Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra.

Background: The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the 'benthic associated clade' of the order Syngnathiformes. The 'benthic associated clade' so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in 'long-snouted' syngnatiformes such as seahorses and pipefishes. Findings: Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies' long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp and a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.7%. Conclusions: The chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.

Time Dependence of Fluoride Uptake in Hydroxyapatite.

Fluoridation of enamel is believed to provide an effective tool to protect teeth from caries, but there is still little information on the time scale of fluoride uptake. In this study, highly compressed pellets of hydroxyapatite are used as first-order model systems to approximate the mineral component of natural enamel for investigations on the time-dependence of fluoride uptake. We found that both the overall amount of fluoride as well as the mean thickness of the fluoridated surface layer cannot be extended to any values just by increasing the application time of a fluoride containing agent. Instead, both parameters start to become constant on a time scale of about 3 min. The present results as obtained on a synthetic model "tooth" show that the time scale to provide the maximum amount of fluoride possible is of the same order of magnitude as that in usual daily practice in dental care when applying toothpastes or mouth rinses.

Synthesis of Hydroxyapatite Substrates: Bridging the Gap between Model Surfaces and Enamel.

Hydroxyapatite substrates are common biomaterials, yet samples of natural teeth do not meet the demands for well-defined, highly reproducible properties. Pellets of hydroxyapatite were produced via the field assisted sintering technology (FAST) as well as via pressureless sintering (PLS). The applied synthesis routes provide samples of very high density (95%-99% of the crystallographic density) and of very low surface roughness (lower than 1 nm when averaged per 1 µm2). The chemical composition of the raw material (commercial HAP powder) as well as the crystalline structure is maintained by the sintering processes. These specimens can therefore be considered as promising model surfaces for studies on the interactions of biomaterial with surfaces of biological relevance, as demonstrated for the adsorption of BSA proteins.

Reduced adhesion of oral bacteria on hydroxyapatite by fluoride treatment.

The mechanisms of action of fluoride have been discussed controversially for decades. The cavity-preventive effect for teeth is often traced back to effects on demineralization. However, an effect on bacterial adhesion was indicated by indirect macroscopic studies. To characterize adhesion on fluoridated samples on a single bacterial level, we used force spectroscopy with bacterial probes to measure adhesion forces directly. We tested the adhesion of Streptococcus mutans , Streptococcus oralis , and Staphylococcus carnosus on smooth, high-density hydroxyapatite surfaces, pristine and after treatment with fluoride solution. All bacteria species exhibit lower adhesion forces after fluoride treatment of the surfaces. These findings suggest that the decrease of adhesion properties is a further key factor for the cariostatic effect of fluoride besides the decrease of demineralization.

Nanosurgery of cells and chromosomes using near-infrared twelve-femtosecond laser pulses.

ABSTRACT. Laser-assisted surgery based on multiphoton absorption of near-infrared laser light has great potential for high precision surgery at various depths within the cells and tissues. Clinical applications include refractive surgery (fs-LASIK). The non-contact laser method also supports contamination-free cell nanosurgery. In this paper we describe usage of an ultrashort femtosecond laser scanning microscope for sub-100 nm surgery of human cells and metaphase chromosomes. A mode-locked 85 MHz Ti:Sapphire laser with an M-shaped ultrabroad band spectrum (maxima: 770 nm/830 nm) and an in situ pulse duration at the target ranging from 12 fs up to 3 ps was employed. The effects of laser nanoprocessing in cells and chromosomes have been quantified by atomic force microscopy. These studies demonstrate the potential of extreme ultrashort femtosecond laser pulses at low mean milliwatt powers for sub-100 nm surgery of cells and cellular organelles.

Elemental depth profiling of fluoridated hydroxyapatite: saving your dentition by the skin of your teeth?

Structural and chemical changes that arise from fluoridation of hydroxyapatite (Ca(5)(PO(4))(3)OH or "HAp"), as representing the synthetic counterpart of tooth enamel, are investigated by X-ray photoelectron spectroscopy (XPS). Elemental depth profiles with a depth resolution on the nanometer scale were determined to reveal the effect of fluoridation in neutral (pH = 6.2) and acidic agents (pH = 4.2). With respect to the chemical composition and the crystal structure, XPS depth profiling reveals different effects of the two treatments. In both cases, however, the fluoridation affects the surface only on the nanometer scale, which is in contrast to recent literature with respect to XPS analysis on dental fluoridation, where depth profiles of F extending to several micrometers were reported. In addition to the elemental depth profiles, as published in various other studies, we also present quantitative depth profiles of the compounds CaF(2), Ca(OH)(2), and fluorapatite (FAp) that were recently proposed by a three-layer model concerning the fluoridation of HAp in an acidic agent. The analysis of our experimental data exactly reproduces the structural order of this model, however, on a scale that differs by nearly 2 orders of magnitude from previous predictions. The results also reveal that the amount of Ca(OH)(2) and FAp is small compared to that of CaF(2). Therefore, it has to be asked whether such narrow Ca(OH)(2) and FAp layers really can act as protective layers for the enamel.