Development of a modified SEDEX phosphorus speciation method for ancient rocks and modern iron-rich sediments

We report the development of a modified method for evaluating different reservoirs of sedimentary phosphorus (P) in ancient marine sedimentary rocks and in modern Fe-rich sediments. Utilising the existing SEDEX scheme for P partitioning in modern sediments, we initially demonstrate limitations in the application of the original scheme to sediments and rocks containing crystalline hematite and magnetite. We tested additional extractions for these crystalline Fe phases, using both synthetic minerals, and modern and ancient sediments. The addition of 6 h oxalate and 6 h citrate-dithionate-acetate extractions considerably enhanced the total recovery of synthetic magnetite and hematite to 88.7 ± 1.1% and 76.9 ± 3.8%, respectively. In addition, application of the 6 h oxalate extraction to synthetic P-containing magnetite recovered 93.9 ± 1.7% of the Fe present and 88.2 ± 12.8% of the co-precipitated P. Based upon these results we developed a modified SEDEX extraction scheme. The modified scheme was applied to modern Fe-rich sediments from Golfo Dulce, Costa Rica, which resulted in 16% higher Fe-bound P recovery. Application of the scheme to a variety of ancient marine rocks increased the recovery of Fe-bound P by up to 22%. We also highlight the potential for authigenic carbonate fluorapatite to convert to more crystalline apatite in ancient rocks during deep burial and metamorphism. We suggest that in such systems minimum and maximum estimates of the total reactive P pool may be calculated with and without the inclusion of crystalline P. It is noted that the application of the revised method may have important implications for understanding the cycling of P in ancient marine environments

Readiness to implement a national quality framework: evidence from Irish early childhood care and education centres

This study examined the factors associated with childcare staff members' readiness to implement quality standards in early childhood settings in Ireland. To coincide with a new government policy that provides every three-year-old child with access to a free preschool year, a framework designed to improve the quality of early childhood care and education centres (ECCECs) is being rolled out nationally. The new quality framework details the first national set of best practice standards for early childhood care and education in Ireland. This study measured support for this change in childcare practices in one pilot community, which introduced the framework prior to national roll-out. The study used the Organizational Change Recipients' Belief Scale to determine how readiness for change was associated with job satisfaction and the work environment in childcare settings. One hundred and twenty surveys were completed by childcare staff in nine pilot ECCECs. The surveys were distributed in 2009 and therefore capture staff attitudes towards the introduction of the new quality framework. The results show that individual staff characteristics had little association with support for the implementation of the quality framework, while factors related to group dynamics were significantly associated with readiness for change. Specifically, a positive work environment and greater job satisfaction were associated with a lower belief that there is a need for the national quality framework, but a higher belief that the childcare staff will be supported by management when the quality framework is introduced

Shallow water anoxia in the Mesoproterozoic ocean: Evidence from the Bashkir Meganticlinorium, Southern Urals

The apparent lag between the first permanent rise of atmospheric oxygen to appreciable levels and oxygenation of the deep ocean has focused efforts in deciphering the evolution of seawater chemistry across the Proterozoic Eon (2.5–0.542 Ga). It is generally accepted that from ∼1.85 Ga oxic shallow marine waters were widespread while the deep ocean remained dominantly ferruginous (Fe(II)-rich), with episodic euxinia confined to productive continental margins and intracontinental basins. The geochemical record that informs this picture, however, is currently sparse, and further studies are required to adequately evaluate temporal and spatial variability in ocean redox conditions across this vast expanse of time. Here, we report Fe-S-C systematics, alongside major (Al, Mn) and trace metal (Mo, U) data for ∼1.6–0.8 Ga marine sediments from the Bashkir Meganticlinorium (BMA), Southern Urals, Russia. Our Fe speciation data reveal a water column dominated by ferruginous conditions, no evidence for euxinia, and oxygenated waters confined to only the shallowest, near-coastal settings. Trace metal data support these findings, with Mo and U enrichment factors in anoxic sediments implying the operation of a particulate Fe (oxyhydr)oxide shuttle under ferruginous conditions as the main mechanism for generating moderate authigenic Mo enrichments. Sulfur isotope systematics imply that predominantly low dissolved sulfate concentrations prevailed throughout the deposition of the BMA succession, which, in combination with a low organic carbon loading, promoted the development of ferruginous, rather than euxinic, water column conditions. The restriction of oxic conditions to the shallowest, near-coastal depositional settings within the Bashkir basin contrasts to other redox studies from this period. Such discrepancies highlight major uncertainty in our understanding of the temporal and spatial evolution of water column redox chemistry across the Mesoproterozoic Era, and signify the need for further detailed work to constrain the chemical evolution of the oceans during this crucial time period

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study.

Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories

New insights into the ∼74ka Toba eruption from sulfur isotopes of polar ice cores

Abstract. The ∼74 ka Toba eruption was one of the largest volcanic events of the Quaternary. There is much interest in determining the impact of such a large event, particularly on the climate and hominid populations at the time. Although the Toba eruption has been identified in both land and marine archives as the Youngest Toba Tuff, its precise place in the ice core record is ambiguous. Several volcanic sulfate signals have been identified in both Antarctic and Greenland ice cores and span the Toba eruption 40Ar/39Ar age uncertainty. Here, we measure sulfur isotope compositions in Antarctic ice samples from the Dome C (EDC) and Dronning Maud Land (EDML) ice cores at high temporal resolution across 11 of these potential Toba sulfate peaks to identify candidates with sulfur mass-independent fractionation (S-MIF), indicative of an eruption whose plume reached altitudes at or above the stratospheric ozone layer. Using this method, we identify several candidate sulfate peaks that contain stratospheric sulfur. We further narrow down potential candidates based on the isotope signatures by identifying sulfate peaks that are due to a volcanic event at tropical latitudes. In one of these sulfate peaks at 73.67 ka, we find the largest ever reported magnitude of S-MIF in volcanic sulfate in polar ice, with a Δ33S value of −4.75 ‰. As there is a positive correlation between the magnitude of the S-MIF signal recorded in ice cores and eruptive plume height, this could be a likely candidate for the Toba super-eruption, with a plume top height in excess of 45 km. These results support the 73.7±0.3 ka (1σ) 40Ar/39Ar age estimate for the eruption, with ice core ages of our candidates with the largest magnitude S-MIF at 73.67 and 73.74 ka. Finally, since these candidate eruptions occurred on the transition into Greenland Stadial 20, the relative timing suggests that Toba was not the trigger for the large Northern Hemisphere cooling at this time although we cannot rule out an amplifying effect. Royal Societ

Children with cystic fibrosis are infected with multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles

BACKGROUND: Children with cystic fibrosis (CF) can develop life-threatening infections of Mycobacterium abscessus. These present a significant clinical challenge, particularly when the strains involved are resistant to antibiotics. Recent evidence of within-patient subclones of M. abscessus in adults with CF suggests the possibility that within-patient diversity may be relevant for the treatment of pediatric CF patients. METHODS: We performed whole genome sequencing (WGS) on 32 isolates of M. abscessus from multiple body sites for two patients with CF undergoing treatment at Great Ormond Street Hospital, UK, in 2015. RESULTS: We found evidence of extensive diversity within patients over time. Clustering analysis of single nucleotide variants (SNVs) revealed that each patient harboured multiple subpopulations, which were differentially abundant between sputum, lung samples, chest wounds, and pleural fluid. Sputum isolates did not reflect overall within-patient diversity, including failing to detect subclones with mutations previously associated with macrolide resistance (rrl 2058/2059). Some variants were present at intermediate frequencies before lung transplant. The time of transplant coincided with extensive variation, suggesting that this event is particularly disruptive for the microbial community, but transplant did not clear the M. abscessus infection and both patients died as a result of this infection. CONCLUSIONS: Isolates of M. abscessus from sputum do not always reflect the entire diversity present within the patient, which can include subclones with differing antimicrobial resistance profiles. Awareness of this phenotypic variability, with sampling of multiple body sites in conjunction with WGS, may be necessary to ensure the best treatment for this vulnerable patient group

Millennial scale persistence of organic carbon bound to iron in Arctic marine sediments

Burial of organic material in marine sediments represents a dominant natural mechanism of long-term carbon sequestration globally, but critical aspects of this carbon sink remain unresolved. Investigation of surface sediments led to the proposition that on average 10-20% of sedimentary organic carbon is stabilised and physically protected against microbial degradation through binding to reactive metal (e.g. iron and manganese) oxides. Here we examine the long-term efficiency of this rusty carbon sink by analysing the chemical composition of sediments and pore waters from four locations in the Barents Sea. Our findings show that the carbon-iron coupling persists below the uppermost, oxygenated sediment layer over thousands of years. We further propose that authigenic coprecipitation is not the dominant factor of the carbon-iron bounding in these Arctic shelf sediments and that a substantial fraction of the organic carbon is already bound to reactive iron prior deposition on the seafloor

Natural enemies from South Africa for biological control of Lagarosiphon major (Ridl.) Moss ex Wager (Hydrocharitaceae) in Europe

The non-native invasive plant, Lagarosiphon major (Hydrocharitaceae) is a submersed aquatic macrophyte that poses a significant threat to water bodies in Europe. Dense infestations prove difficult to manage using traditional methods. In order to initiate a biocontrol programme, a survey for natural enemies of Lagarosiphon was conducted in South Africa. Several phytophagous species were recorded for the first time, with at least three showing notable promise as candidate agents. Amongst these, a leaf-mining fly, Hydrellia sp. (Ephydridae) that occurred over a wide distribution causes significant leaf damage despite high levels of parasitism by braconid wasps. Another yet unidentified fly was recorded mining the stem of L. major. Two leaf-feeding and shoot boring weevils, cf. Bagous sp. (Curculionidae) were recorded damaging the shoot tips and stunting the growth of the stem. Several leaf-feeding lepidopteran species (Nymphulinae) were frequently recorded, but are expected to feed on a wide range of plant species and are not considered for importation before other candidates are assessed. The discovery of several natural enemies in the country of origin improves the biological control prospects of L. major in Europe

IFNβ Protects Neurons from Damage in a Murine Model of HIV-1 Associated Brain Injury.

Infection with human immunodeficiency virus-1 (HIV-1) causes brain injury. Type I interferons (IFNα/β) are critical mediators of any anti-viral immune response and IFNβ has been implicated in the temporary control of lentiviral infection in the brain. Here we show that transgenic mice expressing HIV-1 envelope glycoprotein 120 in their central nervous system (HIVgp120tg) mount a transient IFNβ response and provide evidence that IFNβ confers neuronal protection against HIVgp120 toxicity. In cerebrocortical cell cultures, neuroprotection by IFNβ against gp120 toxicity is dependent on IFNα receptor 1 (IFNAR1) and the β-chemokine CCL4, as IFNAR1 deficiency and neutralizing antibodies against CCL4, respectively, abolish the neuroprotective effects. We find in vivo that IFNβ mRNA is significantly increased in HIVgp120tg brains at 1.5, but not 3 or 6 months of age. However, a four-week intranasal IFNβ treatment of HIVgp120tg mice starting at 3.5 months of age increases expression of CCL4 and concomitantly protects neuronal dendrites and pre-synaptic terminals in cortex and hippocampus from gp120-induced damage. Moreover, in vivo and in vitro data suggests astrocytes are a major source of IFNβ-induced CCL4. Altogether, our results suggest exogenous IFNβ as a neuroprotective factor that has potential to ameliorate in vivo HIVgp120-induced brain injury

Place-of-residence errors on death certificates for two contiguous U. S. counties

BACKGROUND: Based on death certificate data, the Texas Department of Health Bureau of Vital Statistics calculates age adjusted all-cause mortality rates for each Texas county yearly. In 1998 the calculated rates for two adjacent Texas counties was disparate. These counties contain one city (Amarillo) and are identical in size. This study examined the accuracy of recorded county of residence for deaths in the two counties in 1998. In our jurisdiction, the county of residence is assigned by funeral homes. METHODS: A random sample of 20% of death certificates was selected. The accuracy of the county of residence was verified by using a large area map, Tax Appraisal District records, and U.S. Census Bureau databases. Inaccuracies in recording the county or zip code of residence was recorded. RESULTS: Eighteen of 354 (5.4%) death certificates recorded the incorrect county and 21 of 354 (5.9%) of death certificates recorded the zip code improperly. There was a 14.4% county recording error rate for one county compared to a 0.82% for the other county. The zip code error rate was similar for the two counties (5.9% vs. 5.8%). Of the county errors, 83% occurred for addresses within a zip code that contained addresses in both counties. CONCLUSION: This study demonstrated a large error rate (14%) in recording county of residence for deaths in one county. A similar rate was not seen in an adjacent county. This led to significant miscalculation of mortality rates for two counties. We believe that errors may have arisen in part from use of internet programs by funeral homes to assign the county of residence. With some of these programs, the county is determined by zip code, and when a zip code straddles two counties, the program automatically assigns the county whose name appears first in the alphabet. This type of error could be avoided if funeral homes determined the county of residence from Tax Appraisal District or Census Bureau records, both of which are available on the internet. This type of error could also be avoided if vital statistics offices verified the county and zip code of residence using official sources