1,720,991 research outputs found
An overview of genomics, phylogenomics and proteomics approaches in ascomycota
Full text linkFungi 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
Data Fusion Approach to Simultaneously Evaluate the Degradation Process Caused by Ozone and Humidity on Modern Paint Materials
Full text linkThe 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
Oxford Nanopore Technologies for Biocodicology: a case study on a 15th-century parchment - Vassallo Y., Waldherr M., Lehner E., Graf A., Cappa F., Hartl A., Schober R., Beccaccioli M., Sterflinger K., Piñar G., Reverberi M.
No full textBiocodicology, a term coined by Sarah Fiddyment in 2019, is an emerging field which studies the biological information stored in manuscripts: fungi/bacteria that colonise and degrade the surface (microbiome), and the animal species used for the manufacturing of the parchment, to better understand the production and the history of the artefact.
The analyses usually used for the identification of the animal are: visual analysis, protein analysis, or DNA analysis. In this field Oxford Nanopore Technologies (ONT) and in particular their portable device MinION it’s a great instrument to investigate the DNA of the microbiome of cultural artefacts, but so far it has never been used to study the microbiome and the animal species of parchment.
Animal DNA found in ancient parchment manuscripts can be considered ancient DNA (aDNA), as it's characterised by short (40-200 bp) fragments and can have different mutations, therefore, until now the sequencing technology used has been Illumina (short-read sequencing). The portable device MinION (ONT) on the other hand, it’s a long-read sequencer, but last year Nanopore released a new Short Fragmented Mode (SFM) and a new chemistry of the flowcell (R10.4.1) which makes it potentially usable for sequencing short fragments.
In this case study we report for the first time the potential of MinION (ONT) for the identification of the animal species (aDNA) and the microbiome of a 15th-century parchment from the Graphic Collection (Kupferstichkabinett) of the Academy of Fine Arts, in Vienna. The results show the feasibility of this technology for this type of studies
Sample preparation and 2-DE procedure for protein expression profiling of black microcolonial fungi
No full textThe ecology and stress adaptation of black rock inhabiting fungi in hot and cold extreme environments are not yet well understood. Two-dimensional gel electrophoresis (2-DE) is a promising tool to study the protein expression profiling and the metabolic status of microorganisms under stress conditions. The sample preparation has been shown to be the bottleneck for high resolution protein separation in 2-DE. For this purpose conditions must be optimized to obtain reliable and reproducible results. In addition, due to a multilayered and strongly melanized cell wall of black microcolonial fungi, special protocols for cell disruption and processing are required. In the present study, the protocol for protein extraction was established and optimized for the black yeast Exophiala jeanselmei MA 2853. The same protocol was successfully examined also for the meristematic fungus Coniosporium perforans MA 1299. Among the three procedures evaluated, trichloroacetic acid (TCA) precipitation, TCA/acetone precipitation, and phenol extraction combined with methanol/ammonium acetate precipitation, the latter showed to be the best method for black yeasts and meristematic fungi. Penicillium chrysogenum was used as reference strain
Potential extinction of Antarctic endemic fungal species as consequence of Global Warming
No full textCryomyces spp. are fungi adapted to the harsh conditions of the McMurdo Dry Valleys in the Antarctic. The structure of their cell wall is one of the main factors for their uncommon ability to survive external stressors. The cells are, in fact, embedded in a thick and strongly melanised cell wall encrusted with black rigid plaques giving a supplementary protection and making them practically impregnable and refractory even to commercial enzymes including chitinases and glucanases. The Antarctic fungus Lecanicillium muscarium CCFEE 5003, able to produce an arsenal of lytic enzymes, including chitinases and glucanases, is known for its ability to degrade the cell walls of different food spoiling and opportunistic fungi as well as plant pathogenic Oomycota. Active cells of Cryomyces spp. were cultivated in dual culture with the mycoparasitic fungus both in liquid and solid media. Light microscope observations revealed that the cell walls of Cryomyces were heavily decayed. This resulted in the release of protoplasts. Hyphae penetration was evident with both scanning and transmission electron microscope observations. Due to its ecological amplitude (i.e. temperature growth range 0–28 °C), the parasitic fungus could easily expand its area of distribution as a consequence of global warming by invading new areas towards the interior of the continent. The establishment of interactions with organisms living at present in border ecosystems may lead to extinction of extremely specialized and poorly competitive entitie
Facile preparation of organic-inorganic hydrogels containing silver or essential oil with antimicrobial effects
No full textHydrogels (HGs) based on Poly-(vinyl)alcohol (PVA), sodium alginate (SA) and borax were appropriately modified with both poly(ethylene)oxide (PEO) and ZnAl layered double hydroxide (LDH) to create a network in which active molecules can be loaded and confined. PEO acts as a porogen agent in the PVA matrix, reducing the crosslinking degree of the polymer and favouring the retention of organic apolar species. LDH, in nitrate or chloride form, organically modified with SA (LDH/N@SA and LDH/C@SA), reinforces the polymeric network, improving its mechanical properties. Moreover, LDH/N@SA and LDH/C@SA were used to grow and anchor nanoparticles of Ag and Ag/AgCl, becoming fillers of HGs containing active species. An additional sample was prepared by incorporating thyme essential oil (EO) in a HG prepared with LDH/C@SA. These systems provided a sustained release of silver ions and EO and a very efficient swelling in water. The HGs subjected to antimicrobial tests, exhibited good antimicrobial activity against both Gram-positive (Staphylococcus epidermidis and S. aureus) and Gram-negative (Pseudomonas aeruginosa) bacteria and yeast (Candida albicans). These characteristics make the HGs suitable to be proposed as patches for wound healing
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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