Fluorescent analysis of photosynthetic microbes and Polycyclic Aromatic Hydrocarbons linked to optical remote sensing

Fluorescence analysis, being a non-invasive technique, has become one of the most powerful and widely used techniques for microbiologists and chemists to study various types of sample from photosynthetic microbes to hydrocarbons. The work reported here focuses on experimental results of fluorescent features of photosynthetic microbial species (cyanobacteria) and also five different crude oil samples. The cyanobacteria samples were collected from the Baltic Sea at the end of July 2011 and were associated with cyanobacterial bloom events, and the crude oil samples were from various oil spill events. The aim of the study was to find fluorescent biosignatures of cyanobacteria (initially a species specific to the Baltic Sea) and the fingerprints of crude oil; oil spills can be difficult to differentiate from biogenic films when using Synthetic Aperture Radar (SAR) or sunglint contaminated optical imagery. All samples were measured using a Perkin Elmer LS55 Luminescence spectrometer over a broad range of excitation and emission wavelength from ultraviolet (UV) to near infrared (NIR). The results are presented in Excitation Emission Matrices (EEMs) that exhibit the fluorescent features of each sample. In the EEM of the seawater sample containing cyanobacteria, there is an intense emission peak from tryptophan with fluorescent excitation and emission peaks at 285 and 345 nm respectively. In addition, fluorescent signatures of phycocyanin and chlorophyll-a are present with excitation and emission centre wavelengths at 555 nm, 645 nm and 390 nm, 685 nm, respectively. Additionally, the fluorescence signatures of Polycyclic Aromatic Hydrocarbons (PAHs) are present in the EEMs of crude oil samples with excitation and emission peaks at 285 nm and 425 nm. This study underpins further research on how to distinguish cyanobacteria species by their fluorescence signatures and the potential role that PAHs play in detection of cyanobacteria fluorescence features

Martian sub-surface ionising radiation: biosignatures and geology

The surface of Mars, unshielded by thick atmosphere or global magnetic field, is exposed to high levels of cosmic radiation. This ionising radiation field is deleterious to the survival of dormant cells or spores and the persistence of molecular biomarkers in the subsurface, and so its characterisation is of prime astrobiological interest. Here, we present modelling results of the absorbed radiation dose as a function of depth through the Martian subsurface, suitable for calculation of biomarker persistence. A second major implementation of this dose accumulation rate data is in application of the optically stimulated luminescence technique for dating Martian sediments. <br><br> We present calculations of the dose-depth profile in the Martian subsurface for various scenarios: variations of surface composition (dry regolith, ice, layered permafrost), solar minimum and maximum conditions, locations of different elevation (Olympus Mons, Hellas basin, datum altitude), and increasing atmospheric thickness over geological history. We also model the changing composition of the subsurface radiation field with depth compared between Martian locations with different shielding material, determine the relative dose contributions from primaries of different energies, and discuss particle deflection by the crustal magnetic fields

Conjugacy of one-dimensional one-sided cellular automata is undecidable

Two cellular automata are strongly conjugate if there exists a shift-commuting conjugacy between them. We prove that the following two sets of pairs $(F,G)$ of one-dimensional one-sided cellular automata over a full shift are recursively inseparable: (i) pairs where $F$ has strictly larger topological entropy than $G$, and (ii) pairs that are strongly conjugate and have zero topological entropy. Because there is no factor map from a lower entropy system to a higher entropy one, and there is no embedding of a higher entropy system into a lower entropy system, we also get as corollaries that the following decision problems are undecidable: Given two one-dimensional one-sided cellular automata $F$ and $G$ over a full shift: Are $F$ and $G$ conjugate? Is $F$ a factor of $G$? Is $F$ a subsystem of $G$? All of these are undecidable in both strong and weak variants (whether the homomorphism is required to commute with the shift or not, respectively). It also immediately follows that these results hold for one-dimensional two-sided cellular automata.Comment: 12 pages, 2 figures, accepted for SOFSEM 201

Physiography and Late Quaternary-Holocene Processes of Northeastern Gulf of Mexico Outer Continental Shelf off Mississippi and Alabama

High-resolution multibeam mapping of the mid- and outer continental shelf and upper slope off Mississippi and Alabama reveals a complex bathymetry that reflects conditions during the last eustatic rise and the present high stand of sea level. The most prominent bathymetric features are pinnacles and hardgrounds that are scattered throughout the area. These features generally stand \u3c10 m above the surrounding seafloor, cover large areas, and display a variety of morphologies. Almost all the reef pinnacles and hardgrounds have zones of high acoustic backscatter on their summits and on the seafloor immediately adjacent to their southwest walls. In addition, they also have erosional moats on the seafloor to the southwest. Large fields of bedforms are scattered throughout the mapped area. The asymmetries and orientations of the bedforms suggest that they were formed by excursions of the northeast-flowing Loop Current. In contrast, the pervasive ponding of sediment on the northeast sides of bathymetric highs indicates that one of the predominant directions of sediment transport has been to the south and southwest. The shelf break is a zone of numerous landslides of various sizes and complexities. The morphology of several landslide scars indicates that some of the failures occurred recently. One large reef-capped salt dome was mapped in the area, surrounded by a large field of pockmarks. Fields of pockmarks are also scattered on the shelf. The growth and demise of the reefs are related to the fluctuating transgression of eustatic sea level during the last deglaciation. Two episodes of reef drowning are correlated with the increased rates of sea-level rise during documented melt-water pulses; the first occurred from 14.8 to 14.2 ka and the second from 11.8 to 11.2 ka. Rates of sea-level rise exceeded the maximum growth rate of hermatypic corals only during these two intervals since the last glacial maximum and thus drowned the coral communities

Cyanobacteria and microalgae in supporting human habitation on Mars

Establishing the first human presence on Mars will be the most technically challenging undertaking yet in the exploration beyond our planet. The remoteness of Mars from Earth, the inhospitable surface conditions including low atmospheric pressure and cold temperatures, and the need for basic resources including water, pose a formidable challenge to this endeavour. The intersection of multiple disciplines will be required to provide solutions for temporary and eventually permanent Martian habitation. This review considers the role cyanobacteria and eukaryotic microalgae (collectively referred to here as ‘microalgae’) may have in supporting missions to the red planet. The current research using these microorganisms in biological life support systems is discussed, with a systematic analysis of their usage in each system conducted. The potential of microalgae to provide astronauts with oxygen, food, bio-polymers and pharmaceuticals is considered. An overview of microalgal experiments in space missions across the last 60 years is presented, and the research exploring the technical challenges of cultivation on Mars is discussed. From these findings, an argument for culturing microalgae in subterranean bioreactors is proposed. Finally, future synthetic biology approaches for enhancing the cyanobacterial/microalgal role in supporting human deep-space exploration are presented. We show that microalgae hold significant promise for providing solutions to many problems faced by the first Martian settlers, however these can only be realised with significant infrastructure and a reliable power source

An Origin-of-Life Reactor to Simulate Alkaline Hydrothermal Vents

Chemiosmotic coupling is universal: practically all cells harness electrochemical proton gradients across membranes to drive ATP synthesis, powering biochemistry. Autotrophic cells, including phototrophs and chemolithotrophs, also use proton gradients to power carbon fixation directly. The universality of chemiosmotic coupling suggests that it arose very early in evolution, but its origins are obscure. Alkaline hydrothermal systems sustain natural proton gradients across the thin inorganic barriers of interconnected micropores within deep-sea vents. In Hadean oceans, these inorganic barriers should have contained catalytic Fe(Ni)S minerals similar in structure to cofactors in modern metabolic enzymes, suggesting a possible abiotic origin of chemiosmotic coupling. The continuous supply of H2 and CO2 from vent fluids and early oceans, respectively, offers further parallels with the biochemistry of ancient autotrophic cells, notably the acetyl CoA pathway in archaea and bacteria. However, the precise mechanisms by which natural proton gradients, H2, CO2 and metal sulphides could have driven organic synthesis are uncertain, and theoretical ideas lack empirical support. We have built a simple electrochemical reactor to simulate conditions in alkaline hydrothermal vents, allowing investigation of the possibility that abiotic vent chemistry could prefigure the origins of biochemistry. We discuss the construction and testing of the reactor, describing the precipitation of thin-walled, inorganic structures containing nickel-doped mackinawite, a catalytic Fe(Ni)S mineral, under prebiotic ocean conditions. These simulated vent structures appear to generate low yields of simple organics. Synthetic microporous matrices can concentrate organics by thermophoresis over several orders of magnitude under continuous open-flow vent conditions

Physiography and Late Quaternary-Holocene Processes of Northeastern Gulf of Mexico Outer Continental Shelf off Mississippi and Alabama

High-resolution multibeam mapping of the mid- and outer continental shelf and upper slope off Mississippi and Alabama reveals a complex bathymetry that reflects conditions during the last eustatic rise and the present high stand of sea level. The most prominent bathymetric features are pinnacles and hardgrounds that are scattered throughout the area. These features generally stand \u3c10 m above the surrounding seafloor, cover large areas, and display a variety of morphologies. Almost all the reef pinnacles and hardgrounds have zones of high acoustic backscatter on their summits and on the seafloor immediately adjacent to their southwest walls. In addition, they also have erosional moats on the seafloor to the southwest. Large fields of bedforms are scattered throughout the mapped area. The asymmetries and orientations of the bedforms suggest that they were formed by excursions of the northeast-flowing Loop Current. In contrast, the pervasive ponding of sediment on the northeast sides of bathymetric highs indicates that one of the predominant directions of sediment transport has been to the south and southwest. The shelf break is a zone of numerous landslides of various sizes and complexities. The morphology of several landslide scars indicates that some of the failures occurred recently. One large reef-capped salt dome was mapped in the area, surrounded by a large field of pock-marks. Fields of pockmarks are also scattered on the shelf. The growth and demise of the reefs are related to the fluctuating transgression of eustatic sea level during the last deglaciation. Two episodes of reef drowning are correlated with the increased rates of sea-level rise during documented melt-water pulses; the first occurred from 14.8 to 14.2 ka and the second from 11.8 to 11.2 ka. Rates of sea-level rise exceeded the maximum growth rate of hermatypic corals only during these two intervals since the last glacial maximum and thus drowned the coral communities

Fluorescence characterization of clinically-important bacteria

Healthcare-associated infections (HCAI/HAI) represent a substantial threat to patient health during hospitalization and incur billions of dollars additional cost for subsequent treatment. One promising method for the detection of bacterial contamination in a clinical setting before an HAI outbreak occurs is to exploit native fluorescence of cellular molecules for a hand-held, rapid-sweep surveillance instrument. Previous studies have shown fluorescence-based detection to be sensitive and effective for food-borne and environmental microorganisms, and even to be able to distinguish between cell types, but this powerful technique has not yet been deployed on the macroscale for the primary surveillance of contamination in healthcare facilities to prevent HAI. Here we report experimental data for the specification and design of such a fluorescence-based detection instrument. We have characterized the complete fluorescence response of eleven clinically-relevant bacteria by generating excitation-emission matrices (EEMs) over broad wavelength ranges. Furthermore, a number of surfaces and items of equipment commonly present on a ward, and potentially responsible for pathogen transfer, have been analyzed for potential issues of background fluorescence masking the signal from contaminant bacteria. These include bedside handrails, nurse call button, blood pressure cuff and ward computer keyboard, as well as disinfectant cleaning products and microfiber cloth. All examined bacterial strains exhibited a distinctive double-peak fluorescence feature associated with tryptophan with no other cellular fluorophore detected. Thus, this fluorescence survey found that an emission peak of 340nm, from an excitation source at 280nm, was the cellular fluorescence signal to target for detection of bacterial contamination. The majority of materials analysed offer a spectral window through which bacterial contamination could indeed be detected. A few instances were found of potential problems of background fluorescence masking that of bacteria, but in the case of the microfiber cleaning cloth, imaging techniques could morphologically distinguish between stray strands and bacterial contamination

The changing characteristics of patients with chronic hepatitis C prescribed direct acting antiviral medicines in general practice since listing of the medicines on the Australian Pharmaceutical Benefits Scheme

Background and Aim: The primary objective of this study was to determine whether the characteristics of patients prescribed direct acting antiviral (DAA) medicines have changed since initial listing of the medicines on the Australian Pharmaceutical Benefits Scheme (PBS). Methods: A cross-sectional study was conducted using data from MedicineInsight, an Australian database of general practice electronic health records, from March 2016 to August 2018. We compared sociodemographic, comorbidity, and clinical characteristics of patients aged at least 18 years who were prescribed at least one DAA in the first 4 months of PBS listing in 2016 with those prescribed at least one DAA in 2018. Results: There were 2251 eligible adult patients prescribed a DAA during the study period, 62% were men and 59% were aged 50 years and older. Patients prescribed DAA medicines initially were older (aged ≥50 years: 67.9% vs 49.3%; P 1 (20.4% vs 8.9%; P < 0.001) than those prescribed DAA medicines in 2018. A greater proportion of patients in regional/remote (46.5% vs 35.6%; P < 0.001) and socioeconomically disadvantaged areas (44.4% vs 34.5%; P = 0.003) accessed treatment in 2018 compared with 2016. Conclusions: Despite evidence of decreasing uptake of DAA medicines across Australia, this study indicates broadened uptake among younger age groups and those residing in regional/remote and socioeconomically disadvantaged areas since 2016. While uptake of DAA medicines in some population subgroups appears to have improved, continuous efforts to improve uptake across the Australian population are essential

Constraints on a potential aerial biosphere on Venus: II. Ultraviolet radiation

Despite the harsh conditions in the atmosphere of Venus, the possibility for an aerial habitable zone exists. A thermal habitable zone is predicted to exist at an altitude range of 62 to 48 km, above which temperatures drop below the lower thermal limit of cell growth and below which temperatures exceed the evaporation temperature. Many biocidal factors must be considered for the complete definition of an aerial habitable zone; in this study we consider the constraint specifically from the perspective of biocidal solar ultraviolet (UV) intensity in the atmosphere. We simulated the penetration of solar ultraviolet and visible light through the atmosphere using a radiative transfer model, to determine the spectral environment (and thus the UV biocidal effect) as a function of altitude in the atmosphere of Venus. At the top of the thermal aerial habitable zone (62 km) the incoming solar irradiance creates a severely challenging UV environment, with extremophiles such as Deinococcus radiodurans expected to be able to endure these UV conditions for approximately 80 s. At an altitude of around 59 km the biologically-weighted UV irradiance drops below that calculated for the Archean Earth, and continues to fall with decreasing altitude until at 54 km it is less than that found currently at the surface of Earth. Crucially, longer wavelength photosynthetically active light continues to penetrate to these altitudes and below, resulting in a solar radiation environment in the venusian atmosphere below around 54 km that screens biologically-damaging UV radiation yet permits the process of photosynthesis. Whilst not claiming to suggest the existence of an aerial habitable zone in general, by considering thermal conditions, ionising radiation and the UV flux environment of the venusian cloud deck alone, we define a potential habitable zone that extends from 59 km to 48 km. This region should form the focus of future remote and in situ astrobiological investigations of Venus