Portable Unit for Metabolic Analysis

The Portable Unit for Metabolic Analysis (PUMA) is an instrument that measures several quantities indicative of human metabolic function. Specifically, this instrument makes time-resolved measurements of temperature, pressure, flow, and the partial pressures of oxygen and carbon dioxide in breath during both inhalation and exhalation. Portable instruments for measuring these quantities have been commercially available, but the response times of those instruments are too long to enable temporal resolution of phenomena on the time scales of human respiration cycles. In contrast, the response time of the PUMA is significantly shorter than characteristic times of human respiration phenomena, making it possible to analyze varying metabolic parameters, not only on sequential breath cycles but also at successive phases of inhalation and exhalation within the same breath cycle. In operation, the PUMA is positioned to sample breath near the subject s mouth. Commercial off-the-shelf sensors are used for three of the measurements: a miniature pressure transducer for pressure, a thermistor for temperature, and an ultrasonic sensor for flow. Sensors developed at Glenn Research Center are used for measuring the partial pressures of oxygen and carbon dioxide: The carbon dioxide sensor exploits the relatively strong absorption of infrared light by carbon dioxide. Light from an infrared source passes through the stream of inhaled or exhaled gas and is focused on an infrared- sensitive photodetector. The oxygen sensor exploits the effect of oxygen in quenching the fluorescence of ruthenium-doped organic molecules in a dye on the tip of an optical fiber. A blue laser diode is used to excite the fluorescence, and the optical fiber carries the fluorescent light to a photodiode, the temporal variation of the output of which bears a known relationship with the rate of quenching of fluorescence and, hence, with the partial pressure of oxygen. The outputs of the sensors are digitized, preprocessed by a small onboard computer, and then sent wirelessly to a desktop computer, where the collected data are analyzed and displayed. In addition to the raw data on temperature, pressure, flow, and mole fractions of oxygen and carbon dioxide, the display can include volumetric oxygen consumption, volumetric carbon dioxide production, respiratory equivalent ratio, and volumetric flow rate of exhaled gas

Portable Unit for Metabolic Analysis

The Portable Unit for Metabolic Analysis measures human metabolic function. The compact invention attaches to the face of a subject and it is able to record highly time-resolved measurements of air temperature and pressure, flow rates during inhalation and exhalation, and oxygen and carbon dioxide partial pressure. The device is capable of `breath-by-breath` analysis and `within-breath` analysis at high temporal resolution

Asymmetric patterns of recovery in two habitat forming seagrass species following simulated overgrazing by urchins

The persistence of seagrass meadows reflects variation in factors that influence their productivity and consumption. Sea urchins (Amblypneustes pallidus) can over-graze seagrass (Amphibolis antarctica) to create sparse meadows in South Australia, but this effect is not observed in adjacent Posidonia sinuosa meadows despite greater densities of inhabiting urchins. To test the effect of urchin grazing on seagrass biomass, we elevated the density of urchins in meadows of A. antarctica and P. sinuosa and quantified seagrass decline. Urchins removed similar amounts of biomass from both seagrass species, but the loss of leaf meristems was 11-times greater in A. antarctica than in P. sinuosa. In a second experiment to assess the recovery of seagrass, we simulated urchin grazing by clipping seagrass to mimic impacts measured in the first experiment, as well as completely removing all above ground biomass in one treatment. Following simulated grazing, P. sinuosa showed a rapid trajectory toward recovery, while A. antarctica meadows continued to decline relative to control treatments. While both A. antarctica and P. sinuosa were susceptible to heavy grazing loss, consumption of the exposed meristems of A. antarctica appears to reduce its capacity to recover, which may increase its vulnerability to long-term habitat phase-shifts and associated cascading ecosystem changes. © 2013 Elsevier B.V.Owen W. Burnell, Sean D. Connell, Andrew D. Irving, Bayden D. Russel

Crop Updates 2006 - Weeds

This session covers thirty seven papers from different authors: 1. ACKNOWLEDGEMENTS, Alexandra Douglas, CONVENOR – WEEDS DEPARTMENT OF AGRICULTURE SPRAY TECHNOLOGY 2. Meeting the variable application goals with new application technology, Thomas M. Wolf, Agriculture and Agri-Food Canada, Saskatoon Research Centre 3. Spray nozzles for grass weed control, Harm van Rees, BCG (Birchip Cropping Group) 4. Boom sprayer setups – achieving coarse droplets with different operating parameters, Bill Gordon, Bill Gordon Consulting 5. Complying with product label requirements, Bill Gordon, Bill Gordon Consulting 6. IWM a proven performer over 5 years in 33 focus paddocks, Peter Newman and Glenn Adam, Department of Agriculture 7. Crop topping of wild radish in lupins and barley, how long is a piece of string? Peter Newman and Glenn Adam, Department of Agriculture 8. Determining the right timing to maximise seed set control of wild radish, Aik Cheam and Siew Lee, Department of Agriculture 9. Why weed wiping varies in success rates in broadacre crops? Aik Cheam1, Katherine Hollaway2, Siew Lee1, Brad Rayner1 and John Peirce1,1Department of Agriculture, 2Department of Primary Industries, Victoria 10. Are WA growers successfully managing herbicide resistant annual ryegrass? Rick Llewellynabc, Frank D’Emdena, Mechelle Owenb and Stephen Powlesb aCRC Australian Weed Management, School of Agricultural and Resource Economics, University of Western Australia; bWA Herbicide Resistance Initiative, University of Western Australia. cCurrent address: CSIRO Sustainable Ecosystems 11. Do herbicide resistant wild radish populations look different? Michael Walsh, Western Australian Herbicide Resistance Initiative, University of Western Australia 12. Can glyphosate and paraquat annual ryegrass reduce crop topping efficacy? Emma Glasfurd, Michael Walsh and Kathryn Steadman, Western Australian Herbicide Resistance Initiative, University of Western Australia 13. Tetraploid ryegrass for WA. Productive pasture phase AND defeating herbicide resistant ryegrass, Stephen Powlesa, David Ferrisab and Bevan Addisonc, aWA Herbicide Resistance Initiative, University of Western Australia; bDepartment of Agriculture, and cElders Limited 14. Long-term management impact on seedbank of wild radish with multiple resistance to diflufenican and triazines, Aik Cheam, Siew Lee, Dave Nicholson and Ruben Vargas, Department of Agriculture 15. East-west crop row orientation improves wheat and barley yields, Dr Shahab Pathan, Dr Abul Hashem, Nerys Wilkins and Catherine Borger3, Department of Agriculture, 3WAHRI, The University ofWestern Australia 16. Competitiveness of different lupin cultivars with wild radish, Dr Shahab Pathan, Dr Bob French and Dr Abul Hashem, Department of Agriculture 17. Managing herbicide resistant weeds through farming systems, Kari-Lee Falconer, Martin Harries and Chris Matthews, Department of Agriculture 18. Lupins tolerate in-row herbicides well, Peter Newman and Martin Harries, Department of Agriculture 19. Summer weeds can reduce wheat grain yield and protein, Dr Abul Hashem1, Dr Shahab Pathan1 and Vikki Osten3, 1Department Agriculture, 3Senior Agronomist, CRC for Australian Weed Management, Queensland Department of Primary Industries and Fisheries 20. Diuron post-emergent in lupins, the full story, Peter Newman and Glenn Adam, Department of Agriculture 21. Double incorporation of trifluralin, Peter Newman and Glenn Adam, Department of Agriculture 22. Herbicide tolerance of narrow leafed and yellow lupins, Harmohinder Dhammu, David Nicholson, Department of Agriculture 23. MIG narrow leaf lupin herbicide tolerance trial, Richard Quinlan, Planfarm Pty Ltd, Trials Coordinator MIG; Debbie Allen, Research Agronomist – MIG 24. Herbicide tolerance of new albus lupins, Harmohinder Dhammu, David Nicholson, Department of Agriculture 25. Field pea x herbicide tolerance, Mark Seymour and Harmohinder Dhammu, Research Officers, and Pam Burgess, Department of Agriculture 26. Faba bean variety x herbicide tolerance, Mark Seymour and Harmohinder Dhammu, Research Officers, and Pam Burgess, Department of Agriculture 27. Herbicide tolerance of new Kabili chickpeas, Harmohinder Dhammu, Owen Coppen and Chris Roberts, Department of Agriculture 28. Timing of phenoxys application in EAG Eagle Rock, Harmohinder Dhammu, David Nicholson, Department of Agriculture 29. Herbicide tolerance of new wheat varieties, Harmohinder Dhammu, David Nicholson, Department of Agriculture 30. Lathyrus sativus x herbicide tolerance, Mark Seymour, Department of Agriculture 31. Tolerance of annual pasture species to herbicides and mixtures containing diuron, Christiaan Valentine and David Ferris, Department of Agriculture 32. The impact of herbicides on pasture legume species – a summary of scientific trial results across 8 years, Christiaan Valentine and David Ferris, Department of Agriculture 33. The impact of spraytopping on pasture legume seed set, Christiaan Valentine and David Ferris, Department of Agriculture 34. Ascochyta interaction with Broadstrike in chickpeas, H.S. Dhammu1, A.K. Basandrai2,3, W.J. MacLeod1, 3 and C. Roberts1, 1Department of Agriculture, 2CSKHPAU, Dhaulakuan, Sirmour (HP), India and 3CLIMA 35. Best management practices for atrazine in broadacre crops, John Moore, Department of Agriculture, Neil Rothnie, Chemistry Centre of WA, Russell Speed, Department of Agriculture, John Simons, Department of Agriculture, and Ted Spadek, Chemistry Centre of WA 36. Biology and management of red dodder (Cuscuta planiflolia) – a new threat to the grains industry, Abul Hashem, Daya Patabendige and Chris Roberts, Department Agriculture 37. Help the wizard stop the green invaders! Michael Renton, Sally Peltzer and Art Diggle, Department of Agricultur

The Emergence and Early Evolution of Biological Carbon-Fixation

The fixation of into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a “phylometabolic” tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery