Pretty in pink? Complementary strategies for analysing pink biofilms on historical buildings.

Salt-weathering is a deterioration mechanism affecting building materials that results from repetitive cycles of salt crystallisation-dissolution in the porous mineral network under changing environmental conditions, causing damage to surfaces. However, an additional biodeterioration phenomenon frequently associated with salt efflorescence is the appearance of coloured biofilms, comprising halotolerant/halophilic microorganisms, containing carotenoid pigments that cause pinkish patinas. In this work, two Austrian historical salt-weathered buildings showing pink biofilms, the St. Virgil's Chapel and the Charterhouse Mauerbach, were investigated. Substrate chemistry (salt concentration/composition) was analysed by ion chromatography and X-ray diffraction to correlate these parameters with the associated microorganisms. Microbiomes were analysed by sequencing full-length 16S rRNA amplicons using Nanopore technology. Data demonstrates that microbiomes are not only influenced by salt concentration, but also by its chemical composition. The chapel showed a high overall halite (NaCl) concentration, but the factor influencing the microbiome was the presence/absence of K+. The K+ areas showed a dominance of Aliifodinibius and Salinisphaera species, capable of tolerating high salt concentrations through the "salt-in" strategy by transporting K+ into cells. Conversely, areas without K+ showed a community shift towards Halomonas species, which favour the synthesis of compatible solutes for salt tolerance. In the charterhouse, the main salts were sulphates. In areas with low concentrations, Rubrobacter species dominated, while in areas with high concentrations, Haloechinothrix species did. Among archaea, Haloccoccus species were dominant in all samples, except at high sulphate concentrations, where Halalkalicoccus prevailed. Finally, the biological pigments visible in both buildings were analysed by Raman spectroscopy, showing the same spectra in all areas investigated, regardless of the building and the microbiomes, demonstrating the presence of carotenoids in the pink biofilms. Comprehensive information on the factors affecting the microbiome associated with salt-weathered buildings should provide the basis for selecting the most appropriate desalination treatment to remove both salt efflorescence and associated biofilms.

Optimizing cultivation conditions for the highest expression of fungal allergens.

BACKGROUND: Any reliable allergy diagnosis depends on the quality of the testing material. In the case of fungal allergy, fungal extracts, typically used as test solutions, exhibit considerable differences in their allergenicity. Better knowledge of fungal allergen expression would enable the production of diagnostic fungal extracts of higher quality and, thus, improve the specificity and sensitivity of fungal allergy diagnosis. OBJECTIVE: Our study aimed to find optimal cultivation conditions for the highest expression of fungal allergens. METHODS: Fungal species (Alternaria alternata, Ulocladium chartarum, Aspergillus fumigatus, Cladosporium herbarum, and Paecilomyces variotii) were cultivated under different conditions, and extracts were prepared from fungal material. To detect the expression of the homologous major allergens Alt a 1 and Ulo c 1 and of different fungal enolases, Western blots with allergen-specific antibodies were carried out. RESULTS: Western blots performed with antibodies directed against Alt a 1 and enolases showed that the expression of fungal allergens is highly species-dependent. Even allergens of closely related fungal species and highly conserved, cross-reactive allergens display different expression patterns. CONCLUSION: This study exhibits the impact of different environmental conditions on the expression of the fungal allergens Alt a 1, Ulo c 1, and different fungal enolases. Furthermore, it broadens the knowledge regarding the expression pattern of the major fungal allergens Alt a 1 and Ulo c 1. Information obtained in this study will help to optimize fungal cultivation to produce diagnostic fungal extracts of high quality and, therefore, improve diagnostic specificity and sensitivity.

Shockwaves Increase In Vitro Resilience of Rhizopus oryzae Biofilm under Amphotericin B Treatment.

Acoustical biophysical therapies, including ultrasound, radial pressure waves, and shockwaves, have been shown to harbor both a destructive and regenerative potential depending on physical treatment parameters. Despite the clinical relevance of fungal biofilms, little work exits comparing the efficacy of these modalities on the destruction of fungal biofilms. This study evaluates the impact of acoustical low-frequency ultrasound, radial pressure waves, and shockwaves on the viability and proliferation of in vitro Rhizopus oryzae biofilm under Amphotericin B induced apoptosis. In addition, the impact of a fibrin substrate in comparison with a traditional polystyrene well-plate one is explored. We found consistent, mechanically promoted increased Amphotericin B efficacy when treating the biofilm in conjunction with low frequency ultrasound and radial pressure waves. In contrast, shockwave induced effects of mechanotransduction results in a stronger resilience of the biofilm, which was evident by a marked increase in cellular viability, and was not observed in the other types of acoustical pressure waves. Our findings suggest that fungal biofilms not only provide another model for mechanistical investigations of the regenerative properties of shockwave therapies, but warrant future investigations into the clinical viability of the therapy.

Data Fusion Approach to Simultaneously Evaluate the Degradation Process Caused by Ozone and Humidity on Modern Paint Materials.

The knowledge of the atmospheric degradation reactions affecting the stability of modern materials is still of current interest. In fact, environmental parameters, such as relative humidity (RH), temperature, and pollutant agents, often fluctuate due to natural or anthropogenic climatic changes. This study focuses on evaluating analytical and statistical strategies to investigate the degradation processes of acrylic and styrene-acrylic paints after exposure to ozone (O3) and RH. A first comparison of FTIR and Py-GC/MS results allowed to obtain qualitative information on the degradation products and the influence of the pigments on the paints' stability. The combination of these results represents a significant potential for the use of data fusion methods. Specifically, the datasets obtained by FTIR and Py-GC/MS were combined using a low-level data fusion approach and subsequently processed by principal component analysis (PCA). It allowed to evaluate the different chemical impact of the variables for the characterization of unaged and aged samples, understanding which paint is more prone to ozone degradation, and which aging variables most compromise their stability. The advantage of this method consists in simultaneously evaluating all the FTIR and Py-GC/MS variables and describing common degradation patterns. From these combined results, specific information was obtained for further suitable conservation practices for modern and contemporary painted films.

Multi-Analytical Investigations of Andy Warhol's "Orange Car Crash": Polymeric Materials in Modern Paints.

This work presents strategic multi-analytical investigations performed on "Orange Car Crash" by Andy Warhol in order to make a well-informed conservation decision. For determining the type of binding medium used in the artwork, Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS) and Thermally Assisted Hydrolysis and Methylation of GC/MS (THM-GC/MS) were employed. The presence of a coating was investigated by Py-GC/MS. Moreover, the comprehension and elucidation of the paint stratigraphy were studied by examining cross-sections of samples taken from both canvases with Optical Microscopy (OM) under reflected visible (Vis) and ultraviolet light (UV) and by Scanning Electron Microscopy with Energy Dispersive X-ray spectroscopy (SEM-EDX). The investigation of possible synthetic organic pigments (SOPs) and extenders was performed by µ-Raman spectroscopy, while micro-Attenuated Total Reflection of Fourier-Transform Attenuated Total Reflection (µ-ATR-FTIR) allowed us to assign each component detected by Py-GC/MS or THM-GC/MS to a specific layer. The data collected from "Orange Car Crash" show mostly the application of acrylic-based paint as well as alkyd with rosin acids-based ink, thus providing fundamental information about the paint stratigraphy and chemical composition of each layer. In addition to the goal of informing an appropriate conservation-restoration strategy, this work represents a rare scientific study of a work by Andy Warhol.

A Multi-Analytical Approach for Studying the Effect of New LED Lighting Systems on Modern Paints: Chemical Stability Investigations.

This study aims to investigate the chemical stability of some modern paint samples exposed to a new Light Emitting Diode (LED)-lighting system and a halogen lamp by using micro-attenuated total reflectance of Fourier transform infrared spectroscopy (µ-ATR-FTIR), µ-Raman, pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), and thermally assisted hydrolysis and methylation of GC/MS (THM-GC/MS). Those investigations were performed before and after the exposure of the samples to lightings for 1250, 2400, 3300, and 5000 h. The results obtained with µ-Raman spectroscopy show the high stability of the selected inorganic pigments after the exposure to the lighting systems; while similar to the UV/Vis/NIR results reported in a previous study, µ-ATR-FTIR and THM-GC/MS results evidence greater chemical changes occurring principally on the linseed oil binder-based mock-ups among the acrylic and alkyd-based samples. Moreover, principal component analyses (PCA) and hierarchical cluster analyses (HCA) of THM-GC/MS results highlight that those changes were mostly dependent on the exposure time and on the type of pigment, while being independent of the lighting system used. Finally, semi-quantitative µ-ATR-FTIR results show slight pigment enrichment at the paint surface due to the auto and photo-oxidative degradation of the linseed oil binder.

The effect of new LED lighting systems on the colour of modern paints.

This research focuses on the investigation of the effect of a new light emitting diode (LED)-lighting system which reproduces indoor museum conditions, on some self-made art paint colours (acrylic-, alkyd-, and linseed oil-based paints) often used in modern-contemporary art. A halogen lamp representing a traditional light source for museum lighting was also considered. Lighting-set-up and lighting optimization parameters were considered while Ultraviolet/Visible/Near Infrared (UV/Vis/NIR) spectrophotometry was used for investigating the colour change of the paint samples. Univariate analyses allowed determining the highest effect of the lighting systems on the linseed oil binder and ultramarine blue PB29 mixture upon ageing, according to the highest total colour change ΔE*ab. In a more specific and detailed way, variance analyses not only demonstrated the strong correlation between the type of binder and pigment used for the paint samples with the colour variation, but also showed that the short-wavelength blue LEDs influenced the change along the yellow-blue b* axis of the yellow and blue samples, whereas the halogen lamp mostly had an impact towards the red-green a* axis of mostly the green specimens.

What about Phenol Formaldehyde (PF) Foam in Modern-Contemporary Art? Insights into the Unaged and Naturally Aged Material by a Multi-Analytical Approach.

The ageing behavior of phenol formaldehyde (PF) foam, a material increasingly used in modern-contemporary art, was investigated by a multi-analytical approach. PF foams with open- and closed-cell structures were selected and analyzed in their unaged and naturally indoor-aged state by employing optical microscopy (OM) and fiber optical reflectance spectroscopy (FORS) for assessing their morphology and color alteration. Micro-Fourier transform infrared spectroscopy (µ-FTIR) was used for determining chemical changes and oxidation processes, and the acidity was monitored by pH measurements. The results clearly showed the extreme sensitivity of both open- and closed-cell PF foams to conditions typically found in indoor museums. OM indicated that the cells of the foams are prone to disrupt, and a tendency towards a red color shift was observed with FORS. µ-FTIR revealed the formation of quinone groups resulting from oxidation reactions. Finally, a slight decrease in the acidity was found by pH measurements.

Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos.

Black fungi are a group of melanotic microfungi characterized by remarkable polyextremotolerance. Due to a broad ecological plasticity and adaptations at the cellular level, it is predicted that they may survive in a variety of extreme environments, including harsh niches on Earth and Mars, and in outer space. However, the molecular mechanisms aiding survival, especially in space, are yet to be fully elucidated. Based on these premises, the rock-inhabiting black fungus Knufia chersonesos (Wt) and its non-melanized mutant (Mut) were exposed to simulated microgravity-one of the prevalent features characterizing space conditions-by growing the cultures in high-aspect-ratio vessels (HARVs). Qualitative and quantitative proteomic analyses were performed on the mycelia and supernatant of culture medium (secretome) to assess alterations in cell physiology in response to low-shear simulated microgravity (LSSMG) and to ultimately evaluate the role of cell-wall melanization in stress survival. Differential expression was observed for proteins involved in carbohydrate and lipid metabolic processes, transport, and ribosome biogenesis and translation via ribosomal translational machinery. However, no evidence of significant activation of stress components or starvation response was detected, except for the scytalone dehydratase, enzyme involved in the synthesis of dihydroxynaphthalene (DNH) melanin, which was found to be upregulated in the secretome of the wild type and downregulated in the mutant. Differences in protein modulation were observed between K. chersonesos Wt and Mut, with several proteins being downregulated under LSSMG in the Mut when compared to the Wt. Lastly, no major morphological alterations were observed following exposure to LSSMG. Similarly, the strains' survivability was not negatively affected. This study is the first to characterize the response to simulated microgravity in black fungi, which might have implications on future astrobiological missions.

Natural sciences at the service of art and cultural heritage: an interdisciplinary area in development and important challenges.

Our cultural heritage is a common asset that tells the story of our shared past, is part of our origin and identity and has wide social relevance. Our works of art and our heritage must be enjoyed, appreciated and preserved for future generations. To this end, a wide and varied group of professionals, including conservators, restorers, curators, bibliographers, historians, archivists, but also scientists, such as biologists, chemists, physicists and bioinformaticians, work side by side to preserve our cultural heritage. Working together in this wide range of disciplines included in the so-called 'heritage sciences' is the only plausible way to contribute to the sustainable preservation of our heritage. The great progress made in recent years in conservation and restoration work, but also in the natural sciences considered within heritage science, has provided powerful tools and strategies for analytical and experimental research into historical and cultural objects that open up new frontiers for their diagnosis, monitoring and protection. Here we highlight some of the advances and challenges faced by the natural sciences at the service of art.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota.

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

The Microbiome of Leonardo da Vinci's Drawings: A Bio-Archive of Their History.

Seven emblematic Leonardo da Vinci's drawings were investigated through third generation sequencing technology (Nanopore). In addition, SEM analyses were carried out to acquire photographic documentation and to infer the nature of the micro-objects removed from the surface of the drawings. The Nanopore generated microbiomes can be used as a "bio-archive" of the drawings, offering a kind of fingerprint for current and future biological comparisons. This information might help to create a biological catalog of the drawings (cataloging), a microbiome-fingerprint for each single analyzed drawing, as a reference dataset for future studies (monitoring) and last but not least a bio-archive of the history of each single object (added value). Results showed a relatively high contamination with human DNA and a surprising dominance of bacteria over fungi. However, it was possible to identify typical bacteria of the human microbiome, which are mere contaminants introduced by handling of the drawings as well as other microorganisms that seem to have been introduced through vectors, such as insects and their droppings, visible through the SEM analyses. All drawings showed very specific bio-archives, but a core microbiome of bacteria and fungi that are repeatedly found in this type of material as true degraders were identified, such as members of the phyla Proteobacteria, Actinobacteria, and Firmicutes among bacteria, and fungi belonging to the classes Sordariomycetes and Eurotiomycetes. In addition, some similarities were observed that could be influenced by their geographical location (Rome or Turin), indicating the influence of this factor and denoting the importance of environmental and storage conditions on the specific microbiomes.

Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.

The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the "Shed light in The daRk lineagES of the fungal tree of life" (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.

Author Correction: Shotgun proteomics reveals putative polyesterases in the secretome of the rock-inhabiting fungus Knufia chersonesos.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Contamination of wounds with fecal bacteria in immuno-suppressed mice.

Immunocompromised patients are predisposed to chronically infected wounds. Especially ulcers in the dorsal region often experience secondary polymicrobial infections. However, current wound infection models mostly use single-strain bacteria. To mimic clinically occurring infections caused by fecal contamination in immunocompromised/immobile patients, which differ significantly from single-strain infections, the present study aimed at the establishment of a new mouse model using infection by fecal bacteria. Dorsal circular excision wounds in immunosuppressed mice were infected with fecal slurry solution in several dilutions up to 1:8,000. Impact of immunosuppressor, bacterial load and timing on development of wound infections was investigated. Wounds were analyzed by scoring, 3D imaging and swab analyses. Autofluorescence imaging was not successful. Dose-finding of cyclophosphamide-induced immunosuppression was necessary for establishment of bacterial wound infections. Infection with fecal slurry diluted 1:166 to 1:400 induced significantly delayed wound healing (p < 0.05) without systemic reactions. Swab analyses post-infection matched the initial polymicrobial suspension. The customized wound score confirmed significant differences between the groups (p < 0.05). Here we report the establishment of a simple, new mouse model for clinically occurring wound infections by fecal bacteria and the evaluation of appropriate wound analysis methods. In the future, this model will provide a suitable tool for the investigation of complex microbiological interactions and evaluation of new therapeutic approaches.

Shotgun proteomics reveals putative polyesterases in the secretome of the rock-inhabiting fungus Knufia chersonesos.

Knufia chersonesos is an ascomycotal representative of black fungi, a morphological group of polyextremotolerant melanotic fungi, whose ability to resort to recalcitrant carbon sources makes it an interesting candidate for degradation purposes. A secretome screening towards polyesterases was carried out for the fungus and its non-melanized mutant, grown in presence of the synthetic copolyester Polybutylene adipate terephthalate (PBAT) as additional or sole carbon source, and resulted in the identification of 37 esterolytic and lipolytic enzymes across the established cultivation conditions. Quantitative proteomics allowed to unveil 9 proteins being constitutively expressed at all conditions and 7 which were instead detected as up-regulated by PBAT exposure. Protein functional analysis and structure prediction indicated similarity of these enzymes to microbial polyesterases of known biotechnological use such as MHETase from Ideonella sakaiensis and CalA from Candida albicans. For both strains, PBAT hydrolysis was recorded at all cultivation conditions and primarily the corresponding monomers were released, which suggests degradation to the polymer's smallest building block. The work presented here aims to demonstrate how investigations of the secretome can provide new insights into the eco-physiology of polymer degrading fungi and ultimately aid the identification of novel enzymes with potential application in polymer processing, recycling and degradation.

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value.

This study provides an example in the emerging field of biocodicology showing how metagenomics can help answer relevant questions that may contribute to a better understanding of the history of ancient manuscripts. To this end, two Slavonic codices dating from the 11th century were investigated through shotgun metagenomics. Endogenous DNA enabled to infer the animal origin of the skins used in the manufacture of the two codices, while nucleic sequences recovered from viruses were investigated for the first time in this material, opening up new possibilities in the field of biocodicology. In addition, the microbiomes colonizing the surface of the parchments served to determine their conservation status and their latent risk of deterioration. The saline environment provided by the parchments selected halophilic and halotolerant microorganisms, which are known to be responsible for the biodegradation of parchment. Species of Nocardiopsis, Gracilibacillus and Saccharopolyspora, but also members of the Aspergillaceae family were detected in this study, all possessing enzymatic capabilities for the biodeterioration of this material. Finally, a relative abundance of microorganisms originating from the human skin microbiome were identified, most probably related to the intensive manipulation of the manuscripts throughout the centuries, which should be taken with caution as they can be potential pathogens.

Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus.

Friedmanniomyces endolithicus is a highly melanized fungus endemic to the Antarctic, occurring exclusively in endolithic communities of the ice-free areas of the Victoria Land, including the McMurdo Dry Valleys, the coldest and most hyper-arid desert on Earth and accounted as the Martian analog on our planet. F. endolithicus is highly successful in these inhospitable environments, the most widespread and commonly isolated species from these peculiar niches, indicating a high degree of adaptation. The nature of its extremo tolerance has not been previously studied. To investigate this, we sequenced genome of F. endolithicus CCFEE 5311 to explore gene content and genomic patterns that could be attributed to its specialization. The predicted functional potential of the genes was assigned by similarity to InterPro and CAZy domains. The genome was compared to phylogenetically close relatives which are also melanized fungi occurring in extreme environments including Friedmanniomyces simplex, Baudoinia panamericana, Acidomyces acidophilus, Hortaea thailandica and Hortaea werneckii. We tested if shared genomic traits existed among these species and hyper-extremotolerant fungus F. endolithicus. We found that some characters for stress tolerance such as meristematic growth and cold tolerance are enriched in F. endolithicus that may be triggered by the exposure to Antarctic prohibitive conditions.