High-resolution screening for marine prokaryotic and eukaryotic taxa with selective preference for PE and PET surfaces

Marine plastic debris serve as substrates for the colonization of a variety of prokaryote and eukaryote organisms. Of particular interest are the microorganisms that have adapted to thrive on plastic as they may contain genes, enzymes or pathways involved in the colonization or metabolism of plastics. We implemented DNA metabarcoding with nanopore MinION sequencing to compare the one-month-old biomes of hydrolysable (polyethylene terephthalate) and non-hydrolysable (polyethylene) plastics surfaces vs. those of glass and the surrounding water in a Mediterranean Sea marina. We sequenced longer 16S rRNA, 18S rRNA and ITS barcode loci for a more comprehensive taxonomic profiling of the bacterial, protist and fungal communities respectively. Long read sequencing enabled high-resolution mapping to genera and species. Using differential abundance screening we identified 32 bacteria and five eukaryotes, that were significantly differentially abundant on PE or PET compared to glass. This approach may be used in the future to characterize the plastisphere communities and to screen for microorganisms with a plastic-metabolism potential.

5-Hydroxymethylcytosine-mediated active demethylation is required for mammalian neuronal differentiation and function

Although high levels of 5-hydroxymethylcytosine (5hmC) accumulate in mammalian neurons, our knowledge of its roles in terminal differentiation or as an intermediate in active DNA demethylation is incomplete. We report high-resolution mapping of DNA methylation and hydroxymethylation, chromatin accessibility, and histone marks in developing postmitotic Purkinje cells (PCs) in Mus musculus. Our data reveal new relationships between PC transcriptional and epigenetic programs, and identify a class of genes that lose both 5-methylcytosine (5mC) and 5hmC during terminal differentiation. Deletion of the 5hmC writers Tet1, Tet2, and Tet3 from postmitotic PCs prevents loss of 5mC and 5hmC in regulatory domains and gene bodies, and hinders transcriptional and epigenetic developmental transitions. Our data demonstrate that Tet-mediated active DNA demethylation occurs in vivo, and that acquisition of the precise molecular properties of adult PCs require continued oxidation of 5mC to 5hmC during the final phases of differentiation.

3D mapping of the submerged Crowie barge using electrical resistivity tomography

This study explores the applicability and effectiveness of electrical resistivity tomography (ERT) as a tool for the high-resolution mapping of submerged and buried shipwrecks in 3D. This approach was trialled through modelling and field studies of Crowie, a paddle steamer barge which sunk at anchor in the Murray River at Morgan, South Australia, in the late 1950s. The mainly metallic structure of the ship is easily recognisable in the ERT data and was mapped in 3D both subaqueously and beneath the sedimentwater interface.The innovative and successful use of ERT in this case study demonstrates that 3D ERT can be used for the detailed mapping of submerged cultural material. It will be particularly useful where other geophysical and diver based mapping techniques may be inappropriate due to shallow water depths, poor visibility, or other constraints.

Spatial Variation in Temperature and Density in the IC 63 PDR from H2 Spectroscopy

We have measured the gas temperature in the IC 63 photodissociation region (PDR) using the S(1) and S(5) pure rotation lines of molecular hydrogen with SOFIA/EXES. We divide the PDR into three regions for analysis based on the illumination from γ Cas: sunny, ridge, and shady. Constructing rotation diagrams for the different regions, we obtain temperatures of T ex = 562 − 43 + 52 K toward the ridge and T ex = 495 − 25 + 28 K in the shady side. The H2 emission was not detected on the sunny side of the ridge, likely due to the photodissociation of H2 in this gas. Our temperature values are lower than the value of T ex = 685 ± 68 K using the S(1), S(3), and S(5) pure rotation lines, derived by Thi et al. using lower spatial resolution ISO-SWS data at a different location of the IC 63 PDR. This difference indicates that the PDR is inhomogeneous and illustrates the need for high-resolution mapping of such regions to fully understand their physics. The detection of a temperature gradient correlated with the extinction into the cloud, points to the ability of using H2 pure rotational line spectroscopy to map the gas temperature on small scales. We used a PDR model to estimate the FUV radiation and corresponding gas densities in IC 63. Our results shows the capability of SOFIA/EXES to resolve and provide detailed information on the temperature in such regions.

Mapping of individual sensory nerve axons from digits to spinal cord with the Transparent Embedding Solvent System

Understanding the connections and projections of neurons has been a fundamental issue for neuroscience. Although strategies have been developed to map the projection of individual axons within the mouse brain, high resolution mapping of individual peripheral nerve axons in peripheral organs or spinal cord has never been achieved. Here, we designed the Transparent Embedding Solvent System (TESOS) method and developed a technical pipeline for imaging, reconstructing and analyzing large samples containing various tissue types at sub-micron resolution. The mouse whole body was reconstructed at micron-scale resolution. We were able to image, reconstruct and analyze the complete axonal projection of individual sensory neurons within an intact mouse paw or spinal cord at sub-micron resolution. Furtherly, we imaged and reconstructed the entire projection course of individual sensory neurons from adult mouse digits to the spinal cord. The TESOS method provides an efficient tool for micron-scale connectome mapping of the peripheral nervous system.