Structured illumination with coded apertures is an efficient method for collecting high-quality X-ray data while reducing radiation dose. These apertures, fabricated using nano-lithography, exhibit minimal absorption at high energies and introduce significant phase shifts in the illumination for dose efficiency. Unlike traditional holotomography, coded apertures eliminate the need for sample motion along the X-ray beam, reducing acquisition time and alignment errors. They also facilitate rapid convergence of iterative algorithms and enable dynamic experiments previously limited by single-distance measurements. At ID16A, we aim to demonstrate the competitiveness of coded apertures compared to multi-distance acquisition, and explore the possibility of single-distance holotomography. For demonstration, we will focus on high-resolution imaging of fruit fly photoreceptor synapses, a challenging application with conventional methods due to low contrast and alignment issues.

If you use this dataset please cite: Visagie CM, Houbraken J, Overy DP, et al. (2025). From chaos to tranquillity: a modern approach to the identification, nomenclature and phylogeny of Aspergillus, Penicillium and other Eurotiales, including an updated accepted species list. Studies in Mycology 112: 117–260. https://doi.org/10.3114/sim.2025.112.04. Eurotiales is a diverse and speciose order and includes economically important genera like Aspergillus, Penicillium, Paecilomyces and Talaromyces. Historically, species identifications based on morphology are challenging. The publication of accepted species lists and the availability of representative DNA sequences for type strains have contributed greatly towards accurate species identification and facilitated the description of many new species. However, despite current advancements, a proportion of newly described species within these taxonomically challenging genera represent, in fact, existing species, which raises obvious concerns. This study thus aimed to further modernise the taxonomy of Eurotiales by addressing key challenges in species identification and classification. Our study objectives were threefold: to review species described after 2023, update the accepted species list, and release a curated DNA sequence dataset to facilitate future species identifications. We conclude that a move to a phylogenetic species concept is necessary but continue to support the inclusion of morphological descriptions and, where possible, associated secondary metabolite, exoenzyme, physiology and ecological data when introducing new species. Our list now contains 1393 species classified into four families and 26 genera, with Aspergillus (n=465), Penicillium (n=598) and Talaromyces (n=236) containing the most species. To aid sequence-based identifications and species descriptions under a phylogenetic species concept, we release a curated DNA reference sequence database containing 18837 DNA sequences (3867 ITS, 5277 BenA, 5110 CaM and 4583 RPB2) generated from 5325 strains. Sequences were selected to best cover the infraspecies variation under our current understanding of each species. The sequence database will be kept up to date as new information becomes available. This manuscript presents a major leap towards our goal to facilitate work with Eurotiales, while providing the taxonomic framework to support research excellence related to this important fungal group.This dataset is curated and kept up to date by the International Commission of Penicillium and Aspergillus (ICPA). If you have questions or suggestions, please get in contact with ICPA members.

Eurotiales is a diverse and speciose order and includes economically important genera like Aspergillus, Penicillium, Paecilomyces and Talaromyces. Historically, species identifications based on morphology are challenging. The publication of accepted species lists and the availability of representative DNA sequences for type strains have contributed greatly towards accurate species identification and facilitated the description of many new species. However, despite current advancements, a proportion of newly described species within these taxonomically challenging genera represent, in fact, existing species, which raises obvious concerns. This study thus aimed to further modernise the taxonomy of Eurotiales by addressing key challenges in species identification and classification. Our study objectives were threefold: to review species described after 2023, update the accepted species list, and release a curated DNA sequence dataset to facilitate future species identifications. We conclude that a move to a phylogenetic species concept is necessary but continue to support the inclusion of morphological descriptions and, where possible, associated secondary metabolite, exoenzyme, physiology and ecological data when introducing new species. Our list now contains 1393 species classified into four families and 26 genera, with Aspergillus (n=465), Penicillium (n=598) and Talaromyces (n=236) containing the most species. To aid sequence-based identifications and species descriptions under a phylogenetic species concept, we release a curated DNA reference sequence database containing 18837 DNA sequences (3867 ITS, 5277 BenA, 5110 CaM and 4583 RPB2) generated from 5325 strains. Sequences were selected to best cover the infraspecies variation under our current understanding of each species. The sequence database will be kept up to date as new information becomes available. This manuscript presents a major leap towards our goal to facilitate work with Eurotiales, while providing the taxonomic framework to support research excellence related to this important fungal group.This dataset is curated and kept up to date by the International Commission of Penicillium and Aspergillus (ICPA). If you have questions or suggestions, please get in contact with ICPA members.

This dataset includes data from a tracking study, where 48 Atlantic salmon kelts were tagged with acoustic transmitters containing pressure sensors (Lotek MM-M-11-28-PM [76kHz], 12 × 65 mm length; Lotek Wireless Inc., Newmarket, ON, Canada) as well as simulated hydraulic data from computational fluid dynamics modelling. The data was collected in 2016 on the River Orkla, central Norway, just upstream of the Bjørset Dam. The data has been used to understand the swimming behaviours of the tagged kelts in an anthropogenically altered flow field (i.e., the area closest to the dam).  The dataset is an xlsx file with two sheets. The first sheet, "Tracking data", contains the positions and timestamps for each detection of each kelt. The second sheet, "Hydraulic data", contains the streamwise velocity (Vx), transverse velocity (Vy), vertical velocity (Vz), and turbulence kinetic energy (k) for each position. Note, the hydraulic data was simulated under three different operational scenarios, as the operation at the hydropower plant changed over the course of the study period. When 's' = 2, this is the simulated hydraulic data just after the hydropower plant spillway opened (discharge via spillway = 8.0 m3/s), when 's' = 3 this is the discharge when the spillway opens further (22.3 m3/s), and 's' = 4 when it is opened to its furthest extent (38.4 m3/s).Variables in spreadsheetstag: this is the unique ID number for an individual kelttop: this is the timestamp for a given detectionx: this is the kelt's longitudinal position, given in UTMy: this is the kelt's latitudinal position, given in UTMz: this is the kelt's depth, given in metres below the surfacebody_length: this is the kelt's body length, measured upon capture, in mms: this refers to the operational scenario that the hydraulic data was simulated forVx: this is the streamwise velocity, measured in m/sVy: this is the transverse velocity, measured in m/sVz: this is the vertical velocity, measured in m/sk: this is the turbulence kinetic energy, measured in m2/s2

This dataset includes data from a tracking study, where 48 Atlantic salmon kelts were tagged with acoustic transmitters containing pressure sensors (Lotek MM-M-11-28-PM [76kHz], 12 × 65 mm length; Lotek Wireless Inc., Newmarket, ON, Canada) as well as simulated hydraulic data from computational fluid dynamics modelling. The data was collected in 2016 on the River Orkla, central Norway, just upstream of the Bjørset Dam. The data has been used to understand the swimming behaviours of the tagged kelts in an anthropogenically altered flow field (i.e., the area closest to the dam).  The dataset is an xlsx file with two sheets. The first sheet, "Tracking data", contains the positions and timestamps for each detection of each kelt. The second sheet, "Hydraulic data", contains the streamwise velocity (Vx), transverse velocity (Vy), vertical velocity (Vz), and turbulence kinetic energy (k) for each position. Note, the hydraulic data was simulated under three different operational scenarios, as the operation at the hydropower plant changed over the course of the study period. When 's' = 2, this is the simulated hydraulic data just after the hydropower plant spillway opened (discharge via spillway = 8.0 m3/s), when 's' = 3 this is the discharge when the spillway opens further (22.3 m3/s), and 's' = 4 when it is opened to its furthest extent (38.4 m3/s).Variables in spreadsheetstag: this is the unique ID number for an individual kelttop: this is the timestamp for a given detectionx: this is the kelt's longitudinal position, given in UTMy: this is the kelt's latitudinal position, given in UTMz: this is the kelt's depth, given in metres below the surfacebody_length: this is the kelt's body length, measured upon capture, in mms: this refers to the operational scenario that the hydraulic data was simulated forVx: this is the streamwise velocity, measured in m/sVy: this is the transverse velocity, measured in m/sVz: this is the vertical velocity, measured in m/sk: this is the turbulence kinetic energy, measured in m2/s2

Amyloids, classically linked to neurodegenerative diseases, also play critical roles in infection and immunity. Phenol-soluble modulins (PSMs) from Staphylococcus aureus are virulent amyloids that contribute to cytotoxicity, immune modulation, and biofilm stability. PSMα3 forms cross-α amyloid fibrils and shares sequence and structural features with LL-37, a human host-defense peptide that assembles into α-helical structures. Here, we uncover RNA as a potent, context-dependent modulator of their aggregation and activity. RNA consistently reduces LL-37’s cytotoxicity toward human cells without compromising its antibacterial function, suggesting a selective host-protective mechanism. In contrast, RNA preserves PSMα3’s cytotoxic and antimicrobial activity over time, likely by promoting liquid–liquid phase separation (LLPS) and stabilizing bioactive fibrillar polymorphs, enabling S. aureus to fine-tune its virulence strategies. At higher concentrations, RNA drives both peptides toward distinct aggregated states, amorphous for LL-37 and fibrillar for PSMα3, underlying their divergent functional outcomes. The amyloid inhibitor EGCG abolishes the bioactivity of both PSMα3 and LL-37, overriding RNA’s modulatory effects. Together, our findings establish RNA as a key modulator of both virulent amyloids and host-defense peptides, with broad implications for microbial immune evasion, innate immunity, and amyloid-associated diseases. Moreover, they highlight phase transitions as a tunable mechanism for regulating peptide bioactivity and a promising therapeutic target across infectious and neurodegenerative conditions.

Amyloids, classically linked to neurodegenerative diseases, also play critical roles in infection and immunity. Phenol-soluble modulins (PSMs) from Staphylococcus aureus are virulent amyloids that contribute to cytotoxicity, immune modulation, and biofilm stability. PSMα3 forms cross-α amyloid fibrils and shares sequence and structural features with LL-37, a human host-defense peptide that assembles into α-helical structures. Here, we uncover RNA as a potent, context-dependent modulator of their aggregation and activity. RNA consistently reduces LL-37’s cytotoxicity toward human cells without compromising its antibacterial function, suggesting a selective host-protective mechanism. In contrast, RNA preserves PSMα3’s cytotoxic and antimicrobial activity over time, likely by promoting liquid–liquid phase separation (LLPS) and stabilizing bioactive fibrillar polymorphs, enabling S. aureus to fine-tune its virulence strategies. At higher concentrations, RNA drives both peptides toward distinct aggregated states, amorphous for LL-37 and fibrillar for PSMα3, underlying their divergent functional outcomes. The amyloid inhibitor EGCG abolishes the bioactivity of both PSMα3 and LL-37, overriding RNA’s modulatory effects. Together, our findings establish RNA as a key modulator of both virulent amyloids and host-defense peptides, with broad implications for microbial immune evasion, innate immunity, and amyloid-associated diseases. Moreover, they highlight phase transitions as a tunable mechanism for regulating peptide bioactivity and a promising therapeutic target across infectious and neurodegenerative conditions.

Amyloids, classically linked to neurodegenerative diseases, also play critical roles in infection and immunity. Phenol-soluble modulins (PSMs) from Staphylococcus aureus are virulent amyloids that contribute to cytotoxicity, immune modulation, and biofilm stability. PSMα3 forms cross-α amyloid fibrils and shares sequence and structural features with LL-37, a human host-defense peptide that assembles into α-helical structures. Here, we uncover RNA as a potent, context-dependent modulator of their aggregation and activity. RNA consistently reduces LL-37’s cytotoxicity toward human cells without compromising its antibacterial function, suggesting a selective host-protective mechanism. In contrast, RNA preserves PSMα3’s cytotoxic and antimicrobial activity over time, likely by promoting liquid–liquid phase separation (LLPS) and stabilizing bioactive fibrillar polymorphs, enabling S. aureus to fine-tune its virulence strategies. At higher concentrations, RNA drives both peptides toward distinct aggregated states, amorphous for LL-37 and fibrillar for PSMα3, underlying their divergent functional outcomes. The amyloid inhibitor EGCG abolishes the bioactivity of both PSMα3 and LL-37, overriding RNA’s modulatory effects. Together, our findings establish RNA as a key modulator of both virulent amyloids and host-defense peptides, with broad implications for microbial immune evasion, innate immunity, and amyloid-associated diseases. Moreover, they highlight phase transitions as a tunable mechanism for regulating peptide bioactivity and a promising therapeutic target across infectious and neurodegenerative conditions.

Additional data and code for paper on Comparative genomic assessment of the Cupriavidus necator species for one-carbon based biomanufacturing

Additional data and code for paper on Comparative genomic assessment of the Cupriavidus necator species for one-carbon based biomanufacturing