Application of bioluminescence ATP measurement for evaluation of fungal viability of foxing spots on old documents

An adenosine triphosphate (ATP) bioluminescence‐based protocol was tested to assess the viability of fungal species in old documents damaged by foxing. Foxing appears as scattered yellow brownish‐red stains, damaging the aesthetics of documents and their long‐term readability. In the field of cultural heritage conservation, the debate over the mechanism of foxing is ongoing. Previous studies found evidence of mold‐like structures in some coloured areas; however, many species have not yet been identified and their role in the phenomenon is not understood. To better understand their involvement in this type of paper decay, we focused our attention first on their viability. We demonstrated the reliability and sensitivity of the ATP bioluminescence assay compared with conventional methods based on cultivation, which has rarely given rise to in vitro growth from foxed papers. From nine books dating back from the 19th and 20th centuries, the mean ATP amount of foxed spots ranged from 0.29 to 3.63 ng/cm², suggesting the presence of strains inside the brownish spots and providing evidence of their viability. Outside the spots, ATP content was considered negligible, with a mean ATP amount of 0 to 0.03 ng/cm². ATP assay appears to be a useful and robust method for the detection and quantification of viable elements in foxing spots. Copyright © 2012 John Wiley & Sons, Ltd.     

Microfungal biodeterioration of historic paper: Preliminary FTIR and microbiological analyses

Paper is subjected to numerous biodeterioration processes, which may cause the irreversible degradation of important documents and works of art. Many chemical and physical factors can affect these processes and their behaviour, and fungi seem to play a key role in biodeteriorating paper materials. This study is mainly aimed at verifying the presence of fungi in biodeteriorated 18th century etchings, and characterizing the paper surface by means of Fourier transform infrared (FTIR) spectroscopy and fluorescence under UV radiation. The laboratory tests highlight the presence of fungal entities from all the samples investigated. Specifically, 14 species were identified; three of them were never isolated from paper until now. Furthermore, the data gathered do not confirm the theory according to which there is a correspondence between fluorescence of the stains under UV radiation and the vitality of microfungi. Finally, possible correlations among paper composition (as determined by FTIR), mode of conservation and fungal attack are presented and discussed.     

A widely applicable analytical system for biological stains: reverse-phase thin layer chromatography

The suitability of reverse-phase thin layer chromatography using a commercial adsorbant and aqueous methanol as an analytical tool for biological stains was investigated. The wide range of applicability of this technique is shown by the fact that of 120 dyes used as biological stains, 84 of diverse chemical character were successfully chromatographed by varying only the water content of the eluent. Unsuccessful chromatography was due either to immobility or streaking. Dyes exhibiting this behavior can be identified prior to chromatography by inspection of their structural formulae. Rf values were found to be significantly correlated with the calculated partition coefficients. This relationship provides information for the identification of dye components revealed by chromatography and a discussion of its use in the chemical characterization of various dyestuffs is presented.     

A Comparison of the Reaction Sites Associated with the Resistance of Coleoptiles of Barley, Oats and Wheat to Infection by Septoria nodorum

A novel technique has been developed to inoculate the outer epidermal cells of coleoptiles of barley, oats and wheat with S. nodorum. Using this technique, which results in a large number of attempted penetrations, the composition of the material deposited at unsuccessful penetration sites in these cereals have been compared. Although the deposits reacted in a similar manner with some histochemical reagents (ammoniacal silver solution, Coppick-Fowler reaction, p-nitrobenzene tetrafluoroborate and Coomassie brilliant blue R250) marked differences occurred between the reactions sites formed by barley and wheat and by oats with other stains (bromophenol blue, nile blue sulphate and Toluidine blue). Chemical treatments used to delignify tissue also revealed differences in these reaction sites. It is concluded that although the reaction sites share some similar components there are significant differences in their chemical structure.     

A Widely Applicable Analytical System for Biological Stains: Reverse-Phase Thin Layer Chromatography

The suitability of reverse-phase thin layer chromatography using a commercial adsorbant and aqueous methanol as an analytical tool for biological stains was investigated. The wide range of applicability of this technique is shown by the fact that of 120 dyes used as biological stains, 84 of diverse chemical character were successfully chromatographed by varying only the water content of the eluent. Unsuccessful chromatography was due either to immobility or streaking. Dyes exhibiting this behavior can be identified prior to chromatography by inspection of their structural formulae. R_f values were found to be significantly correlated with the calculated partition coefficients. This relationship provides information for the identification of dye components revealed by chromatography and a discussion of its use in the chemical characterization of various dyestuffs is presented.     

Biomimetic system for removal of fungal melanin staining on paper

Fungal melanin staining is a problem on many cultural objects, ranging from the French Palaeolithic cave at Lascaux to books and papers in museum collections. Melanin, because it is insoluble and resistant to bleaching, may leave behind undesirable stains long after the fungal infestation has been controlled. Research into removal of melanin stains from paper and other sensitive substrates using industrial biomimetic oxidizing systems has shown considerable success. We studied relative concentration of the bleaching reagents and the reaction kinetics both in liquid suspensions of melanin and on melanized paper samples. Liquid suspension samples were tested for changes in their chemical composition (appearance and relative representation of functional groups and chemical bonds) with FTIR spectrometry. Changes in color of melanized paper samples were investigated with a CIE L*a*b system, where the effectiveness of the treatment (bleaching) was determined as a change in lightness (ΔL). Melanin was oxidized in the liquid suspensions, and the intensity of modification depended on the procedure employed. Bleaching of melanin with the biomimetic copper–pyridine complex proved to be far superior to the effect of white-rot fungal oxidizing enzymes, previously reported on by this group.     

The use of FTIR spectroscopy to monitor modifications in plant cell wall architecture caused by cellulose biosynthesis inhibitors

Fourier Transform InfraRed (FTIR) spectroscopy is a powerful and rapid technique for analyzing cell wall components and putative cross-links, which is able to non-destructively recognize polymers and functional groups and provide abundant information about their in muro organization. FTIR spectroscopy has been reported to be a useful tool for monitoring cell wall changes occurring in muro as a result of various factors, such as growth and development processes, mutations or biotic and abiotic stresses. This mini-review examines the use of FTIR spectroscopy in conjunction with multivariate analyses to monitor cell wall changes related to (1) the exposure of diverse plant materials to cellulose biosynthesis inhibitors (CBIs) and (2) the habituation/dehabituation of plant cell cultures to this kind of herbicides. The spectra analyses show differences not only regarding the inhibitor, but also regarding how long cells have been growing in its presence.Key words: FTIR, cellulose biosynthesis inhibitor, habituation/dehabituation     

Preservation agents influence UV-coloration of plumage in museum bird skins

Plumage colour has always been a major criterion when describing and distinguishing bird taxa. Today, the use of reflection spectrophotometry is the most commonly used technique to study plumage coloration. A major advantage of this method is the opportunity of observing reflection beyond the human colour vision range—including the UV-waveband. Traditional taxonomic and phylogenetic research is often based on bird skins held in collections in natural history museums worldwide. Different agents for preservation have been used to prevent skins from being damaged by arthropod pests. Sometimes, parts of the plumage have been contaminated with stains from preservation agents. When dried, they are almost invisible to the human eye under normal sunlight conditions and cause no obvious change to feather coloration. However, some preservation agents contain fluorescent components which show up brightly when illuminated with UV-light. Furthermore, undetectable to the human eye, stains from these agents annihilate UV-reflection, preventing accurate data collection based on the UV-reflection of bird feathers. Measuring plumage parts which have been accidentally stained will lead to a relative underestimate of UV-reflection. In studying 20,000 samples, we found fluorescent stains in some 300 bird skins of varying ages (1913–2004) in museum collections throughout Europe and the USA. Different preservation agents have been evaluated for their fluorescence properties.     

Detection of Bioactive Exometabolites Produced by the Filamentous Marine Cyanobacterium Geitlerinema sp.

Marine cyanobacteria are noted for their ability to excrete metabolites with biotic properties. This paper focuses on such exometabolites obtained from the culture of the marine filamentous cyanobacterium Geitlerinema sp. strain, their purification and subsequent analyses. By this means the recoveries of the active compounds, a prerequisite for properly determining their concentration, are quantified here for the first time. We demonstrate a new procedure using Amberlite XAD-1180 resin in combination with the eluent isopropanol for extraction of the culture media and gas chromatography as simplified chemical analysis. This procedure reduced necessary bacteria cultivation time (from 150 to 21?days) at low volumes of culture media (300?mL) required for identification of two selected bioactive compounds: 4,4'-dihydroxybiphenyl and harmane.     

Silver stains demonstrating neuroendocrine cells

During the preimmunohistochemical era, silver stains were an important part of the staining arsenal for identifying certain tissue structures and cell types in tissue sections. Some of them were useful for demonstrating endocrine cells, especially in the gastrointestinal tract. Until the late 1950s, silver stains, particularly those identifying endocrine cells, were accompanied by a number of technical difficulties resulting from uncontrolled staining factors. In the 1960s, new silver stains were developed for endocrine cell types and these stains gave reproducible results. One of the “older” silver stains and two of the “newer” ones are emphasized in this presentation, namely the Masson, the Grimelius and the Sevier-Munger techniques. The Masson stain demonstrates the enterochromaffin (EC, serotonin) cells, the Grimelius stain is a broad endocrine cell marker, and the Sevier-Munger technique demonstrates EC and EC-like cells and the C-cells of the thyroid. Especially in the preimmunohistochemical era, these staining methods often were used for histopathological diagnosis, particularly the Grimelius technique. The silver stains were developed empirically, and with few exceptions the chemical background is not known. Staining protocols are included.     

Investigating plant-plant interference by metabolic fingerprinting

New analytical developments in post-genomic technologies are being introduced to the field of plant ecology. FT-IR fingerprinting coupled with chemometrics via cluster analysis is proposed as a tool for correlating global metabolic changes with abiotic or biotic perturbation and/or interactions. The current study concentrates on detecting chemical responses by inter-species competition between a monocotyledon Brachypodium distachyion and a dicotyledon Arabidopsis thaliana. Growth analysis of 42 days old plants showed differences in both species under competition. Clear changes in the FT-IR metabolic fingerprints of B. distachyion in competition with A. thaliana were observed, whilst there were no apparent chemical differences in the A. thaliana plant tissues. This study demonstrates the power of this approach in detecting changes in the global metabolic profiles of plants in response to biotic interactions, and we believe FT-IR is appropriate for rapid screening (10 s per sample) prior to targeted metabolite analyses.     

Silver stains demonstrating neuroendocrine cells

During the preimmunohistochemical era, silver stains were an important part of the staining arsenal for identifying certain tissue structures and cell types in tissue sections. Some of them were useful for demonstrating endocrine cells, especially in the gastrointestinal tract. Until the late 1950s, silver stains, particularly those identifying endocrine cells, were accompanied by a number of technical difficulties resulting from uncontrolled staining factors. In the 1960s, new silver stains were developed for endocrine cell types and these stains gave reproducible results. One of the “older” silver stains and two of the “newer” ones are emphasized in this presentation, namely the Masson, the Grimelius and the Sevier-Munger techniques. The Masson stain demonstrates the enterochromaffin (EC, serotonin) cells, the Grimelius stain is a broad endocrine cell marker, and the Sevier-Munger technique demonstrates EC and EC-like cells and the C-cells of the thyroid. Especially in the preimmunohistochemical era, these staining methods often were used for histopathological diagnosis, particularly the Grimelius technique. The silver stains were developed empirically, and with few exceptions the chemical background is not known. Staining protocols are included.     

How plants cope with biotic interactions

In their natural environment, plants interact with many different organisms. The nature of these interactions may range from positive, for example interactions with pollinators, to negative, such as interactions with pathogens and herbivores. In this special issue, the contributors provide several examples of how plants manage both positive and negative biotic interactions. This review aims to relate their findings to what we know about the complex natural environments in which plants have evolved. Molecular analyses of plant genomes and expression profiles have shown how intricately plants may regulate responses to single or multiple biotic interactions. Plant responses are fine-tuned by signalling hormone interactions. When multiple organisms interact with a single plant this may result in antagonistic or synergistic effects. The emerging fields of ecogenomics and metabolomics undoubtedly will refine our understanding of the multilayered regulation that plants use to manage relationships with their biotic environment. However, we can only understand why plants have such an intricate regulatory apparatus if we consider the ecological context of plant biotic interactions.     

Elm defence against herbivores and pathogens: morphological,chemical and molecular regulation aspects

Elms (Ulmus spp.) have long been appreciated for their environmental tolerance, landscape and ornamental value, and the quality of their wood. Although elm trees are extremely hardy against abiotic stresses such as wind and pollution, they are susceptible to attacks of biotic stressors. Over 100 phytopathogens and invertebrate pests are associated with elms: fungi, bacteria and insects like beetles and moths, and to a lesser extent aphids, mites, viruses and nematodes. While the biology of the pathogen and insect vector of the Dutch elm disease has been intensively studied, less attention has been paid so far to the defence mechanisms of elms to other biotic stressors. This review highlights knowledge of direct and indirect elm defences against biotic stressors focusing on morphological, chemical and gene regulation aspects. First, we report how morphological defence mechanisms via barrier formation and vessel occlusion prevent colonisation and spread of wood- and bark-inhabiting fungi and bacteria. Second, we outline how secondary metabolites such as terpenoids (volatile terpenoids, mansonones and triterpenoids) and phenolics (lignans, coumarins, flavonoids) in leaves and bark are involved in constitutive and induced chemical defence mechanisms of elms. Third, we address knowledge on how the molecular regulation of elm defence is orchestrated through the interaction of a huge variety of stress- and defence-related genes. We conclude by pointing to the gaps of knowledge on the chemical and molecular mechanisms of elm defence against pest insects and diseases. An in-depth understanding of defence mechanisms of elms will support the development of sustainable integrated management of pests and diseases attacking elms.     

Distribution patterns of the small mammals (Insectivora and Rodentia) in a transitional zone between the Eurosiberian and the Mediterranean regions

To determine, by means of quantitative analyses, the distribution patterns of the insectivores and rodents in Catalonia using physiographical regions as Operative Geographical Units (OGUs). Catalonia (north‐eastern Iberian Peninsula). Based on the presence/absence of twenty‐five small mammals in thirteen physiographical regions, which were used as OGUs, the following aspects were studied: (a) identification of biotic boundaries; (b) determination of chorological association of species; (c) climatic characterization of the biotic regions and the chorotypes. Groups of biotic regions and species were established, and their statistical significance was tested. The possible effect of several climatic factors on these groupings was studied using discriminant analyses. A significant biotic boundary was found to separate the central and eastern Pyrenees from the remaining physiographical regions. The climatic variables that defined this boundary were related to the severity and the availability of environmental energy. Four chorotypes were identified. One chorotype was constituted by Pyrenean or Pre‐Pyrenean species, an association determined by their mid‐European requirements; another chorotype was formed by Eurosiberian species, but showed a variable degree of tolerance to Mediterranean conditions; a third chorotype included species with a wide distribution that are Mediterranean, anthropic, generalist or have very specific habitats; and finally the fourth chorotype was constituted by a strictly Mediterranean species. The climatic factors that accounted for the distribution of these chorotypes were the mean July temperature and the mean annual precipitation. We conclude that the axial zone of the Pyrenees, except the coastal portion, determines two biotic regions in Catalonia. As for the classification of species, using quantitative techniques for the first time, we offer a new biogeographicalal configuration for the small mammals in this temperate‐Mediterranean transition.     

Effects of actinobacteria on plant disease suppression and growth promotion

Biological control and plant growth promotion by plant beneficial microbes has been viewed as an alternative to the use of chemical pesticides and fertilizers. Bacteria and fungi that are naturally associated with plants and have a beneficial effect on plant growth by the alleviation of biotic and abiotic stresses were isolated and developed into biocontrol (BCA) and plant growth-promoting agents (PGPA). Actinobacteria are a group of important plant-associated spore-forming bacteria, which have been studied for their biocontrol, plant growth promotion, and interaction with plants. This review summarizes the effects of actinobacteria as BCA, PGPA, and its beneficial associations with plants.     

Investigating Influential Factors on Bacterioplankton Community Composition: Results from a Field Study of Five Mesotrophic Lakes

In order to investigate which biotic and abiotic factors may have an impact on the community composition of bacterioplankton, five mesotrophic lakes were studied. The composition of the bacterioplankton communities was determined by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Multivariate statistical analyses of the gel patterns, in relation to each other and to the chemical, biological, and physical parameters of the lakes, were performed. The analyses showed that the import of allochthonous bacteria and the interaction with other plankton organisms (for example, grazing) in the lakes probably had an impact on the composition of the communities.     

Biotic interactions hold the key to understanding metacommunity organisation

Biotic interactions are fundamental drivers governing biodiversity locally, yet their effects on geographical variation in community composition (i.e. incidence-based) and community structure (i.e. abundance-based) at regional scales remain controversial. Ecologists have only recently started to integrate different types of biotic interactions into community assembly in a spatial context, a theme that merits further empirical quantification. Here, we applied partial correlation networks to infer the strength of spatial dependencies between pairs of organismal groups and mapped the imprints of biotic interactions on the assembly of pond metacommunities. To do this, we used a comprehensive empirical dataset from Mediterranean landscapes and adopted the perspective that community assembly is best represented as a network of interacting organismal groups. Our results revealed that the co-variation among the beta diversities of multiple organismal groups is primarily driven by biotic interactions and, to a lesser extent, by the abiotic environment. These results suggest that ignoring biotic interactions may undermine our understanding of assembly mechanisms in spatially extensive areas and decrease the accuracy and performance of predictive models. We further found strong spatial dependencies in our analyses which can be interpreted as functional relationships among several pairs of organismal groups (e.g. macrophytes–macroinvertebrates, fish–zooplankton). Perhaps more importantly, our results support the notion that biotic interactions make crucial contributions to the species sorting paradigm of metacommunity theory and raise the question of whether these biologically-driven signals have been equally underappreciated in other aquatic and terrestrial ecosystems. Although more research is still required to empirically capture the importance of biotic interactions across ecosystems and at different spatial resolutions and extents, our findings may allow decision makers to better foresee the main consequences of human-driven impacts on inland waters, particularly those associated with the addition or removal of key species.