543 research outputs found
Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets
Marine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling coverage and application of methods (e.g. phylogenetic trees) that are not well suited to identify relatively recent divergence and ongoing gene flow. In this paper, we show how these issues can be overcome by inferring phylogenetic haplotype networks from global metabarcoding datasets. We use the Chaetoceros curvisetus (Bacillariophyta) species complex as study case. Using two complementary metabarcoding datasets (Ocean Sampling Day and Tara Oceans), we equally resolve the cryptic complex in terms of number of inferred species. We detect new hypothetical species in both datasets. Gene flow between most of species is absent, but no barcoding gap exists. Some species have restricted distribution patterns whereas others are widely distributed. Closely related taxa occupy contrasting biogeographic regions, suggesting that geographic and ecological differentiation drive speciation. In conclusion, we show the potential of the analysis of metabarcoding data with evolutionary approaches for systematic and phylogeographic studies of marine protists
Aberrant DNA methylation and expression of SPDEF and FOXA2 in airway epithelium of patients with COPD
Background: Goblet cell metaplasia, a common feature of chronic obstructive pulmonary disease (COPD), is associated with mucus hypersecretion which contributes to the morbidity and mortality among patients. Transcription factors SAM-pointed domain-containing Ets-like factor (SPDEF) and forkhead box protein A2 (FOXA2) regulate goblet cell differentiation. This study aimed to (1) investigate DNA methylation and expression of SPDEF and FOXA2 during goblet cell differentiation and (2) compare this in airway epithelial cells from patients with COPD and controls during mucociliary differentiation. Methods: To assess DNA methylation and expression of SPDEF and FOXA2 during goblet cell differentiation, primary airway epithelial cells, isolated from trachea (non-COPD controls) and bronchial tissue (patients with COPD), were differentiated by culture at the air-liquid interface (ALI) in the presence of cytokine interleukin (IL)-13 to promote goblet cell differentiation. Results: We found that SPDEF expression was induced during goblet cell differentiation, while FOXA2 expression was decreased. Importantly, CpG number 8 in the SPDEF promoter was hypermethylated upon differentiation, whereas DNA methylation of FOXA2 promoter was not changed. In the absence of IL-13, COPD-derived ALI-cultured cells displayed higher SPDEF expression than control-derived ALI cultures, whereas no difference was found for FOXA2 expression. This was accompanied with hypomethylation of CpG number 6 in the SPDEF promoter and also hypomethylation of CpG numbers 10 and 11 in the FOXA2 promoter. Conclusions: These findings suggest that aberrant DNA methylation of SPDEF and FOXA2 is one of the factors underlying mucus hypersecretion in COPD, opening new avenues for epigenetic-based inhibition of mucus hypersecretion
A Comparison of Three Different Bioinformatics Analyses of the 16S–23S rRNA Encoding Region for Bacterial Identification
Rapid and reliable identification of bacterial pathogens directly from patient samples is required for optimizing antimicrobial therapy. Although Sanger sequencing of the 16S ribosomal RNA (rRNA) gene is used as a molecular method, species identification and discrimination is not always achievable for bacteria as their 16S rRNA genes have sometimes high sequence homology. Recently, next generation sequencing (NGS) of the 16S–23S rRNA encoding region has been proposed for reliable identification of pathogens directly from patient samples. However, data analysis is laborious and time-consuming and a database for the complete 16S–23S rRNA encoding region is not available. Therefore, a better, faster, and stronger approach is needed for NGS data analysis of the 16S–23S rRNA encoding region. We compared speed and diagnostic accuracy of different data analysis approaches: de novo assembly followed by Basic Local Alignment Search Tool (BLAST), operational taxonomic unit (OTU) clustering, or mapping using an in-house developed 16S–23S rRNA encoding region database for the identification of bacterial species. De novo assembly followed by BLAST using the in-house database was superior to the other methods, resulting in the shortest turnaround time (2 h and 5 min), approximately 2 h less than OTU clustering and 4.5 h less than mapping, and a sensitivity of 80%. Mapping was the slowest and most laborious data analysis approach with a sensitivity of 60%, whereas OTU clustering was the least laborious approach with 70% sensitivity. Although the in-house database requires more sequence entries to improve the sensitivity, the combination of de novo assembly and BLAST currently appears to be the optimal approach for data analysis
Optimized Trigger for Ultra-High-Energy Cosmic-Ray and Neutrino Observations with the Low Frequency Radio Array
When an ultra-high energy neutrino or cosmic ray strikes the Lunar surface a
radio-frequency pulse is emitted. We plan to use the LOFAR radio telescope to
detect these pulses. In this work we propose an efficient trigger
implementation for LOFAR optimized for the observation of short radio pulses.Comment: Submitted to Nuclear Instruments and Methods in Physics Research
Section
Transcriptional profiling of macaque microglia reveals an evolutionary preserved gene expression program
Microglia are tissue-resident macrophages of the central nervous system (CNS), and important for CNS development and homeostasis. In the adult CNS, microglia monitor environmental changes and react to tissue damage, cellular debris, and pathogens. Here, we present a gene expression profile of purified microglia isolated from the rhesus macaque, a non-human primate, that consists of 666 transcripts. The macaque microglia transcriptome was intersected with the transcriptional programs of microglia from mouse, zebrafish, and human CNS tissues, to determine (dis)similarities. This revealed an extensive overlap of 342 genes between the transcriptional profile of macaque and human microglia, and showed that the gene expression profile of zebrafish is most distant when compared to other species. Furthermore, an evolutionair core based on the overlapping gene expression signature from all four species was identified. This study presents a macaque microglia transcriptomics profile, and identifies a gene expression program in microglia that is preserved across species, underscoring their CNS-tailored tissue macrophage functions as innate immune cells with CNS-surveilling properties
Radial decoupling of small and large dust grains in the transitional disk RX J1615.3-3255
We present H-band (1.6 {\mu}m) scattered light observations of the
transitional disk RX J1615.3-3255, located in the ~1 Myr old Lupus association.
From a polarized intensity image, taken with the HiCIAO instrument of the
Subaru Telescope, we deduce the position angle and the inclination angle of the
disk. The disk is found to extend out to 68 12 AU in scattered light and
no clear structure is observed. Our inner working angle of 24 AU does not allow
us to detect a central decrease in intensity similar to that seen at 30 AU in
the 880 {\mu}m continuum observations. We compare the observations with
multiple disk models based on the Spectral Energy Distribution (SED) and submm
interferometry and find that an inner rim of the outer disk at 30 AU containing
small silicate grains produces a polarized intensity signal which is an order
of magnitude larger than observed. We show that a model in which the small dust
grains extend smoothly into the cavity found for large grains is closer to the
actual H-band observations. A comparison of models with different dust size
distributions suggests that the dust in the disk might have undergone
significant processing compared to the interstellar medium.Comment: 8 pages, 7 figures, 4 tables. Accepted for publication in A&
- …