Multiphase imaging of freezing particle suspensions by confocal microscopy

Ice-templating is a well-established processing route for porous ceramics. Because of the structure/properties relationships, it is essential to better understand and control the solidification microstructures. Ice-templating is based on the segregation and concentration of particles by growing ice crystals. What we understand so far of the process is based on either observations by optical or X-ray imaging techniques, or on the characterization of ice-templated materials. However, in situ observations at particle-scale are still missing. Here we show that confocal microscopy can provide multiphase imaging of ice growth and the segregation and organization of particles. We illustrate the benefits of our approach with the observation of particles and pore ice in the frozen structure, the dynamic evolution of the freeze front morphology, and the impact of PVA addition on the solidification microstructures. These results prove in particular the importance of controlling both the temperature gradient and the growth rate during ice-templating.Comment: 20 pages, 9 figure

Initiator tRNA genes template the 3\u27 CCA end at high frequencies in bacteria.

BACKGROUND: While the CCA sequence at the mature 3\u27 end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically. RESULTS: In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0.8. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes template CCA at the highest average frequency (74.1%) over all functional classes except selenocysteine and pyrrolysine tRNA genes (88.1% and 100% respectively). Across bacterial phyla and a wide range of genome sizes, many lineages exist in which predominantly initiator tRNA genes template CCA. Convergent and parallel retention of CCA templating in initiator tRNA genes evolved in independent histories of reductive genome evolution in Bacteria. Also, in a majority of cyanobacterial and actinobacterial genera, predominantly initiator tRNA genes template CCA. We also found that a surprising fraction of archaeal tRNA genes template CCA. CONCLUSIONS: We suggest that cotranscriptional synthesis of initiator tRNA CCA 3\u27 ends can complement inefficient processing of initiator tRNA precursors, bootstrap rapid initiation of protein synthesis from a non-growing state, or contribute to an increase in cellular growth rates by reducing overheads of mass and energy to maintain nonfunctional tRNA precursor pools. More generally, CCA templating in structurally non-conforming tRNA genes can afford cells robustness and greater plasticity to respond rapidly to environmental changes and stimuli

Joint UK Land Environment Simulator (JULES) Version 2.2 User Manual

The Joint UK Land Environment Simulator (JULES) is a computer model that simulates many soil and vegetation processes. This document describes how to run version 2.2 of JULES. It primarily describes the format of the input and output files, and does not include detailed descriptions of the science and representation of the processes in the model. The first version of JULES was based on the Met Office Surface Exchange System (MOSES), the land surface model used in the Unified Model (UM) of the UK Met Office. After that initial split, the MOSES and JULES code bases evolved separately, but with JULES2.1 these differences were reconciled, so that all versions since v2.1 have had identical code in both the standalone version (as described here) and in the UM

Dewetting of thin films on heterogeneous substrates: Pinning vs. coarsening

We study a model for a thin liquid film dewetting from a periodic heterogeneous substrate (template). The amplitude and periodicity of a striped template heterogeneity necessary to obtain a stable periodic stripe pattern, i.e. pinning, are computed. This requires a stabilization of the longitudinal and transversal modes driving the typical coarsening dynamics during dewetting of a thin film on a homogeneous substrate. If the heterogeneity has a larger spatial period than the critical dewetting mode, weak heterogeneities are sufficient for pinning. A large region of coexistence between coarsening dynamics and pinning is found.Comment: 4 pages, 4 figure

The Microscopic Structure of Adsorbed Water on Hydrophobic Surfaces under Ambient Conditions

The interaction of water vapor with hydrophobic surfaces is poorly understood. We utilize graphene templating to preserve and visualize the microscopic structures of adsorbed water on hydrophobic surfaces. Three well-defined surfaces [H–Si(111), graphite, and functionalized mica] were investigated, and water was found to adsorb as nanodroplets (~10–100 nm in size) on all three surfaces under ambient conditions. The adsorbed nanodroplets were closely associated with atomic-scale surface defects and step-edges and wetted all the hydrophobic substrates with contact angles < ~10°, resulting in total water adsorption that was similar to what is found for hydrophilic surfaces. These results point to the significant differences between surface processes at the atomic/nanometer scales and in the macroscopic world

Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase

Non homologous end-joining (NHEJ)-mediated repair of DNA double-strand breaks in prokaryotes requires Ku and a specific multidomain DNA ligase (LigD). We present crystal structures of the primase/polymerisation domain (PolDom) of Mycobacterium tuberculosis LigD, alone and complexed with nucleotides. The PolDom structure combines the general fold of the archaeo-eukaryotic primase (AEP) superfamily with additional loops and domains that together form a deep cleft on the surface, likely used for DNA binding. Enzymatic analysis indicates that the PolDom of LigD, even in the absence of accessory domains and Ku proteins, has the potential to recognise DNA end-joining intermediates. Strikingly, one of the main signals for the specific and efficient binding of PolDom to DNA is the presence of a 5'-phosphate group, located at the single/double-stranded junction at both gapped and 3'-protruding DNA molecules. Although structurally unrelated, Pol lambda and Pol mu, the two eukaryotic DNA polymerases involved in NHEJ, are endowed with a similar capacity to bind a 5'-phosphate group. Other properties that are beneficial for NHEJ, such as the ability to generate template distortions and realignments of the primer, displayed by Pol lambda and Pol mu, are shared by the PolDom of bacterial LigD. In addition, PolDom can perform non-mutagenic translesion synthesis on termini containing modified bases. Significantly, ribonucleotide insertion appears to be a recurrent theme associated with NHEJ, maximised in this case by the deployment of a dedicated primase, although its in vivo relevance is unknown