A global perspective on bacterial diversity in the terrestrial deep subsurface.

While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

Storage and export of microbial biomass across the western Greenland Ice Sheet.

The Greenland Ice Sheet harbours a wealth of microbial life, yet the total biomass stored or exported from its surface to downstream environments is unconstrained. Here, we quantify microbial abundance and cellular biomass flux within the near-surface weathering crust photic zone of the western sector of the ice sheet. Using groundwater techniques, we demonstrate that interstitial water flow is slow (~10-2 m d-1), while flow cytometry enumeration reveals this pathway delivers 5 × 108 cells m-2 d-1 to supraglacial streams, equivalent to a carbon flux up to 250 g km-2 d-1. We infer that cellular carbon accumulation in the weathering crust exceeds fluvial export, promoting biomass sequestration, enhanced carbon cycling, and biological albedo reduction. We estimate that up to 37 kg km-2 of cellular carbon is flushed from the weathering crust environment of the western Greenland Ice Sheet each summer, providing an appreciable flux to support heterotrophs and methanogenesis at the bed.

MEF2C transcription factor is associated with the genetic and epigenetic risk architecture of schizophrenia and improves cognition in mice.

Large-scale consortia mapping the genomic risk architectures of schizophrenia provide vast amounts of molecular information, with largely unexplored therapeutic potential. We harnessed publically available information from the Psychiatric Genomics Consortium, and report myocyte enhancer factor 2C (MEF2C) motif enrichment in sequences surrounding the top scoring single-nucleotide polymorphisms within risk loci contributing by individual small effect to disease heritability. Chromatin profiling at base-pair resolution in neuronal nucleosomes extracted from prefrontal cortex of 34 subjects, including 17 cases diagnosed with schizophrenia, revealed MEF2C motif enrichment within cis-regulatory sequences, including neuron-specific promoters and superenhancers, affected by histone H3K4 hypermethylation in disease cases. Vector-induced short- and long-term Mef2c upregulation in mouse prefrontal projection neurons consistently resulted in enhanced cognitive performance in working memory and object recognition paradigms at baseline and after psychotogenic drug challenge, in conjunction with remodeling of local connectivity. Neuronal genome tagging in vivo by Mef2c-Dam adenine methyltransferase fusion protein confirmed the link between cognitive enhancement and MEF2C occupancy at promoters harboring canonical and variant MEF2C motifs. The multilayered integrative approaches presented here provide a roadmap to uncover the therapeutic potential of transcriptional regulators for schizophrenia and related disorders.

Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge.

Liquid water occurs below glaciers and ice sheets globally, enabling the existence of an array of aquatic microbial ecosystems. In Antarctica, large subglacial lakes are present beneath hundreds to thousands of metres of ice, and scientific interest in exploring these environments has escalated over the past decade. After years of planning, the first team of scientists and engineers cleanly accessed and retrieved pristine samples from a West Antarctic subglacial lake ecosystem in January 2013. This paper reviews the findings to date on Subglacial Lake Whillans and presents new supporting data on the carbon and energy metabolism of resident microbes. The analysis of water and sediments from the lake revealed a diverse microbial community composed of bacteria and archaea that are close relatives of species known to use reduced N, S or Fe and CH4 as energy sources. The water chemistry of Subglacial Lake Whillans was dominated by weathering products from silicate minerals with a minor influence from seawater. Contributions to water chemistry from microbial sulfide oxidation and carbonation reactions were supported by genomic data. Collectively, these results provide unequivocal evidence that subglacial environments in this region of West Antarctica host active microbial ecosystems that participate in subglacial biogeochemical cycling.

Role of outer membrane c-type cytochromes MtrC and OmcA in Shewanella oneidensis MR-1 cell production, accumulation, and detachment during respiration on hematite.

The iron-reducing bacterium Shewanella oneidensis MR-1 has the capacity to contribute to iron cycling over the long term by respiring on crystalline iron oxides such as hematite when poorly crystalline phases are depleted. The ability of outer membrane cytochromes OmcA and MtrC of MR-1 to bind to and transfer electrons to hematite has led to the suggestion that they function as terminal reductases when this mineral is used as a respiratory substrate. Differences in their redox behavior and hematite-binding properties, however, indicate that they play different roles in the electron transfer reaction. Here, we investigated how these differences in cytochrome behavior with respect to hematite affected biofilm development when the mineral served as terminal electron acceptor (TEA). Upon attachment to hematite, cells of the wild-type (WT) strain as well as those of a ΔomcA mutant but not those of a ΔmtrC mutant replicated and accumulated on the mineral surface. The results indicate that MtrC but not OmcA is required for growth when this mineral serves as TEA. While an OmcA deficiency did not impede cell replication and accumulation on hematite prior to achievement of a maximum surface cell density comparable to that established by WT cells, OmcA was required for efficient electron transfer and cell attachment to hematite once maximum surface cell density was achieved. OmcA may therefore play a role in overcoming barriers to electron transfer and cell attachment to hematite imposed by reductive dissolution of the mineral surface from cell respiration associated with achievement of high surface cell densities.

Selective detection of luminescence from semiconductor quantum dots by nanosecond time-gated imaging with a colour-masked CCD detector.

Quantum dots are of considerable interest as highly detectable labels with broad absorption, narrow spectral emission and good quantum yields. The luminescence emission has a longer decay time than that of the most common fluorophores, leading to facile rejection of much background emission (such as autofluorescence from biological samples) by means of gated detection. Here, it is shown that a new technique, true-colour nanosecond time-gated luminescence imaging, can be used for selective detection of quantum dot luminescence and should prove valuable for multiplexed detection on the basis of both spectral emission profile and luminescence decay time.

Prospects for applications of lanthanide-based upconverting surfaces to bioassay and detection.

Biological assays to detect binding interactions are often conducted using fluorescence resonance energy transfer (FRET) but this has several disadvantages that markedly reduce the dynamic range of measurements. The very short range of FRET interactions also causes difficulties when large analytes such as viruses or spores are to be detected. Conventional FRET-based assays can in principle be improved using infrared-excited upconverting lanthanide-based energy donors but this does not address the short range of the FRET process. Here we investigate an alternative mode of energy transfer based on evanescent wave coupling from an erbium-doped waveguide to an absorbed fluorophore and characterise the luminescence from the dopant. The upconverted erbium emission is highly structured with well-separated bands in the violet, green and red spectral regions and very little detectable signal between the peaks. The relative intensity of these bands depends on power-density of infrared excitation. Green emission predominates at low power-density and red emission increases more rapidly as power-density increases, with a smaller violet peak also emerging. The temporal response of the upconverting material to pulsed infrared excitation was investigated and was shown to vary markedly with emission wavelength with the red component being particularly sensitive to the duration of the excitation pulse. A surface monolayer of the fluorescent protein R-phycoerythrin was very easily detected on binding to an upconverting waveguide. The potential advantages and limitations of the evanescent wave excitation technique for fluorescence detection are discussed and avenues for further development are considered.

Total internal reflection fluorescence imaging using an upconverting cover slip for multicolour evanescent excitation.

Total internal reflection fluorescence microscopy is well known as a means of studying surface-bound structures in cell biology. It is usually measured either by coupling a light source to the sample using a prism or with a special objective where light passing through the periphery of the lens illuminates the contact region beyond the critical angle. In this study we present a new and simple approach to total internal reflection fluorescence microscopy where the sample is mounted on a cover slip prepared from a high-index upconverting glass-ceramic. Excitation of the cover slip with a low-cost near-infrared laser diode generates intense narrow-band visible emission within the cover slip, some of which is totally internally reflected. This emission gives rise to an evanescent wave at the interface and hence can excite surface-bound fluorescent species. Depending on the excitation conditions the cover slip can generate violet, green and red emission and hence can excite a wide range of fluorescent labels. Fluorescence emission from the sample can be detected in spectral regions where the direct emission from the cover slip is very weak. The advantages and limitations of the technique are discussed in comparison with conventional total internal reflection fluorescence microscopy measurements and prospects for novel total internal reflection fluorescence microscopy geometries are considered.

Metallization of fluid nitrogen and the mott transition in highly compressed low-Z fluids.

Electrical conductivities are reported for degenerate fluid nitrogen at pressures up to 180 GPa (1.8 Mbar) and temperatures of approximately 7000 K. These extreme quasi-isentropic conditions were achieved with multiple-shock compression generated with a two-stage light-gas gun. Nitrogen undergoes a nonmetal-metal transition at 120 GPa, probably in the monatomic state. These N data and previous conductivity data for H, O, Cs, and Rb are used to develop a general picture of the systematics of the nonmetal-metal transition in these fluids. Specifically, the density dependences of electrical conductivities in the semiconducting fluid are well correlated with the radial extent of the electronic charge-density distributions of H, N, O, Cs, and Rb atoms. These new data for N scale with previous data for O, as expected from their similar charge-density distributions.

Direct modulation of the effective sensitivity of a CCD detector: a new approach to time-resolved fluorescence imaging.

In this paper a novel approach to frequency-domain fluorescence lifetime imaging (FLIM) is described. In a CCD camera a single pixel is defined by a charge pattern on a group of electrodes. By modulation of the pattern of voltages defining the pixel structure it is possible to modulate the sensitivity of the CCD at radio frequency. The modulation enhances the noise performance of the CCD, in contrast to the deterioration in performance seen when an intensifier stage is similarly modulated. The new technology has potential applications to a wide range of assays as well as in conventional FLIM applications. Unlike intensifier-based systems, the directly modulated CCD is physically small, inexpensive, robust and offers superior resolution and noise performance.

Measurement of nanosecond time-resolved fluorescence with a directly gated interline CCD camera.

CCD cameras coupled optically to gated image intensifiers have been used for fast time-resolved measurements for some years. Image intensifiers have disadvantages, however, and for some applications it would be better if the image sensor could be gated directly at high speed. Control of the 'charge drain' function on an interline-transfer CCD allows the sensor to be switched rapidly from an insensitive state. The temporal and spatial properties of the charge drain are explored in the present paper and it is shown that nanosecond time resolution with acceptable spatial uniformity can be achieved for a small commercial sensor. A fluorescence lifetime imaging system is demonstrated, based on a repetitively pulsed laser excitation source synchronized to the CCD control circuitry via a programmable delay unit.

An unusual case of chronic neuropathic pain responds to an optimum frequency of intravenous ketamine infusions.

The effective treatment of patients suffering from a variety of difficult pain syndromes, including phantom pain and other neuropathic pains, remains a clinical challenge. Neuropathic pain has been shown to respond to drugs that block the N-methyl-D-aspartate (NMDA) receptor, such as ketamine and amantidine. A 44-year-old woman with a previous right-sided forequarter amputation presented to the Palliative Medicine Team complaining of neuropathic pain in her left arm, which was neurologically intact. The pain was treated with repeated infusions of intravenous ketamine. Twenty-one infusions were given over a period of four months. The pain intensity experienced by the patient lessened as the frequency of the ketamine infusions increased. This finding has not been described previously and supports the theory that there may be an optimum frequency of ketamine infusions to achieve adequate pain control.

High pressure insulator-metal transition in molecular fluid oxygen.

We report the first experimental evidence for a metallic phase in fluid molecular oxygen. Our electrical conductivity measurements of fluid oxygen under dynamic quasi-isentropic compression show that a nonmetal-metal transition occurs at 3.4 fold compression, 4500 K, and 1.2 Mbar. We discuss the main features of the electrical conductivity dependence on density and temperature and give an interpretation of the nature of the electrical transport mechanisms in fluid oxygen at these extreme conditions.

Fast laser-induced solute release from liposomes sensitized with photochromic lipid: effects of temperature, lipid host, and sensitizer concentration.

Liposomes of gel-phase phospholipid have been prepared containing a photochromic lipid sensitizer. A fast UV laser pulse isomerizes the sensitizer destabilizing the lipid bilayer structure and causing release of trapped solute. The kinetics of solute release have been investigated as a function of host lipid chain length, sensitizer concentration, and temperature, and the limits of liposome stability have been established. At low concentrations of sensitizer, pulsed laser irradiation induces some solute release when continuous UV illumination is ineffective. Although rates of solute release usually increase with temperature, at low sensitizer concentration in a rigid host, leakage at first increases but then decreases rapidly above a threshold temperature. The results presented are relevant to the design of photostimulated drug delivery systems and to potential applications of photosensitive liposomes as caging agents for biological effectors.

Metallization and electrical conductivity of hydrogen in Jupiter.

Electrical conductivities of molecular hydrogen in Jupiter were calculated by scaling electrical conductivities measured at shock pressures in the range of 10 to 180 gigapascals (0.1 to 1.8 megabars) and temperatures to 4000 kelvin, representative of conditions inside Jupiter. Jupiter's magnetic field is caused by convective dynamo motion of electrically conducting fluid hydrogen. The data imply that Jupiter should become metallic at 140 gigapascals in the fluid, and the electrical conductivity in the jovian molecular envelope at pressures up to metallization is about an order of magnitude larger than expected previously. The large magnetic field is produced in the molecular envelope closer to the surface than previously thought.

Fluorescence lifetime imaging: an emerging technique in fluorescence microscopy.

Fluorescence microscopy is an important tool for biological research, in part because of the extremely high detection sensitivity that can be achieved, but also because fluorescent molecules can be used as probes on account of their environmental responsiveness, for example to measure intracellular pH or metal ion concentration. Unfortunately, the environmental sensitivity can sometimes be a source of problems because of enhancement or 'quenching', which can make it very difficult to relate emission intensity to the amount of fluorophore present. The measured intensity is essentially proportional to the product of the amount of fluorophore present in the sample and the local quantum yield of the fluorophore (the quantum yield can be thought of as the probability that an excited molecule decays by fluorescence emission rather than by other non-radiative processes). This is a particular difficulty in an environment such as a cell or tissue slice in which quantum yield and flurophore concentration can both vary within the sample. Ideally we would wish to be able to measure the quantum yield of fluorescence as well as the fluorescence intensity, as this would allow environmental effects to be compensated for. Unfortunately, this is not at all easy, and indirect means to achieve the same goal are more appropriate. A recently introduced technique, fluorescence lifetime imaging (Morgan et al. 1992, Wang et al. 1992), offers one such means to improve quantification of fluorescence microscopy. In addition, as will be explained, the technique offers the prospect of significantly improving detection sensitivity in appropriate circumstances.

Fast solute release from photosensitive liposomes: an alternative to 'caged' reagents for use in biological systems.

The kinetics of release of soluble marker trapped in liposomes of gel phase phospholipid containing a photoisomerisable phospholipid analogue have been investigated. Marker release is triggered by UV laser flash photolysis at 355 nm. A markedly temperature-dependent release rate is seen, and above 25 degrees C millisecond release kinetics can be achieved. These results suggest that such liposomes might find application as an alternative to conventional 'caged' reagents for photo-triggered reagent release in biological research.

Liposome fusion and lipid exchange on ultraviolet irradiation of liposomes containing a photochromic phospholipid.

A photochromic phospholipid, 1,2-bis[4-4(4-n-butylphenylazo) phenylbutyroyl] phosphatidylcholine (Bis-Azo PC) has been incorporated into liposomes of gel- and liquid-crystalline- phase phospholipids. Liposomes of gel-phase phospholipid are stable in the presence of the trans photostationary state Bis-Azo PC and can encapsulate fluorescent marker dye. On photoisomerization to the cis photostationary state, trapped marker is rapidly released. Liposomes containing Bis-Azo PC can rapidly fuse together after UV isomerization, this process continuing in the dark. Exposure to white light causes reversion of Bis-Azo Pc to the trans form and halts dye leakage and vesicle fusion. Both unilamellar and multilamellar liposomes are able to fuse together on UV exposure. On UV photolysis, liposomes containing Bis-Azo PC do not fuse with a large excess of unlabeled liposomes, but transfer of Bis-Azo PC can be demonstrated spectrophotometrically. Vesicles of pure gel-phase lipid containing trapped marker dye but initially no Bis-Azo PC become leaky as a result of this lipid transfer. Liposomes composed of liquid-crystalline-phase phosphatidylcholine- containing Bis-Azo PC neither leak trapped marker no fuse together on photolysis, nor do liquid-crystalline-phase liposomes fuse with gel-phase liposomes under these conditions. These results are discussed together with some possible applications of liposome photodestabilization.