Evaluating molecular diagnostic techniques for seed detection of Pseudomonas savastanoi pv. phaseolicola, causal agent of halo blight disease in mungbean (Vigna radiata)

Halo blight of mungbean (Vigna radiata var. radiata) is caused by the bacterium Pseudomonas savastanoi pv. phaseolicola. This pathogen is transmitted via infected seed, facilitating the spread of the disease into new cultivated areas. Prospective mungbean seed crops are currently subjected to visual inspection as a means of determining disease status, however, this is a poor method that relies on visible symptoms and does not account for latent infections. A range of molecular diagnostics targeting P. savastanoi pv. phaseolicola have been developed, but these have not been deployed on seeds. Quantitative PCR (qPCR) SYBR assay, hydrolysis probe, and conventional PCR, using the same primers were optimised against a plate-truthed dilution series of P. savastanoi pv. phaseolicola. The detection limit of the conventional PCR assay was approximately 9,000 CFU µl-1, while both qPCR assays could detect 9 CFU µl-1. These tests were then used to screen DNA extracted from 200 g allotments of 38 seed lots comprising six mungbean cultivars representing the primary Australian production area, and two seed lots of known infection status. Of these, the pathogen was detected in six seed lots by conventional PCR. The SYBR assay and hydrolysis probe methods detected 20 and 24 infected seed lots respectively. This shows that the hydrolysis probe method was the most effective at diagnosing the presence of P. savastanoi pv. phaseolicola in mungbean seed, providing a valuable molecular diagnostic to aid in integrated disease management and seed certification, substantially mitigating losses to halo blight disease

Diagnosis and management of halo blight in Australian mungbeans: A review

Mungbean (Vigna radiata L. Wilczek var. radiata) is an important food crop cultivated on over 6 Mha throughout the world. Its short duration of 55-70 days, capacity to fix atmospheric nitrogen, and exceptional grain nutritional profile makes the crop a staple for smallholder and subsistence farmers. In Australia, mungbean is grown as a high-value export crop and established as a main summer rotation for dryland farmers. A major threat to the integrity of the industry is halo blight, a bacterial disease leading to necrotic lesions surrounded by a chlorotic halo that stunts and ultimately kills the plant. Caused by Pseudomonas savastanoi pv. Phaseolicola, this seed-borne disease is extremely difficult to control, resulting in significant yield loss and production volatility. The challenge of managing halo blight is exacerbated by a wide host range that includes many legume and weed species, and the presence of multiple epidemiologically significant strains. Molecular technologies could play a pivotal role in addressing these issues. This review synthesises current and emerging technologies to develop improved management strategies for the control of halo blight in mungbean. © CSIRO 2019 Open Access

Can the surgical checklist reduce the risk of wrong site surgery in orthopaedics? - can the checklist help? Supporting evidence from analysis of a national patient incident reporting system

<p>Abstract</p> <p>Background</p> <p>Surgical procedures are now very common, with estimates ranging from 4% of the general population having an operation per annum in economically-developing countries; this rising to 8% in economically-developed countries. Whilst these surgical procedures typically result in considerable improvements to health outcomes, it is increasingly appreciated that surgery is a high risk industry. Tools developed in the aviation industry are beginning to be used to minimise the risk of errors in surgery. One such tool is the World Health Organization's (WHO) surgery checklist. The National Patient Safety Agency (NPSA) manages the largest database of patient safety incidents (PSIs) in the world, already having received over three million reports of episodes of care that could or did result in iatrogenic harm. The aim of this study was to estimate how many incidents of wrong site surgery in orthopaedics that have been reported to the NPSA could have been prevented by the WHO surgical checklist.</p> <p>Methods</p> <p>The National Reporting and Learning Service (NRLS) database was searched between 1^stJanuary 2008- 31^stDecember 2008 to identify all incidents classified as wrong site surgery in orthopaedics. These incidents were broken down into the different types of wrong site surgery. A Likert-scale from 1-5 was used to assess the preventability of these cases if the checklist was used.</p> <p>Results</p> <p>133/316 (42%) incidents satisfied the inclusion criteria. A large proportion of cases, 183/316 were misclassified. Furthermore, there were fewer cases of actual harm [9% (12/133)] versus 'near-misses' [121/133 (91%)]. Subsequent analysis revealed a smaller proportion of 'near-misses' being prevented by the checklist than the proportion of incidents that resulted in actual harm; 18/121 [14.9% (95% CI 8.5 - 21.2%)] versus 10/12 [83.3% (95%CI 62.2 - 104.4%)] respectively. Summatively, the checklist could have been prevented 28/133 [21.1% (95%CI 14.1 - 28.0%)] patient safety incidents.</p> <p>Discussion</p> <p>Orthopaedic surgery is a high volume specialty with major technical complexity in terms of equipment demands and staff training and familiarity. There is therefore an increased propensity for errors to occur. Wrong-site surgery still occurs in this specialty and is a potentially devastating situation for both the patient and surgeon. Despite the limitations of inclusion and reporting bias, our study highlights the need to match technical precision with patient safety. Tools such as the WHO surgical checklist can help us to achieve this.</p

Planning Considerations Related to Collecting and Analyzing Samples of the Martian Soils

The Mars Sample Return (MSR) End-to-End International Science Analysis Group (E2E-iSAG [1]) established scientific objectives associ-ated with Mars returned-sample science that require the return and investigation of one or more soil samples. Soil is defined here as loose, unconsolidated materials with no implication for the presence or absence of or-ganic components. The proposed Mars 2020 (M-2020) rover is likely to collect and cache soil in addition to rock samples [2], which could be followed by future sample retrieval and return missions. Here we discuss key scientific consid-erations for sampling and caching soil samples on the proposed M-2020 rover, as well as the state in which samples would need to be preserved when received by analysts on Earth. We are seeking feedback on these draft plans as input to mission requirement formulation. A related planning exercise on rocks is reported in an accompanying abstract [3]

Modulation of the Metabiome by Rifaximin in Patients with Cirrhosis and Minimal Hepatic Encephalopathy

Hepatic encephalopathy (HE) represents a dysfunctional gut-liver-brain axis in cirrhosis which can negatively impact outcomes. This altered gut-brain relationship has been treated using gut-selective antibiotics such as rifaximin, that improve cognitive function in HE, especially its subclinical form, minimal HE (MHE). However, the precise mechanism of the action of rifaximin in MHE is unclear. We hypothesized that modulation of gut microbiota and their end-products by rifaximin would affect the gut-brain axis and improve cognitive performance in cirrhosis. Aim To perform a systems biology analysis of the microbiome, metabolome and cognitive change after rifaximin in MHE. Methods Twenty cirrhotics with MHE underwent cognitive testing, endotoxin analysis, urine/serum metabolomics (GC and LC-MS) and fecal microbiome assessment (multi-tagged pyrosequencing) at baseline and 8 weeks post-rifaximin 550 mg BID. Changes in cognition, endotoxin, serum/urine metabolites (and microbiome were analyzed using recommended systems biology techniques. Specifically, correlation networks between microbiota and metabolome were analyzed before and after rifaximin. Results There was a significant improvement in cognition(six of seven tests improved,pVeillonellaceaeand increase inEubacteriaceae was observed. Rifaximin resulted in a significant reduction in network connectivity and clustering on the correlation networks. The networks centered onEnterobacteriaceae, Porphyromonadaceae and Bacteroidaceae indicated a shift from pathogenic to beneficial metabolite linkages and better cognition while those centered on autochthonous taxa remained similar. Conclusions Rifaximin is associated with improved cognitive function and endotoxemia in MHE, which is accompanied by alteration of gut bacterial linkages with metabolites without significant change in microbial abundance. Trial Registration ClinicalTrials.gov NCT0106913

Type 2 alveolar cells are stem cells in adult lung

Gas exchange in the lung occurs within alveoli, air-filled sacs composed of type 2 and type 1 epithelial cells (AEC2s and AEC1s), capillaries, and various resident mesenchymal cells. Here, we use a combination of in vivo clonal lineage analysis, different injury/repair systems, and in vitro culture of purified cell populations to obtain new information about the contribution of AEC2s to alveolar maintenance and repair. Genetic lineage-tracing experiments showed that surfactant protein C–positive (SFTPC-positive) AEC2s self renew and differentiate over about a year, consistent with the population containing long-term alveolar stem cells. Moreover, if many AEC2s were specifically ablated, high-resolution imaging of intact lungs showed that individual survivors undergo rapid clonal expansion and daughter cell dispersal. Individual lineage-labeled AEC2s placed into 3D culture gave rise to self-renewing “alveolospheres,” which contained both AEC2s and cells expressing multiple AEC1 markers, including HOPX, a new marker for AEC1s. Growth and differentiation of the alveolospheres occurred most readily when cocultured with primary PDGFRα+ lung stromal cells. This population included lipofibroblasts that normally reside close to AEC2s and may therefore contribute to a stem cell niche in the murine lung. Results suggest that a similar dynamic exists between AEC2s and mesenchymal cells in the human lung

Monitoring human growth and development: a continuum from the womb to the classroom

A comprehensive set of fully integrated anthropometric measures is needed to evaluate human growth from conception to infancy so that consistent judgments can be made about the appropriateness of fetal and infant growth. At present, there are 2 barriers to this strategy. First, descriptive reference charts, which are derived from local, unselected samples with inadequate methods and poor characterization of their putatively healthy populations, commonly are used rather than prescriptive standards. The use of prescriptive standards is justified by the extensive biologic, genetic, and epidemiologic evidence that skeletal growth is similar from conception to childhood across geographic populations, when health, nutrition, environmental, and health care needs are met. Second, clinicians currently screen fetuses, newborn infants, and infants at all levels of care with a wide range of charts and cutoff points, often with limited appreciation of the underlying population or quality of the study that generated the charts. Adding to the confusion, infants are evaluated after birth with a single prescriptive tool: the World Health Organization Child Growth Standards, which were derived from healthy, breastfed newborn infants, infants, and young children from populations that have been exposed to few growth-restricting factors. The International Fetal and Newborn Growth Consortium for the 21st Century Project addressed these issues by providing international standards for gestational age estimation, first-trimester fetal size, fetal growth, newborn size for gestational age, and postnatal growth of preterm infants, all of which complement the World Health Organization Child Growth Standards conceptually, methodologically, and analytically. Hence, growth and development can now, for the first time, be monitored globally across the vital first 1000 days and all the way to 5 years of age. It is clear that an integrative approach to monitoring growth and development from pregnancy to school age is desirable, scientifically supported, and likely to improve care, referral patterns, and reporting systems. Such integration can be achieved only through the use of international growth standards, especially in increasingly diverse, mixed ancestry populations. Resistance to new scientific developments has been hugely problematic in medicine; however, we are confident that the obstetric and neonatal communities will join their pediatric colleagues worldwide in the adoption of this integrative strategy

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

Embryonic stem (ES) cell self-renewal efficiency is determined by the Nanog protein level. However, the protein partners of Nanog that function to direct self-renewal are unclear. Here, we identify a Nanog interactome of over 130 proteins including transcription factors, chromatin modifying complexes, phosphorylation and ubiquitination enzymes, basal transcriptional machinery members, and RNA processing factors. Sox2 was identified as a robust interacting partner of Nanog. The purified Nanog–Sox2 complex identified a DNA recognition sequence present in multiple overlapping Nanog/Sox2 ChIP-Seq data sets. The Nanog tryptophan repeat region is necessary and sufficient for interaction with Sox2, with tryptophan residues required. In Sox2, tyrosine to alanine mutations within a triple-repeat motif (S X T/S Y) abrogates the Nanog–Sox2 interaction, alters expression of genes associated with the Nanog-Sox2 cognate sequence, and reduces the ability of Sox2 to rescue ES cell differentiation induced by endogenous Sox2 deletion. Substitution of the tyrosines with phenylalanine rescues both the Sox2–Nanog interaction and efficient self-renewal. These results suggest that aromatic stacking of Nanog tryptophans and Sox2 tyrosines mediates an interaction central to ES cell self-renewal

Sociological and Communication-Theoretical Perspectives on the Commercialization of the Sciences

Both self-organization and organization are important for the further development of the sciences: the two dynamics condition and enable each other. Commercial and public considerations can interact and "interpenetrate" in historical organization; different codes of communication are then "recombined." However, self-organization in the symbolically generalized codes of communication can be expected to operate at the global level. The Triple Helix model allows for both a neo-institutional appreciation in terms of historical networks of university-industry-government relations and a neo-evolutionary interpretation in terms of three functions: (i) novelty production, (i) wealth generation, and (iii) political control. Using this model, one can appreciate both subdynamics. The mutual information in three dimensions enables us to measure the trade-off between organization and self-organization as a possible synergy. The question of optimization between commercial and public interests in the different sciences can thus be made empirical.Comment: Science & Education (forthcoming

Grain Surface Models and Data for Astrochemistry

AbstractThe cross-disciplinary field of astrochemistry exists to understand the formation, destruction, and survival of molecules in astrophysical environments. Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. A broad consensus has been reached in the astrochemistry community on how to suitably treat gas-phase processes in models, and also on how to present the necessary reaction data in databases; however, no such consensus has yet been reached for grain-surface processes. A team of ∼25 experts covering observational, laboratory and theoretical (astro)chemistry met in summer of 2014 at the Lorentz Center in Leiden with the aim to provide solutions for this problem and to review the current state-of-the-art of grain surface models, both in terms of technical implementation into models as well as the most up-to-date information available from experiments and chemical computations. This review builds on the results of this workshop and gives an outlook for future directions