Modern microbiology: Embracing complexity through integration across scales

Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century

PCOC National Report on Outcomes in Palliative Care in Australia July to December 2011

The Palliative Care Outcomes Collaboration (PCOC) was established in mid-2005 and is funded under the National Palliative Care Program supported by the Australian Government Department of Health and Ageing. The goal of the PCOC is to use standardised, validated, clinical assessment tools to benchmark and measure outcomes in palliative care; and assist palliative care services to improve the quality of care. Further information on the tools can be found at www.pcoc.org.au. Each service involved in PCOC submits data every six months. The data are then collated and fed back to services to inform service improvement. Participation in PCOC is voluntary. There are three levels of data items - patient, episode and phase. The broad detail is found at the patient level, where the data items look at patient demographics. At the episode level, the items focus on characterising each setting of palliative care. They also describe the reasons behind why and how palliative care episodes start/end, the level of support patients receive both before and after an episode and (where applicable) the setting in which the patient died. The clinical focus of the data is at the phase level. The items at this level describe the patient\u27s stage of illness, functional impairment as well as their levels of pain and symptom distress. The items at the phase level are used to quantify patient outcomes, and are the focus of the PCOC benchmarks. The current PCOC data set (Version 2) was introduced in July 2007 following consultation with palliative care services and approval by PCOC\u27s Scientific and Clinical Advisory Committee. The data set includes five clinical assessment tools: Phases of Care, Palliative Care Problem Severity Score (PCPSS), Symptom Assessment Scale (SAS), Australia-modified Karnofsky Performance Status Scale (AKPS) and Resource Utilisation Groups - Activities of Daily Living (RUG-ADL). The items included in the PCOC data set serve the dual purpose of: - defining a common clinical language to allow communication between palliative care providers - facilitating the routine collection of national palliative care data for the purpose of reporting and benchmarking to drive quality improvement. Revised phase definitions were implemented in January 2012 but the data in this report does not reflect the revised definitions

Polarization signatures of unresolved radio sources

We investigate how the imprint of Faraday rotation on radio spectra can be used to determine the geometry of radio sources and the strength and structure of the surrounding magnetic fields. We model spectra of Stokes Q and U for frequencies between 200 MHz and 10 GHz for Faraday screens with large-scale or small-scale magnetic fields external to the source. These sources can be uniform or 2D Gaussians on the sky with transverse linear gradients in rotation measure (RM), or cylinders or spheroids with an azimuthal magnetic field. At high frequencies, the spectra of all these models can be approximated by the spectrum of a Gaussian source; this is independent of whether the magnetic field is large scale or small scale. A sinc spectrum in polarized flux density is not a unique signature of a volume where synchrotron emission and Faraday rotation are mixed. A turbulent Faraday screen with a large field coherence length produces a spectrum which is similar to the spectrum of a partial coverage model. At low and intermediate frequencies, such a Faraday screen produces a significantly higher polarized signal than Burn's depolarization model, as shown by a random walk model of the polarization vectors. We calculate RM spectra for four frequency windows. Sources are strongly depolarized at low frequencies, but RMs can be determined accurately if the sensitivity of the observations is sufficient. Finally, we show that RM spectra can be used to differentiate between turbulent foreground models and partial coverage models

Quantifying heavy metals sequestration by sulfate-reducing bacteria in an acid mine drainage-contaminated natural wetland

Bioremediation strategies that depend on bacterial sulfate reduction for heavy metals remediation harness the reactivity of these metals with biogenic aqueous sulfide. Quantitative knowledge of the degree to which specific toxic metals are partitioned into various sulfide, oxide, or other phases is important for predicting the long-term mobility of these metals under environmental conditions. Here we report the quantitative partitioning into sedimentary biogenic sulfides of a suite of metals and metalloids associated with acid mine drainage contamination of a natural estuarine wetland for over a century

Thermal tides in the Martian middle atmosphere as seen by the Mars Climate Sounder

The first systematic observations of the middle atmosphere of Mars (35–80km) with the Mars Climate Sounder (MCS) show dramatic patterns of diurnal thermal variation, evident in retrievals of temperature and water ice opacity. At the time of writing, the data set of MCS limb retrievals is sufficient for spectral analysis within a limited range of latitudes and seasons. This analysis shows that these thermal variations are almost exclusively associated with a diurnal thermal tide. Using a Martian general circulation model to extend our analysis, we show that the diurnal thermal tide dominates these patterns for all latitudes and all seasons

Patient Outcomes in Palliative Care, Report 13 (January - June 2012) - Western Australia

PCOC aims to assist services to improve the quality of the palliative care they provide through the analysis and benchmarking of patient outcomes. In this, the thirteenth PCOC report, data submitted for the January - June 2012 period are summarised and patient outcomes benchmarked to enable participating services to assess their performance and identify areas in which they may improve. This report is broken into four sections: Section 1 provides a summary of the data included in this report. Section 2 summarises each of the four outcome measures and presents national benchmarking results for a selection of these measures. Section 3 presents a more detailed analysis of the outcome measures and benchmarks. Section 4 provides descriptive analysis at each of the patient, episode and phase data levels. In each of the four sections, data and analysis for services in WA is presented alongside the national figures for comparative purposes. The national figures reflect all palliative care services who submitted data for the January - June 2012 period. A full list of these services can be found at www.pcoc.org.au The four outcome measures included in this report were first introduced in the reporting period January to June 2009 (Report 7). There is strong sectoral support for national benchmarks and a consensus that such benchmarks can drive service innovation regardless of model of care. Benchmarking provides opportunities to understand the services that are provided, the outcomes patients experience and also to generate research opportunities focused on how to demonstrate variations in practice and outcomes

Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community.

The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C. psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria.IMPORTANCE CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence

Infrared-Faint Radio Sources: A New Population of High-redshift Radio Galaxies

We present a sample of 1317 Infrared-Faint Radio Sources (IFRSs) that, for the first time, are reliably detected in the infrared, generated by cross-correlating the Wide-Field Infrared Survey Explorer (WISE) all-sky survey with major radio surveys. Our IFRSs are brighter in both radio and infrared than the first generation IFRSs that were undetected in the infrared by the Spitzer Space Telescope. We present the first spectroscopic redshifts of IFRSs, and find that all but one of the IFRSs with spectroscopy has z > 2. We also report the first X-ray counterparts of IFRSs, and present an analysis of radio spectra and polarization, and show that they include Gigahertz-Peaked Spectrum, Compact Steep Spectrum, and Ultra-Steep Spectrum sources. These results, together with their WISE infrared colours and radio morphologies, imply that our sample of IFRSs represents a population of radio-loud Active Galactic Nuclei at z > 2. We conclude that our sample consists of lower-redshift counterparts of the extreme first generation IFRSs, suggesting that the fainter IFRSs are at even higher redshift.Comment: 23 pages, 17 figures. Submitted to MNRA