Microbial and Geochemical aspects of Selenium cycling in an Estuarine system: Lake Macquarie N.S.W.

ABSTRACT This work examined the role of micro-organisms in the biogeochemical cycling of selenium within the benthic ecosystem of Lake Macquarie, a coastal lake in New South Wales with a history of anthropogenic heavy metal contamination. Certain micro-organisms possess the ability to oxidise or reduce selenium (Fleming and Alexander, 1973; Doran and Alexander, 1977), and microbial volatilisation of selenium from contaminated sediments and soils utilising naturally-occurring microflora has been shown in overseas research (Thompson-Eagle and Frankenberger, 1992) to be a potentially effective remediation strategy. In examining the impact of micro-organisms upon the oxidation state of selenium in Lake Macquarie sediments, this work also investigated and characterised selenium (and heavy metal) concentrations, speciation and geochemical phase associations (an indicator of potential bioavailability) in the sediments. Seven distinct bacterial species indigenous to Lake Macquarie were identified in this work with the ability to reduce selenium as selenite to elemental selenium, and selenium as selenate to organic forms of selenium, including volatile methylated selenium compounds. Metabolic parameters calculated for these organisms compared favourably with those reported in the literature by other researchers. Mixed populations of sediment micro-organisms were also isolated and studied in this work for their selenite and selenate reduction abilities. Total reduction of added selenite at levels up to 100 mg/L was recorded for a number of the organisms studied in this work. A maximum specific uptake rate for selenite of 3040 mgSe(IV).(gcells)-1.(h)-1 for one isolate (Shewanella putrefaciens) was determined, exceeding rates reported in the literature by other authors. Use of the indigenous micro-organisms from Lake Macquarie for the bioremediation of selenium containing waste streams was also examined in this work and selenium reduction in an immobilised cell reactor was demonstrated with such organisms. Concentrations, speciation, sediment core profiles and geochemical phase associations for selenium were determined for sediment samples collected at a variety of sites throughout Lake Macquarie and from Wyee Creek, a selenium-impacted fluvial input to the lake. The maximum concentration of selenium obtained in this work for the lake proper was 4.04 mg/kg, considerably lower than values reported over a decade ago (Batley, 1987) but consistent with reported reductions of selenium input into the lake from the lead-zinc smelter. Selective extraction methodology (Tessier et al. and BCR methods) studied geochemical phase association of selenium in Lake Macquarie sediments and found up to 44% of selenium was in bioavailable forms. Of interest and environmental concern was levels of selenium found in sediments of Wyee Creek, which previously received overflows from the ash dam associated with the Vales Point Power Station. Sediment selenium levels of up to 300 mg/kg were determined for this creek. These were an order of magnitude or more greater than those recorded for the lake itself and are of concern as to the potential impact on benthic organisms and those animals, including humans, who consume them. While this work can only provide a 'snapshot' of conditions within Lake Macquarie at the time of the sampling events recorded herein, it does make several important contributions to the understanding of selenium biogeochemistry in Lake Macquarie. These include: presentation of the hypothesis that selenium levels in surficial sediments being deposited in the north of the lake have decreased in recent years as a result of selenium reduction measures undertaken by the lead-zinc smelter; determination that up to 44% of selenium in surficial sediments from the lake is associated with sediment phases in which selenium has the potential to become remobilized and hence possibly bioavailable; and documentation of selenium concentrations in Wyee Creek, identifying the area as having selenium concentrations an order of magnitude or more greater than the lake itself. Concerning the role played by microorganisms in the biogeochemical cycling of selenium in Lake Macquarie, this work has: identified individual isolated and mixed cultures of bacteria that can reduce selenium as selenite to lower oxidation states; identified individual isolated and mixed cultures of bacteria that can reduce selenium as selenate to lower oxidation states; identified volatile methylated selenium compounds in the headspace gases of microorganisms reducing selenate; determined Minimum Inhibitory Concentrations for selenate and selenite for organisms isolated from Lake Macquarie; identified casein hydrolysate as a preferred carbon source for selenium reducing microorganisms from Lake Macquarie; and demonstrated that bioremediation of selenium contaminated waste streams using indigenous organisms from Lake Macquarie is feasible on the laboratory scale. Further research areas suggested by this work include: additional investigations of elevated selenium levels in Wyee Creek sediments; determination of the role of microbes in in-situ selenium reduction; and optimisation of selenium biotreatment/bioremediation of selenium-containing waste streams and sediments. In summary, this work, in rejecting the null hypothesis that the oxidation states of selenium in sediments from Lake Macquarie, NSW, are independent of microbial activity and accepting the alternate hypothesis that these oxidation states are not independent of microbial activity, contributes to the understanding of the role of microorganisms in the biogeochemical cycling of selenium, having applicability to both the specific ecosystem of Lake Macquarie, NSW, and also to selenium cycling in the environment in general. In addition, this work has identified selenium contamination in Wyee Creek, one of the fluvial inputs to Lake Macquarie, which was previously been undocumented in the literature and which may pose significant potential risk to humans and the ecosystem due to sediment selenium levels one or more orders of magnitude higher than those recorded in the lake itself. Finally, this work has also identified a number of microorganisms indigenous to Lake Macquarie with the ability to reduce selenium from toxic, mobile forms to less toxic, immobile or volatile forms, and these organisms have been shown to have the potential for use in treatment of selenium contaminated waste streams and also in the bioremediation of selenium-contaminated sediments

Microbial and Geochemical aspects of Selenium cycling in an Estuarine system: Lake Macquarie N.S.W.

ABSTRACT This work examined the role of micro-organisms in the biogeochemical cycling of selenium within the benthic ecosystem of Lake Macquarie, a coastal lake in New South Wales with a history of anthropogenic heavy metal contamination. Certain micro-organisms possess the ability to oxidise or reduce selenium (Fleming and Alexander, 1973; Doran and Alexander, 1977), and microbial volatilisation of selenium from contaminated sediments and soils utilising naturally-occurring microflora has been shown in overseas research (Thompson-Eagle and Frankenberger, 1992) to be a potentially effective remediation strategy. In examining the impact of micro-organisms upon the oxidation state of selenium in Lake Macquarie sediments, this work also investigated and characterised selenium (and heavy metal) concentrations, speciation and geochemical phase associations (an indicator of potential bioavailability) in the sediments. Seven distinct bacterial species indigenous to Lake Macquarie were identified in this work with the ability to reduce selenium as selenite to elemental selenium, and selenium as selenate to organic forms of selenium, including volatile methylated selenium compounds. Metabolic parameters calculated for these organisms compared favourably with those reported in the literature by other researchers. Mixed populations of sediment micro-organisms were also isolated and studied in this work for their selenite and selenate reduction abilities. Total reduction of added selenite at levels up to 100 mg/L was recorded for a number of the organisms studied in this work. A maximum specific uptake rate for selenite of 3040 mgSe(IV).(gcells)-1.(h)-1 for one isolate (Shewanella putrefaciens) was determined, exceeding rates reported in the literature by other authors. Use of the indigenous micro-organisms from Lake Macquarie for the bioremediation of selenium containing waste streams was also examined in this work and selenium reduction in an immobilised cell reactor was demonstrated with such organisms. Concentrations, speciation, sediment core profiles and geochemical phase associations for selenium were determined for sediment samples collected at a variety of sites throughout Lake Macquarie and from Wyee Creek, a selenium-impacted fluvial input to the lake. The maximum concentration of selenium obtained in this work for the lake proper was 4.04 mg/kg, considerably lower than values reported over a decade ago (Batley, 1987) but consistent with reported reductions of selenium input into the lake from the lead-zinc smelter. Selective extraction methodology (Tessier et al. and BCR methods) studied geochemical phase association of selenium in Lake Macquarie sediments and found up to 44% of selenium was in bioavailable forms. Of interest and environmental concern was levels of selenium found in sediments of Wyee Creek, which previously received overflows from the ash dam associated with the Vales Point Power Station. Sediment selenium levels of up to 300 mg/kg were determined for this creek. These were an order of magnitude or more greater than those recorded for the lake itself and are of concern as to the potential impact on benthic organisms and those animals, including humans, who consume them. While this work can only provide a 'snapshot' of conditions within Lake Macquarie at the time of the sampling events recorded herein, it does make several important contributions to the understanding of selenium biogeochemistry in Lake Macquarie. These include: presentation of the hypothesis that selenium levels in surficial sediments being deposited in the north of the lake have decreased in recent years as a result of selenium reduction measures undertaken by the lead-zinc smelter; determination that up to 44% of selenium in surficial sediments from the lake is associated with sediment phases in which selenium has the potential to become remobilized and hence possibly bioavailable; and documentation of selenium concentrations in Wyee Creek, identifying the area as having selenium concentrations an order of magnitude or more greater than the lake itself. Concerning the role played by microorganisms in the biogeochemical cycling of selenium in Lake Macquarie, this work has: identified individual isolated and mixed cultures of bacteria that can reduce selenium as selenite to lower oxidation states; identified individual isolated and mixed cultures of bacteria that can reduce selenium as selenate to lower oxidation states; identified volatile methylated selenium compounds in the headspace gases of microorganisms reducing selenate; determined Minimum Inhibitory Concentrations for selenate and selenite for organisms isolated from Lake Macquarie; identified casein hydrolysate as a preferred carbon source for selenium reducing microorganisms from Lake Macquarie; and demonstrated that bioremediation of selenium contaminated waste streams using indigenous organisms from Lake Macquarie is feasible on the laboratory scale. Further research areas suggested by this work include: additional investigations of elevated selenium levels in Wyee Creek sediments; determination of the role of microbes in in-situ selenium reduction; and optimisation of selenium biotreatment/bioremediation of selenium-containing waste streams and sediments. In summary, this work, in rejecting the null hypothesis that the oxidation states of selenium in sediments from Lake Macquarie, NSW, are independent of microbial activity and accepting the alternate hypothesis that these oxidation states are not independent of microbial activity, contributes to the understanding of the role of microorganisms in the biogeochemical cycling of selenium, having applicability to both the specific ecosystem of Lake Macquarie, NSW, and also to selenium cycling in the environment in general. In addition, this work has identified selenium contamination in Wyee Creek, one of the fluvial inputs to Lake Macquarie, which was previously been undocumented in the literature and which may pose significant potential risk to humans and the ecosystem due to sediment selenium levels one or more orders of magnitude higher than those recorded in the lake itself. Finally, this work has also identified a number of microorganisms indigenous to Lake Macquarie with the ability to reduce selenium from toxic, mobile forms to less toxic, immobile or volatile forms, and these organisms have been shown to have the potential for use in treatment of selenium contaminated waste streams and also in the bioremediation of selenium-contaminated sediments

Discovery of the Interstellar Chiral Molecule Propylene Oxide (CH3_3CHCH2_2O)

Life on Earth relies on chiral molecules, that is, species not superimposable on their mirror images. This manifests itself in the selection of a single molecular handedness, or homochirality, across the biosphere. We present the astronomical detection of a chiral molecule, propylene oxide (CH$_3$CHCH$_2$O), in absorption toward the Galactic Center. Propylene oxide is detected in the gas phase in a cold, extended molecular shell around the embedded, massive protostellar clusters in the Sagittarius B2 star-forming region. This material is representative of the earliest stage of solar system evolution in which a chiral molecule has been found

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security

Proceedings of the 3rd Biennial Conference of the Society for Implementation Research Collaboration (SIRC) 2015: advancing efficient methodologies through community partnerships and team science

It is well documented that the majority of adults, children and families in need of evidence-based behavioral health interventionsi do not receive them [1, 2] and that few robust empirically supported methods for implementing evidence-based practices (EBPs) exist. The Society for Implementation Research Collaboration (SIRC) represents a burgeoning effort to advance the innovation and rigor of implementation research and is uniquely focused on bringing together researchers and stakeholders committed to evaluating the implementation of complex evidence-based behavioral health interventions. Through its diverse activities and membership, SIRC aims to foster the promise of implementation research to better serve the behavioral health needs of the population by identifying rigorous, relevant, and efficient strategies that successfully transfer scientific evidence to clinical knowledge for use in real world settings [3]. SIRC began as a National Institute of Mental Health (NIMH)-funded conference series in 2010 (previously titled the “Seattle Implementation Research Conference”; $150,000 USD for 3 conferences in 2011, 2013, and 2015) with the recognition that there were multiple researchers and stakeholdersi working in parallel on innovative implementation science projects in behavioral health, but that formal channels for communicating and collaborating with one another were relatively unavailable. There was a significant need for a forum within which implementation researchers and stakeholders could learn from one another, refine approaches to science and practice, and develop an implementation research agenda using common measures, methods, and research principles to improve both the frequency and quality with which behavioral health treatment implementation is evaluated. SIRC’s membership growth is a testament to this identified need with more than 1000 members from 2011 to the present.ii SIRC’s primary objectives are to: (1) foster communication and collaboration across diverse groups, including implementation researchers, intermediariesi, as well as community stakeholders (SIRC uses the term “EBP champions” for these groups) – and to do so across multiple career levels (e.g., students, early career faculty, established investigators); and (2) enhance and disseminate rigorous measures and methodologies for implementing EBPs and evaluating EBP implementation efforts. These objectives are well aligned with Glasgow and colleagues’ [4] five core tenets deemed critical for advancing implementation science: collaboration, efficiency and speed, rigor and relevance, improved capacity, and cumulative knowledge. SIRC advances these objectives and tenets through in-person conferences, which bring together multidisciplinary implementation researchers and those implementing evidence-based behavioral health interventions in the community to share their work and create professional connections and collaborations

PURE ROTATIONAL SPECTROSCOPY OF PANHs II: ACRIDINE. POSSIBLE APPLICATIONS IN THz COHERENT CONTROL SPECTROSCOPY

Author Institution: Department of Chemistry, California Institute of Technology, Pasadena, CA 91125; Divisions of Geological & Planetary Sciences and Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA 91125Recent developments in THz pulse generation have allowed for the synthesis of short (sub-ps), high power ($>$10 MV/cm) pulses capable of controlling low energy vibrations, such as large amplitude torsions or bending modes. Clusters of polycyclic aromatic nitrogen heterocycles (PANHs) with water are good candidates for this research since a significant amount of theoretical and experimental work has already been undertaken on these species. A thorough understanding of the rotational spectra of these molecules is essential for assessing their suitability in far-IR/THz coherent control studies and is also of astrochemical interest. A promising target in this regard is the PANH acridine. Here we present the pure-rotational spectrum of the acridine monomer recorded with a direct absorption mm/sub-mm wave spectrometer and discuss the results in the context of future applications to coherent control of large amplitude motions of small aromatic water clusters