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Karsten, U.

Publications and source records attributed to Karsten, U..

2 recordsLinked to original sources

Discovery of a novel UV-absorbing mycosporine-like amino acid in Vertebrata lanosa using an expanded combinatorial structure database incorporating non-proteinogenic amino acids and organic solutes

Mycosporine-like amino acids (MAAs) are among nature's most effective sunscreen compounds, capable of converting harmful ultraviolet radiation into harmless heat, and are widely distributed in marine organisms such as red macroalgae. Although decades of research have led to numerous discoveries, the rate of new MAA identifications has declined. To address this, we considerably expanded our previously developed combinatorial MAA database, increasing the number of covered structures tenfold. Following a comprehensive literature search for plausible but undescribed building blocks, the database now incorporates an extensive set of proteinogenic and non-proteinogenic amino acids, as well as other marine organic osmolytes, in combination with all (currently) known MAA scaffolds. This expanded resource was integrated into our identification platform, which combines UHPLC-VWD-HRMS2 analysis, feature-based molecular networking, and bioinformatics-driven annotation. Application of this updated workflow enabled the isolation and structural elucidation of a novel MAA, mycosporine-cysteinolic acid, from the red marine macroalga Vertebrata lanosa. Altogether, this study provides a valuable extension of the bioinformatics-based MAA screening pipeline, enhancing the annotation and discovery of novel MAAs in natural matrices.

plant biology↗

New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts

We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hyper-variable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (ca. 350 bp) is suitable for Illumina MiSeq, the most cost-effective platform for molecular environmental surveys. We provide barcoded primers, an economical alternative to multiple libraries for multiplex sequencing of over a hundred samples. In silico, our primers matched 68% of the cercozoan sequences of the reference database and performed better than previously proposed new generation sequencing primers. In mountain grasslands soils and in biological soil crusts from a variety of climatic regions, we were able to detect cercozoan sequences encompassing nearly the whole range of the phylum. We obtained 901 OTUs at 97% similarity threshold from 26 samples, with ca. 50,000 sequences per site, and only 8% of non-cercozoan sequences. We could contribute to a further increase of the diversity of Cercozoa, since only 43% of the OTUs were 97-100% similar to any known sequence. Our study thus provides an advanced tool for cercozoan metabarcoding and to investigate their diversity and distribution in the environment.

bioinformatics↗