Biology subjects

Janssen, E. M.- L.

Publications and source records attributed to Janssen, E. M.- L..

3 recordsLinked to original sources

bioRxiv2025

A critical assessment of aptamer and CRISPR-Cas12a-based biosensors for small molecule detection

Analyte detection through aptamer-induced signal generation by CRISPR-Cas enzymes has rapidly emerged as a popular biosensing approach. Here, we investigated the implementability and analytical performance of this setup for the detection of diverse small molecule analytes. We selected nine aptamers from the literature targeting seven analytes and tested a commonly used assay design whereby analyte binding by the aptamer liberates a short complementary DNA strand, which in turn activates Cas12a to generate a fluorescence signal. After extensive optimization, the assay functioned for only two of the seven analytes, and several previously reported results could not be reproduced. While Cas12a fluorescence detection was robust, the low success rate is likely due to aptamers not functioning reliably, underscoring the need for careful aptamer validation. Overall, our study provides a critical assessment of aptamer-Cas12a assay performances and discusses potential strengths, limitations, and pitfalls of this biosensing strategy.

biochemistry↗

bioRxiv2020

Comprehensive database of secondary metabolites from cyanobacteria

Cyanobacteria form harmful mass blooms in freshwater and marine environments around the world. A range of secondary metabolites has been identified from cultures of cyanobacteria and biomass collected from cyanobacterial bloom events. A comprehensive database is necessary to correctly identify cyanobacterial metabolites and advance research on their abundance, persistence and toxicity in natural environments. We consolidated open access databases and manually curated missing information from the literature published between 1970 and March 2020. The result is the database CyanoMetDB, which includes more than 2000 entries based on more than 750 literature references. This effort has more than doubled the total number of entries with complete literature metadata and structural composition (SMILES codes) compared to publicly available databases to this date. Over the past decade, more than one hundred additional secondary metabolites have been identified yearly. We organized all entries into structural classes and conducted substructure searches of the provided SMILES codes. This approach demonstrated, for example, that 65% of the compounds carry at least one peptide bond, 57% are cyclic compounds, and 30% carry at least one halogen atom. Structural searches by SMILES code can be further specified to identify structural motifs that are relevant for analytical approaches, research on biosynthetic pathways, bioactivity-guided analysis, or to facilitate predictive science and modeling efforts on cyanobacterial metabolites. This database facilitates rapid identification of cyanobacterial metabolites from toxic blooms, research on the biosynthesis of cyanobacterial natural products, and the identification of novel natural products from cyanobacteria. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/038703v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@3504f7org.highwire.dtl.DTLVardef@d92680org.highwire.dtl.DTLVardef@6ea103org.highwire.dtl.DTLVardef@10cd983_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2016

Magnitude and mechanism of siderophore-mediated competition in bacterial interactions

Whether microbial interactions are predominantly cooperative or competitive is a central question in microbial ecology, and determines the composition and stability of microbial communities. The secretion of iron chelators called siderophores is a model system for cooperative interactions, even though these chelators can also mediate competition by depriving competitors of iron. Using a genetically engineered experimental system based on the Pseudomonas aeruginosa siderophore pyochelin, we found that secreting siderophores to inhibit a competitor can lead to higher benefits than secreting siderophores to make iron available. Based on thermodynamic modeling, we propose that competitive inhibition by siderophores is efficient in kinetically controlled saturated systems, where dissolution of precipitated iron phases is slow. Under these conditions, met in many natural environments, secreted siderophores temporarily reduce the concentration of available iron and can thus induce growth inhibition in a competing strain, even at high iron concentrations. These findings give insight into the function of siderophores: In addition to its cooperative nature, siderophore secretion could also be a widespread mechanism for mediating competitive interactions. Our functional investigation reveals a complexity in microbial interaction networks that would remain hidden when focusing on genomic information alone.

microbiology↗