Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The tuatara genome reveals ancient features of amniote evolution.

The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2-is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.

Reactivity Switch of Platinum with Gallium: From Reverse Water Gas Shift to Methanol Synthesis.

The development of efficient catalysts for the hydrogenation of CO2 to methanol using "green" H2 is foreseen to be a key step to close the carbon cycle. In this study, we show that small and narrowly distributed alloyed PtGa nanoparticles supported on silica, prepared via a surface organometallic chemistry (SOMC) approach, display notable activity for the hydrogenation of CO2 to methanol, reaching a 7.2 molCH3OH h-1 molPt-1 methanol formation rate with a 54% intrinsic CH3OH selectivity. This reactivity sharply contrasts with what is expected for Pt, which favors the reverse water gas shift reaction, albeit with poor activity (2.6 molCO2 h-1 molPt-1). In situ XAS studies indicate that ca. 50% of Ga is reduced to Ga0 yielding alloyed PtGa nanoparticles, while the remaining 50% persist as isolated GaIII sites. The PtGa catalyst slightly dealloys under CO2 hydrogenation conditions and displays redox dynamics with PtGa-GaOx interfaces responsible for promoting both the CO2 hydrogenation activity and methanol selectivity. Further tailoring the catalyst interface by using a carbon support in place of silica enables to improve the methanol formation rate by a factor of ∼5.

The importance of both catalyst and process design in unlocking sustainable carbon feedstocks through syngas.

As part of its move towards net zero, the chemical industry, over time, will transition away from fossil-based chemical feedstocks towards more sustainable, 'green' carbon-biomass, recycled waste and captured carbon dioxide. One gateway to transforming these feedstocks into the vital chemicals and fuels society relies on is via synthesis gas or 'syngas'-a gaseous mixture of chemical building blocks (H2, CO and CO2). While today the majority of syngas is produced via steam reforming of natural gas, commercially available technologies are enabling syngas production and transformation from sustainable feedstocks. The optimization of sustainable syngas technologies would not be possible without the integrated development of both catalyst and process technology and the associated skills in chemistry and chemical engineering. This paper covers three example technologies that are unlocking the role of syngas as a gateway to sustainable fuels and chemicals and highlights the innovative developments in catalyst and process design that have enabled their optimization and commercialization. This article is part of the discussion meeting issue 'Green carbon for the chemical industry of the future'.

Targeting the BRAF pathway in haematological diseases.

Since the recognition of BRAF V600E mutations in the majority of cases of hairy cell leukaemia, Erdheim-Chester disease and Langerhans cell histiocytosis, the targeted oral kinase inhibitors dabrafenib and vemurafenib have been adapted for their treatment. Like other targeted agents, these drugs produce high response rates and predictable but unique side effects. Physician familiarity is essential for the effective use of these agents. We review the Australian experience of BRAF/MEK inhibitor therapy in these rare haematological cancers.

Evaluating the Cytometric Detection and Enumeration of the Wine Bacterium, Oenococcus oeni.

Flow cytometry is a high-throughput tool for determining microbial abundance in a range of medical, environmental, and food-related samples. For wine, determining the abundance of Saccharomyces cerevisiae is well-defined and reliable. However, for the most common wine bacterium, Oenococcus oeni, using flow cytometry to determine cell concentration poses some challenges. O. oeni most often occurs in doublets or chains of varying lengths that can be greater than seven cells. This wine bacterium is also small, at 0.2-0.6 µm and may exhibit a range of morphologies including binary fission and aggregated complexes. This work demonstrates a straightforward approach to determining the suitability of flow cytometry for the chain-forming bacteria, O. oeni, and considerations when using flow cytometry for the enumeration of small microorganisms (<0.5 µm). © 2020 International Society for Advancement of Cytometry.

Changes of viral and prokaryote abundances in a high rate algal pond using flow cytometry detection.

High rate algal ponds (HRAPs) are shallow, mixed systems for wastewater treatment, which use sunlight exposure for disinfection. Little is known regarding the relationships between the bacteria and viruses within HRAP systems. Uniquely, flow cytometry permits the rapid identification of bacterial and viral populations in wastewater samples, separating populations based on genome and particle size. Treated wastewater samples were collected from an HRAP at Kingston on Murray, South Australia. Flow cytometry analysis detected bacterial populations and discriminated virus-like particles (VLP) and large VLP (LVLP). Rapid, short term, fluctuations in the abundance of all three populations were observed. Changes in the abundance of these populations was compared; wastewater composition was used as metadata for the comparisons. Linear regression determined relationships in abundances between bacteria and LVLP (R2 0.2985); LVLP and VLP (R2 0.5829) and bacteria and VLP (R2 0.5778) all with p-values of <0.001. Bacterial, LVLP and VLP abundance positively correlated with each other, indicating potential microbial interactions. Overall, the results suggest a parasitic relationship was occurring and driving the abundances of bacteria and viruses within the system.

X-ray physico-chemical imaging during activation of cobalt-based Fischer-Tropsch synthesis catalysts.

The imaging of catalysts and other functional materials under reaction conditions has advanced significantly in recent years. The combination of the computed tomography (CT) approach with methods such as X-ray diffraction (XRD), X-ray fluorescence (XRF) and X-ray absorption near-edge spectroscopy (XANES) now enables local chemical and physical state information to be extracted from within the interiors of intact materials which are, by accident or design, inhomogeneous. In this work, we follow the phase evolution during the initial reduction step(s) to form Co metal, for Co-containing particles employed as Fischer-Tropsch synthesis (FTS) catalysts; firstly, working at small length scales (approx. micrometre spatial resolution), a combination of sample size and density allows for transmission of comparatively low energy signals enabling the recording of 'multimodal' tomography, i.e. simultaneous XRF-CT, XANES-CT and XRD-CT. Subsequently, we show high-energy XRD-CT can be employed to reveal extent of reduction and uniformity of crystallite size on millimetre-sized TiO2 trilobes. In both studies, the CoO phase is seen to persist or else evolve under particular operating conditions and we speculate as to why this is observed.This article is part of a discussion meeting issue 'Providing sustainable catalytic solutions for a rapidly changing world'.

Do ectotherms partition thermal resources? We still do not know.

Partitioning of the niche space is a mechanism used to explain the coexistence of similar species. Ectotherms have variable body temperatures and their body temperatures influence performance and, ultimately, fitness. Therefore, many ectotherms use behavioral thermoregulation to avoid reduced capacities associated with body temperatures far from the optimal temperature for performance. Several authors have proposed that thermal niche partitioning in response to interspecific competition is a mechanism that allows the coexistence of similar species of ectotherms. We reviewed studies on thermal resource partitioning to evaluate the evidence for this hypothesis. In almost all studies, there was insufficient evidence to conclude unequivocally that thermal resource partitioning allowed species coexistence. Future studies should include sites where species are sympatric and sites where they are allopatric to rule out alternative mechanisms that cause differences in thermal traits between coexisting species. There is evidence of conservatism in the evolution of most thermal traits across a wide range of taxa, but thermal performance curves and preferred temperatures do respond to strong selection under laboratory conditions. Thus, there is potential for selection to act on thermal traits in response to interspecific competition. Nevertheless, more stringent tests of the thermal resource partitioning hypothesis are required before we can assess whether it is widespread in communities of ectotherms in nature.

A step-by-step method to quantify coloration with digital photography.

Coloration is often used in biological studies, for example when studying social signaling or antipredator defense. Yet, few detailed and standardized methods are available to measure coloration using digital photography. Here we provide a step-by-step guide to help researchers quantify coloration from digital images. We first identify the do's and don'ts of taking pictures for coloration analysis. We then describe how to i) extract reflectance values with the software ImageJ; ii) fit and apply linearization equations to reflectance values; iii) scale and select the areas of interest in ImageJ; iv) standardize pictures; and v) binarize and measure the proportion of different colors in an area of interest. We apply our methodological protocol to digital pictures of painted turtles (Chrysemys picta), but the approach could be easily adapted to any species. More specifically, we wished to calculate the proportion of red and yellow on the neck and head of turtles. With this protocol, our main aims are to make coloration analyses with digital photography:•More accessible to researchers without a background in photography.•More consistent between studies.

A survey of severe asthma in Canada: results from the CASCADE practice reflective program.

BACKGROUND: Since the last guidance was published by the Canadian Thoracic Society, there have been several advances in the clinical management of severe asthma. To gain a better understanding of the current standards of care and treatment patterns of patients, the CASCADE practice reflective program was established to conduct a real-world analysis of severe asthma management among specialists in Canada with a goal of identifying areas of opportunity to enhance patient management and outcomes. METHODS: The CASCADE program was a two-part practice reflective and assessment program delivered through an on-line portal for selected specialists (Respirologists and Allergists) in Canada. The program consisted of a one-time overview survey of physician practice to establish overall practice parameters, followed by a review of at least 5 severe asthma patients to establish the current landscape of severe asthma management. RESULTS: The program collected practice overview surveys from 78 specialists (52 Respirologists, 24 Allergists, and 2 General practice physicians with an interest in respiratory disease) in 8 provinces. Practices included a variety of types in both large metropolitan centres and smaller regional settings. There were 503 patients reviewed and included in the program. Most (65%) patients were currently using a biologic treatment, 30% were biologic naive, and 5% had used a biologic treatment in the past. Most patients (53%) were reported to have mixed allergic and eosinophilic phenotypes, despite a perception that allergic, eosinophilic and mixed phenotypes were evenly balanced in the physician practice. Overall, patients currently treated with biologic agents had parameters suggesting higher control and were more satisfied with treatment. However, there was less than optimal treatment satisfaction for more than half of all patients, particularly for those patients not treated with a biologic agent. CONCLUSIONS: Phenotyping is hampered by poor availability for several assessments, and the full range of treatments are not currently fully utilized, partly due to physician familiarity with the agents and partly due to prescribing restrictions. Even when treated with biologic agents, patient satisfaction can still be improved.

Effects of ophidiomycosis on movement, survival, and reproduction of eastern foxsnakes (Pantherophis vulpinus).

Ophidiomycosis (snake fungal disease) is caused by the fungal pathogen Ophidiomyces ophidiicola, which causes dermal lesions, occasional systemic infections, and in some cases, mortality. To better understand potential conservation implications of ophidiomycosis (i.e., population-level effects), we investigated its impacts on individual fitness in a population of endangered eastern foxsnakes (Pantherophis vulpinus). We tracked 38 foxsnakes over 6 years and quantified body condition, movement patterns, oviposition rates, and survival. Body condition, distance travelled, and oviposition rates were similar between snakes with and without ophidiomycosis. Interestingly, snakes that tested positive for the pathogen travelled farther, suggesting that movement through a greater diversity of habitats increases risk of exposure. Ophidiomycosis did not negatively affect survival, and most apparently infected snakes persisted in a manner comparable to snakes without ophidiomycosis. Only one mortality was directly attributed to ophidiomycosis, although infected snakes were overrepresented in a sample of snakes killed by predators. Overall, our results suggest that ophidiomycosis may have sublethal effects on eastern foxsnakes, but do not suggest direct effects on survival, ovipositioning, or viability of the study population.

Chemical Imaging of Carbide Formation and Its Effect on Alcohol Selectivity in Fischer Tropsch Synthesis on Mn-Doped Co/TiO2 Pellets.

X-ray diffraction/scattering computed tomography (XRS-CT) was used to create two-dimensional images, with 20 µm resolution, of passivated Co/TiO2/Mn Fischer-Tropsch catalyst extrudates postreaction after 300 h on stream under industrially relevant conditions. This combination of scattering techniques provided insights into both the spatial variation of the different cobalt phases and the influence that increasing Mn loading has on this. It also demonstrated the presence of a wax coating throughout the extrudate and its capacity to preserve the Co/Mn species in their state in the reactor. Correlating these findings with catalytic performance highlights the crucial phases and active sites within Fischer-Tropsch catalysts required for understanding the tunability of the product distribution between saturated hydrocarbons or oxygenate and olefin products. In particular, a Mn loading of 3 wt % led to an optimum equilibrium between the amount of hexagonal close-packed Co and Co2C phases resulting in maximum oxygenate selectivity. XRS-CT revealed Co2C to be located on the extrudates' periphery, while metallic Co phases were more prevalent toward the center, possibly due to a lower [CO] ratio there. Reduction at 450 °C of a 10 wt % Mn sample resulted in MnTiO3 formation, which inhibited carbide formation and alcohol selectivity. It is suggested that small MnO particles promote Co carburization by decreasing the CO dissociation barrier, and the Co2C phase promotes CO nondissociative adsorption leading to increased oxygenate selectivity. This study highlights the influence of Mn on the catalyst structure and function and the importance of studying catalysts under industrially relevant reaction times.

Tuning the Size of TiO2-Supported Co Nanoparticle Fischer-Tropsch Catalysts Using Mn Additions.

Modifying traditional Co/TiO2-based Fischer-Tropsch (FT) catalysts with Mn promoters induces a selectivity shift from long-chain paraffins toward commercially desirable alcohols and olefins. In this work, we use in situ gas cell scanning transmission electron microscopy (STEM) with energy-dispersive X-ray spectroscopy (EDS) elemental mapping, and near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) to demonstrate how the elemental dispersion and chemical structure of the as-calcined materials evolve during the H2 activation heat treatment required for industrial CoMn/TiO2 FT catalysts. We find that Mn additions reduce both the mean Co particle diameter and the size distribution but that the Mn remains dispersed on the support after the activation step. Density functional theory calculations show that the slower surface diffusion of Mn is likely due to the lower number of energetically accessible sites for the Mn on the titania support and that favorable Co-Mn interactions likely cause greater dispersion and slower sintering of Co in the Mn-promoted catalyst. These mechanistic insights into how the introduction of Mn tunes the Co nanoparticle size can be applied to inform the design of future-supported nanoparticle catalysts for FT and other heterogeneous catalytic processes.

SEASONAL AND INTERSPECIFIC VARIATION IN THE PREVALENCE OF OPHIDIOMYCES OPHIDIICOLA AND OPHIDIOMYCOSIS IN A COMMUNITY OF FREE-RANGING SNAKES.

Ophidiomycosis in snakes is caused by the fungus Ophidiomyces ophidiicola. Clinical signs associated with the disease range from minor skin lesions to severe swelling of the face. In some cases, the fungus invades the snake's underlying muscle and bone and internal organs; disease severity appears to peak during brumation. We quantified the prevalence of O. ophidiicola and ophidiomycosis in free-ranging snakes to explore seasonal variation in detection of the pathogen and disease. We collected skin swabs (n=464 samples) from seven species of free-ranging snakes (n=336) from Rondeau Provincial Park (Ontario, Canada) and tested the swabs for O. ophidiicola using quantitative PCR. We also assessed individuals for lesions consistent with ophidiomycosis and monitored changes in gross lesions over time in recaptured individuals. Eastern foxsnakes (Pantherophis vulpinus) had the highest prevalence of O. ophidiicola (24/84) and of lesions consistent with ophidiomycosis (34/84). On other species (Nerodia sipedon, Storeria dekayi, Thamnophis sirtalis, and Thamnophis sauritus), we detected the pathogen on only 4/229 snakes and observed gross lesions consistent with ophidiomycosis on 24/229 snakes. Body length of eastern foxsnakes was associated with detection of O. ophidiicola, suggesting that eastern foxsnakes' large size increases the risk of pathogen exposure relative to the other, smaller, species at our study site. Ophidiomyces ophidiicola and lesions consistent with ophidiomycosis were detected most frequently in eastern foxsnakes soon after emergence from brumation and less frequently later in the active season (O. ophidiicola: April=29.8%, October=3.9%; lesions: April=36.1%, October=5.5%). This decrease corresponded with resolution of lesions in 6/13 resampled eastern foxsnakes. Considering the seasonal cycle of O. ophidiicola and ophidiomycosis when planning disease surveillance research may improve detection probabilities for ophidiomycosis in Nearctic snakes.

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software.

BACKGROUND: Computational biology provides software tools for testing and making inferences about biological data. In the face of increasing volumes of data, heuristic methods that trade software speed for accuracy may be employed. We have studied these trade-offs using the results of a large number of independent software benchmarks, and evaluated whether external factors, including speed, author reputation, journal impact, recency and developer efforts, are indicative of accurate software. RESULTS: We find that software speed, author reputation, journal impact, number of citations and age are unreliable predictors of software accuracy. This is unfortunate because these are frequently cited reasons for selecting software tools. However, GitHub-derived statistics and high version numbers show that accurate bioinformatic software tools are generally the product of many improvements over time. We also find an excess of slow and inaccurate bioinformatic software tools, and this is consistent across many sub-disciplines. There are few tools that are middle-of-road in terms of accuracy and speed trade-offs. CONCLUSIONS: Our findings indicate that accurate bioinformatic software is primarily the product of long-term commitments to software development. In addition, we hypothesise that bioinformatics software suffers from publication bias. Software that is intermediate in terms of both speed and accuracy may be difficult to publish-possibly due to author, editor and reviewer practises. This leaves an unfortunate hole in the literature, as ideal tools may fall into this gap. High accuracy tools are not always useful if they are slow, while high speed is not useful if the results are also inaccurate.

Remote assessment of diabetic foot ulcers using a novel wound imaging system.

Telemedicine allows experts to assess patients in remote locations, enabling quality convenient, cost-effective care. To help assess foot wounds remotely, we investigated the reliability of a novel optical imaging system employing a three-dimensional camera and disposable optical marker. We first examined inter- and intraoperator measurement variability (correlation coefficient) of five clinicians examining three different wounds. Then, to assess of the system's ability to identify key clinically relevant features, we had two clinicians evaluate 20 different wounds at two centers, recording observations on a standardized form. Three other clinicians recorded their observations using only the corresponding three-dimensional images. Using the in-person assessment as the criterion standard, we assessed concordance of the remote with in-person assessments. Measurement variation of area was 3.3% for intraoperator and 11.9% for interoperator; difference in clinician opinion about wound boundary location was significant. Overall agreement for remote vs. in-person assessments was good, but was lowest on the subjective clinical assessments, e.g., value of debridement to improve healing. Limitations of imaging included inability to show certain characteristics, e.g., moistness or exudation. Clinicians gave positive feedback on visual fidelity. This pilot study showed that a clinician viewing only the three-dimensional images could accurately measure and assess a diabetic foot wound remotely.

Microbial disruption in the gut promotes cerebral endothelial dysfunction.

Cerebrovascular disease is a group of conditions characterized by disorders of the cerebral vessels. Endothelial dysfunction renders the vasculature at risk of impaired blood flow and increases the potential of developing cerebrovascular disease. The gut microbiota has been recently identified as a possible risk factor of cerebrovascular disease. However, a direct link between gut microbiota and cerebral vascular function has not been established. Therefore, the aim of this study was to determine the effect of gut bacterial disruption on cerebral endothelial function. Male inbred Sprague-Dawley rats were randomly assigned to receive either drinking water with (n = 4) or without (n = 4) a cocktail of nonabsorbable broad-spectrum antibiotics (streptomycin, neomycin, bacitracin, and polymyxin B). Three weeks of antibiotic treatment resulted in a significant reduction in bacterial load and shifts within the bacterial sub-populations as assessed using flow cytometry. Using pressure myography, we found that spontaneous tone significantly increased and L-NAME-induced vasoconstriction was significantly blunted in middle cerebral arteries (MCAs) harvested from antibiotic-treated rats. ATP-mediated dilations were significantly blunted in MCAs from antibiotic-treated rats compared to their control counterparts. Immunoblotting revealed that the eNOS-P/total eNOS ratio was significantly reduced in cerebral artery lysates from antibiotic-treated rats compared to controls. Our findings suggest that disruption of the gut microbiota leads to cerebral endothelial dysfunction through reduction of eNOS activity. This study highlights the potential of the microbiota as a target to reverse endothelial dysfunction and a preventative approach to reducing risk of stroke and aneurysms.

Revisiting Ophidiomycosis (Snake Fungal Disease) After a Decade of Targeted Research.

Emerging infectious diseases (EIDs) are typically characterized by novelty (recent detection) and by increasing incidence, distribution, and/or pathogenicity. Ophidiomycosis, also called snake fungal disease, is caused by the fungus Ophidiomyces ophidiicola (formerly "ophiodiicola"). Ophidiomycosis has been characterized as an EID and as a potential threat to populations of Nearctic snakes, sparking over a decade of targeted research. However, the severity of this threat is unclear. We reviewed the available literature to quantify incidence and effects of ophidiomycosis in Nearctic snakes, and to evaluate whether the evidence supports the ongoing characterization of ophidiomycosis as an EID. Data from Canada remain scarce, so we supplemented the literature review with surveys for O. ophidiicola in the Canadian Great Lakes region. Peer-reviewed reports of clinical signs consistent with ophidiomycosis in free-ranging, Nearctic snakes date back to at least 1998, and retrospective molecular testing of samples extend the earliest confirmed record to 1986. Diagnostic criteria varied among publications (n = 33), confounding quantitative comparisons. Ophidiomycosis was diagnosed or suspected in 36/121 captive snakes and was fatal in over half of cases (66.7%). This result may implicate captivity-related stress as a risk factor for mortality from ophidiomycosis, but could also reflect reporting bias (i.e., infections are more likely to be detected in captive snakes, and severe cases are more likely to be reported). In contrast, ophidiomycosis was diagnosed or suspected in 441/2,384 free-ranging snakes, with mortality observed in 43 (9.8 %). Ophidiomycosis was only speculatively linked to population declines, and we found no evidence that the prevalence of the pathogen or disease increased over the past decade of targeted research. Supplemental surveys and molecular (qPCR) testing in Ontario, Canada detected O. ophidiicola on 76 of 657 free-ranging snakes sampled across ~136,000 km2. The pathogen was detected at most sites despite limited and haphazard sampling. No large-scale mortality was observed. Current evidence supports previous suggestions that the pathogen is a widespread, previously unrecognized endemic, rather than a novel pathogen. Ophidiomycosis may not pose an imminent threat to Nearctic snakes, but further research should investigate potential sublethal effects of ophidiomycosis such as altered reproductive success that could impact population growth, and explore whether shifting environmental conditions may alter host susceptibility.

The microbial abundance dynamics of the paediatric oral cavity before and after sleep.

Objective: Microhabitats in the oral cavity differ in microbial taxonomy. However, abundance variations of bacterial and viral communities within these microhabitats are not fully understood. Aims and Hypothesis: To assess the spatial distribution and dynamics of the microbial abundances within 6 microhabitats of the oral cavity before and after sleep. We hypothesise that the abundance distributions of these microbial communities will differ among oral sites. Methods: Using flow cytometry, bacterial and virus-like particle (VLP) abundances were enumerated for 6 oral microhabitats before and after sleep in 10 healthy paediatric sleepers. Results: Bacterial counts ranged from 7.2 ± 2.8 × 105 at the palate before sleep to 1.3 ± 0.2 × 108 at the back of the tongue after sleep, a difference of 187 times. VLPs ranged from 1.9 ± 1.0 × 106 at the palate before sleep to 9.2 ± 5.0 × 107 at the back of the tongue after sleep, a difference of 48 times. Conclusion: The oral cavity is a dynamic numerically heterogeneous environment where microbial communities can increase by a count of 100 million during sleep. Quantification of the paediatric oral microbiome complements taxonomic diversity information to show how biomass varies and shifts in space and time.