The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization

An analysis of the seven genes of the tryptophan pathway in the Sargasso Sea metagenome shows that the majority of contigs and scaffolds contain whole or split operons that are similar to previously analyzed trp gene organizations

Direct Measurements of Island Growth and Step-Edge Barriers in Colloidal Epitaxy

Epitaxial growth, a bottom-up self-assembly process for creating surface nano- and microstructures, has been extensively studied in the context of atoms. This process, however, is also a promising route to self-assembly of nanometer- and micrometer-scale particles into microstructures that have numerous technological applications. To determine whether atomic epitaxial growth laws are applicable to the epitaxy of larger particles with attractive interactions, we investigated the nucleation and growth dynamics of colloidal crystal films with single-particle resolution. We show quantitatively that colloidal epitaxy obeys the same two-dimensional island nucleation and growth laws that govern atomic epitaxy. However, we found that in colloidal epitaxy, step-edge and corner barriers that are responsible for film morphology have a diffusive origin. This diffusive mechanism suggests new routes toward controlling film morphology during epitaxy

Dislocations and Vacancies in Two-Dimensional Mixed Crystals of Spheres and Dimers

In colloidal crystals of spheres, dislocation motion is unrestricted. On the other hand, recent studies of relaxation in crystals of colloidal dimer particles have demonstrated that the dislocation dynamics in such crystals are reminiscent of glassy systems. The observed glassy dynamics arise as a result of dislocation cages formed by certain dimer orientations. In the current study, we use experiments and simulations to investigate the transition that arises when a pure sphere crystal is doped with an increasing concentration of dimers. Specifically, we focus on both dislocation caging and vacancy motion. Interestingly, we find that any nonzero fraction of dimers introduces finite dislocation cages, suggesting that glassy dynamics are present for any mixed crystal. However, we have also identified a vacancy-mediated uncaging mechanism for releasing dislocations from their cages. This mechanism is dependent on vacancy diffusion, which slows by orders of magnitude as the dimer concentration is increased. We propose that in mixed crystals with low dimer concentrations vacancy diffusion is fast enough to uncage dislocations and delay the onset of glassy dislocation dynamics

A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus 'relic' prophage

Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment

Restricted Dislocation Motion in Crystals of Colloidal Dimer Particles

At high area fractions, monolayers of colloidal dimer particles form a degenerate crystal (DC) structure in which the particle lobes occupy triangular lattice sites while the particles are oriented randomly along any of the three lattice directions. We report that dislocation glide in DCs is blocked by certain particle orientations. The mean number of lattice constants between such obstacles is 4.6 +/- 0.2 in experimentally observed DC grains and 6.18 +/- 0.01 in simulated monocrystalline DCs. Dislocation propagation beyond these obstacles is observed to proceed through dislocation reactions. We estimate that the energetic cost of dislocation pair separation via such reactions in an otherwise defect free DC grows linearly with final separation, hinting that the material properties of DCs may be dramatically different from those of 2-D crystals of spheres

Entropy Driven Crystal Formation on Highly Strained Substrates

In heteroepitaxy, lattice mismatch between the deposited material and the underlying surface strongly affects nucleation and growth processes. The effect of mismatch is well studied in atoms with growth kinetics typically dominated by bond formation with interaction lengths on the order of one lattice spacing. In contrast, less is understood about how mismatch affects crystallization of larger particles, such as globular proteins and nanoparticles, where interparticle interaction energies are often comparable to thermal fluctuations and are short ranged, extending only a fraction of the particle size. Here, using colloidal experiments and simulations, we find particles with short-range attractive interactions form crystals on isotropically strained lattices with spacings significantly larger than the interaction length scale. By measuring the free-energy cost of dimer formation on monolayers of increasing uniaxial strain, we show the underlying mismatched substrate mediates an entropy-driven attractive interaction extending well beyond the interaction length scale. Remarkably, because this interaction arises from thermal fluctuations, lowering temperature causes such substrate-mediated attractive crystals to dissolve. Such counterintuitive results underscore the crucial role of entropy in heteroepitaxy in this technologically important regime. Ultimately, this entropic component of lattice mismatched crystal growth could be used to develop unique methods for heterogeneous nucleation and growth of single crystals for applications ranging from protein crystallization to controlling the assembly of nanoparticles into ordered, functional superstructures. In particular, the construction of substrates with spatially modulated strain profiles would exploit this effect to direct self-assembly, whereby nucleation sites and resulting crystal morphology can be controlled directly through modifications of the substrate

Glassy Dislocation Dynamics in 2D Colloidal Dimer Crystals

Although glassy relaxation is typically associated with disorder, here we report on a new type of glassy dynamics relating to dislocations within 2D crystals of colloidal dimers. Previous studies have demonstrated that dislocation motion in dimer crystals is restricted by certain particle orientations. Here, we drag an optically trapped particle through such dimer crystals, creating dislocations. We find a two-stage relaxation response where initially dislocations glide until encountering particles that cage their motion. Subsequent relaxation occurs logarithmically slowly through a second process where dislocations hop between caged configurations. Finally, in simulations of sheared dimer crystals, the dislocation mean squared displacement displays a caging plateau typical of glassy dynamics. Together, these results reveal a novel glassy system within a colloidal crystal

Safety and efficacy of an intra-oral electrostimulator for the relief of dry mouth in patients with chronic graft versus host disease: case Series

Objectives: Patients with chronic graft-versus-host disease (cGVHD) often suffer from dry mouth and oral mu - cosal lesions. The primary objective of this study was to investigate the safety of an intra-oral electrostimulator (GenNarino) in symptomatic cGVHD patients. The secondary objective was to study the impact on the salivary gland involvement of cGVHD patients. Study Design: This paper presents a case series. The study included patients treated for 4 weeks, randomly as - signed to the active device and then crossed-over to a sham-device or vice versa. The patients and clinicians were blind to the treatment delivered. Data regarding oral mucosal and salivary gland involvement were collected. Results: Six patients were included in this series. Most of the intraoral areas with manifestations of cGVHD were not in contact with the GenNarino device. Two patients developed mild mucosal lesions in areas in contact with the GenNarino during the study. However, only one of them had a change in the National Institutes of Health (NIH) score for oral cGVHD. The unstimulated and stimulated salivary flow rate increased in 4 out of the 5 pa - tients included in this analysis. Symptoms of dry mouth and general oral comfort improved. Conclusion: This study suggests that GenNarino is safe in cGVHD patients with respect to oral tissues. Furthermore the use of GenNarino resulted in subjective and objective improvements in dry mouth symptoms. A large scale study is needed to confirm the impact and safety of GenNarino on systemic cGVHD

Archaeal diversity in the Dead Sea: Microbial survival under increasingly harsh conditions

The Dead Sea is rapidly drying out. The lake is supersaturated with NaCl, and precipitated of halite from the water column has led to a decrease in sodium content, while concentrations of magnesium and calcium greatly increased, making the lake an ever more extreme environment for microbial life. In the past decades, blooms of algae (Dunaliella) and halophilic Archaea were twice observed in the lake (1980-1982 and 1992-1995), triggered by massive inflow of freshwater floods, but no conditions suitable for renewed microbial growth have occurred since. To examine whether the Death Sea in its current state (density 1.24 g ml-1, water activity about 0.67) still supports life of halophilic Archaea, we collected particulate matter from a depth of 5 m at an offshore station by means of tangential filtration. Presence of bacterioruberin carotenoids, albeit at low concentrations, in the particulate material showed the members of the Halobactericacae were still present in the lake\u27s water column. Amplification of 16S rRNA genes from the biomass yielded genes with less than 95% identify with environmental sequences reported from other environments and only 85-95% identity with cultivated Halobacteriaceae. It is thus shown that the Dead Sea, in spite of the ever more adverse conditions to life, supports a unique and varied community of halophilic Archaea. We have also isolated a number of strains of Halobacteriaceae from the samples collected, and their characterization is currently in progress