74 min, made contact periodically with the floor and supercoiled repeatedly. The supercoils moved over the floor toward the tether at approximately 0.06 mm/min, 4 times faster than the fiber growth rate. Over a period of 800 minutes the fiber grew to 23 mm in length and was entirely retracted back to the tether by a process involving 29 supercoils. CONCLUSIONS: The rate at which growing bacterial macrofibers rotated about the axis of the fiber shaft measured at various locations along fibers in structures prevented from rotating at one end reveal that the rate varied linearly from zero at the blocked end to maximum at the distal end. The increasing number of twisting cells in growing fibers caused the distal end to continuously rotate faster. When the free end was intermittently prevented from rotating a torque developed which was relieved by supercoiling. On a solid surface the supercoils moved toward the end permanently blocked from rotating as a result of supercoil rolling over the surface and the formation of new supercoils that reduced fiber length between the initial supercoil and the wire tether. All of the motions are ramifications of cell growth with twist and the highly ordered multicellular state of macrofibers

Ekman veering, internal waves, and turbulence observed under Arctic sea ice

Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 44 (2014): 1306–1328, doi:10.1175/JPO-D-12-0191.1.The ice–ocean system is investigated on inertial to monthly time scales using winter 2009–10 observations from the first ice-tethered profiler (ITP) equipped with a velocity sensor (ITP-V). Fluctuations in surface winds, ice velocity, and ocean velocity at 7-m depth were correlated. Observed ocean velocity was primarily directed to the right of the ice velocity and spiraled clockwise while decaying with depth through the mixed layer. Inertial and tidal motions of the ice and in the underlying ocean were observed throughout the record. Just below the ice–ocean interface, direct estimates of the turbulent vertical heat, salt, and momentum fluxes and the turbulent dissipation rate were obtained. Periods of elevated internal wave activity were associated with changes to the turbulent heat and salt fluxes as well as stratification primarily within the mixed layer. Turbulent heat and salt fluxes were correlated particularly when the mixed layer was closest to the freezing temperature. Momentum flux is adequately related to velocity shear using a constant ice–ocean drag coefficient, mixing length based on the planetary and geometric scales, or Rossby similarity theory. Ekman viscosity described velocity shear over the mixed layer. The ice–ocean drag coefficient was elevated for certain directions of the ice–ocean shear, implying an ice topography that was characterized by linear ridges. Mixing length was best estimated using the wavenumber of the beginning of the inertial subrange or a variable drag coefficient. Analyses of this and future ITP-V datasets will advance understanding of ice–ocean interactions and their parameterizations in numerical models.Support for this study and the overall ITP program was provided by the National Science Foundation and Woods Hole Oceanographic Institution. Support for S. Cole was partially though the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Devonshire Foundation.2014-11-0

Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit

BACKGROUND  Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-genome sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission using the conventional approach of spa typing and overlapping patient stay. METHODS Over 14 months, all unselected patients admitted to an adult intensive care unit (ICU) were serially screened for S. aureus. All available isolates (n = 275) were spa typed and underwent whole-genome sequencing to investigate their relatedness at high resolution. RESULTS Staphylococcus aureus was carried by 185 of 1109 patients sampled within 24 hours of ICU admission (16.7%); 59 (5.3%) patients carried methicillin-resistant S. aureus (MRSA). Forty-four S. aureus (22 MRSA) acquisitions while on ICU were detected. Isolates were available for genetic analysis from 37 acquisitions. Whole-genome sequencing indicated that 7 of these 37 (18.9%) were transmissions from other colonized patients. Conventional methods (spa typing combined with overlapping patient stay) falsely identified 3 patient-to-patient transmissions (all MRSA) and failed to detect 2 acquisitions and 4 transmissions (2 MRSA). CONCLUSIONS Only a minority of S. aureus acquisitions can be explained by patient-to-patient transmission. Whole-genome sequencing provides the resolution to disprove transmission events indicated by conventional methods and also to reveal otherwise unsuspected transmission events. Whole-genome sequencing should replace conventional methods for detection of nosocomial S. aureus transmission

A novel LMX1B mutation in a family with end-stage renal disease of 'unknown cause'

End-stage renal disease (ESRD) presenting in a familial autosomal dominant pattern points to an underlying monogenic cause. Nail-patella syndrome (NPS) is an autosomal dominant disorder that may lead to ESRD caused by mutations in the transcription factor LMX1B. Renal-limited forms of this disease, termed nail-patella-like renal disease (NPLRD), and LMX1B nephropathy have recently been described. We report a large family, from the North East of England, with seven affected members with varying phenotypes of renal disease, ranging from ESRD at 28 years of age to microscopic haematuria and proteinuria and relatively preserved renal function. In this family, there were no extra-renal manifestations to suggest NPS. Genome-wide linkage studies and inheritance by descent (IBD) suggested disease loci on Chromosome 1 and 9. Whole exome sequencing (WES) analysis identified a novel sequence variant (p.R249Q) in the LMX1B gene in each of the three samples submitted, which was confirmed using Sanger sequencing. The variant segregated with the disease in all affected individuals. In silico modelling revealed that R249 is putatively located in close proximity to the DNA phosphoskeleton, supporting a role for this residue in the interaction between the LMX1B homeodomain and its target DNA. WES and analysis of potential target genes, including CD2AP, NPHS2, COL4A3, COL4A4 and COL4A5, did not reveal any co-inherited pathogenic variants. In conclusion, we confirm a novel LMX1B mutation in a large family with an autosomal dominant pattern of nephropathy. This report confirms that LMX1B mutations may cause a glomerulopathy without extra-renal manifestations. A molecular genetic diagnosis of LMX1B nephropathy thus provides a definitive diagnosis, prevents the need for renal biopsies and allows at risk family members to be screened

A framework for considering the utility of models when facing tough decisions in public health: a guideline for policy-makers

The COVID-19 pandemic has brought the combined disciplines of public health, infectious disease and policy modelling squarely into the spotlight. Never before have decisions regarding public health measures and their impacts been such a topic of international deliberation, from the level of individuals and communities through to global leaders. Nor have models-developed at rapid pace and often in the absence of complete information-ever been so central to the decision-making process. However, after nearly 3 years of experience with modelling, policy-makers need to be more confident about which models will be most helpful to support them when taking public health decisions, and modellers need to better understand the factors that will lead to successful model adoption and utilization. We present a three-stage framework for achieving these ends

The management of Staphylococcus aureus bacteremia in the United Kingdom and Vietnam: a multi-centre evaluation.

Background: Staphylococcus aureus bacteremia is a common and serious infection worldwide and although treatment guidelines exist, there is little consensus on optimal management. In this study we assessed the variation in management and adherence to treatment guidelines of S. aureus bacteremia. Methodology/Principal Findings: We prospectively recorded baseline clinical characteristics, management, and in-hospital outcome of all adults with S. aureus bacteremia treated consecutively over one year in eight centres in the United Kingdom, three in Vietnam and one in Nepal. 630 adults were treated for S. aureus bacteremia: 549 in the UK (21% methicillin-resistant), 80 in Vietnam (19% methicillin-resistant) and 1 in Nepal. In the UK, 41% had a removable infection focus (50% intravenous catheter-related), compared to 12% in Vietnam. Significantly (p50% of treatment with oral antibiotics alone (25% versus 4%). UK centres varied significantly (p50% of treatment (range 12-40%), in those treated for longer than 28 days (range 13-54%), and in those given combination therapy (range 14-94%). 24% died during admission: older age, time in hospital before bacteremia, and an unidentified infection focus were independent predictors of in-hospital death (p<0.001). Conclusions/Significance: The management of S. aureus bacteremia varies widely between the UK and Vietnam and between centres in the UK with little adherence to published guidelines. Controlled trials defining optimal therapy are urgently required