Modelling the effect of temperature, water activity and pH on the growth of Serpula lacrymans

Aims: To predict the risk factors for building infestation by Serpula lacrymans, which is one of the most destructive fungi causing timber decay in buildings. Methods and Results: The growth rate was assessed on malt extract agar media at temperatures between 1·5 and 45°C, at water activity (a_w) over the range of 0·800–0·993 and at pH ranges from 1·5 to 11·0. The radial growth rate (μ) and the lag phase (λ) were estimated from the radial growth kinetics via the plots radius vs time. These parameters were then modelled as a function of the environmental factors tested. Models derived from the cardinal model (CM) were used to fit the experimental data and allowed an estimation of the optimal and limit values for fungal growth. Optimal growth rate occurred at 20°C, at high a_w level (0·993) and at a pH range between 4·0 and 6·0. The strain effect on the temperature parameters was further evaluated using 14 strains of S. lacrymans. The robustness of the temperature model was validated on data sets measured in two different wood‐based media (Quercus robur L. and Picea abies). Conclusions: The two‐step procedure of exponential model with latency followed by the CM with inflection gives reliable predictions for the growth conditions of a filamentous fungus in our study. The procedure was validated for the study of abiotic factors on the growth rate of S. lacrymans. Significance and Impact of the Study: This work describes the usefulness of evaluating the effect of physico‐chemical factors on fungal growth in predictive building mycology. Consequently, the developed mathematical models for predicting fungal growth on a macroscopic scale can be used as a tool for risk assessment of timber decay in buildings.     

Initial fungal colonizer affects mass loss and fungal community development in Picea abies logs 6 yr after inoculation

Picea abies logs were inoculated with Resinicium bicolor, Fomitopsis pinicola or left un-inoculated and placed in an old-growth boreal forest. Mass loss and fungal community data were collected after 6 yr to test whether simplification of the fungal community via inoculation affects mass loss and fungal community development. Three techniques were used to survey communities: (1) observation of fruiting structures; (2) culturing on media; and (3) cloning and sequencing of ITS rDNA. Fruit body surveys detected the smallest number of species (18, 3.8 per log), DNA-based methods detected the most species (72, 31.7 per log), and culturing detected an intermediate number (23, 7.2 per log). Initial colonizer affected community development and inoculation with F. pinicola led to significantly greater mass loss. Relationships among fungal community composition, community richness and mass loss are complex and further work is needed to determine whether simplification of fungal communities affects carbon sequestration in forests.     

Microbial responses to a changing environment: implications for the future functioning of terrestrial ecosystems

In this review, we present a conceptual model which links plant communities and saprotrophic microbial communities through the reciprocal exchange of growth-limiting resources. We discuss the numerous ways human-induced environmental change has directly and indirectly impacted this relationship, and review microbial responses that have occurred to date. We argue that compositional shifts in saprotrophic microbial communities underlie functional responses to environmental change that have ecosystem-level implications. Drawing on a long-term, large-scale, field experiment, we illustrate how and why chronic atmospheric N deposition can alter saprotrophic communities in the soil of a wide-spread sugar maple (Acer saccharum) ecosystem in northeastern North America, resulting in the slowing of plant litter decay, the rapid accumulation of soil organic matter, and the accelerated production and loss of dissolved organic carbon (DOC). Compositional shifts in soil microbial communities, mediated by ecological interactions among soil saprotrophs, appear to lie at the biogeochemical heart of ecosystem response to environmental change.     

Phytoplankton Cell Lysis after Water Bloom in a Eutrophic Freshwater Lake Taihu (China)

The phytoplankton lysis rates in the different eutrophic regions of Lake Taihu were determined based on the activities of particle and dissolved esterase, as well as the decay rate of the latter, from August 2009 to March 2010. Two peaks were observed for the chlorophyll a concentration, one in September 2009 and another in January 2010. The highest phytoplankton lysis rates observed in October were associated with the decay of the summer bloom, whereas the minimum lysis rates observed in January were associated with the winter bloom. The highest cell lysis rates in Meiliang Bay, Lake centre, and Gonghu Bay were 0.67, 0.77, and 0.68 d^–1, respectively, whereas the lowest lysis rates in these regions were 0.03, 0.01, and 0.05 d^–1, respectively. Water temperature showed an apparent indirect effect on lysis rate. In addition, a significant inverse relationship was observed between lysis rates and nitrate concentration in the three lake regions, which suggests that phytoplankton cell lysis is associated with changes in nitrate concentration. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Plasmonics in Biology and Plasmon-Controlled Fluorescence

Fluorescence technology is fully entrenched in all aspects of biological research. To a significant extent, future advances in biology and medicine depend on the advances in the capabilities of fluorescence measurements. As examples, the sensitivity of many clinical assays is limited by sample autofluorescence, single-molecule detection is limited by the brightness and photostability of the fluorophores, and the spatial resolution of cellular imaging is limited to about one-half of the wavelength of the incident light. We believe a combination of fluorescence, plasmonics, and nanofabrication can fundamentally change and increase the capabilities of fluorescence technology. Surface plasmons are collective oscillations of free electrons in metallic surfaces and particles. Surface plasmons, without fluorescence, are already in use to a limited extent in biological research. These applications include the use of surface plasmon resonance to measure bioaffinity reactions and the use of metal colloids as light-scattering probes. However, the uses of surface plasmons in biology are not limited to their optical absorption or extinction. We now know that fluorophores in the excited state can create plasmons that radiate into the far field and that fluorophores in the ground state can interact with and be excited by surface plasmons. These reciprocal interactions suggest that the novel optical absorption and scattering properties of metallic nanostructures can be used to control the decay rates, location, and direction of fluorophore emission. We refer to these phenomena as plasmon-controlled fluorescence (PCF). We predict that PCF will result in a new generation of probes and devices. These likely possibilities include ultrabright single-particle probes that do not photobleach, probes for selective multiphoton excitation with decreased light intensities, and distance measurements in biomolecular assemblies in the range from 10 to 200 nm. Additionally, PCF is likely to allow design of structures that enhance emission at specific wavelengths and the creation of new devices that control and transport the energy from excited fluorophores in the form of plasmons, and then convert the plasmons back to light. Finally, it appears possible that the use of PCF will allow construction of wide-field optical microscopy with subwavelength spatial resolution down to 25 nm.     

Microwave-Accelerated and Metal-Enhanced Fluorescence Myoglobin Detection on Silvered Surfaces: Potential Application to Myocardial Infarction Diagnosis

In this short paper, we describe a novel approach to both significantly accelerate and optically amplify fluorescence-based immunoassays. Our approach utilizes metal-enhanced fluorescence (MEF) to intrinsically optically amplify fluorescence signatures, which, when combined with the use of low-power microwaves to kinetically accelerate assays, provides for both ultrafast and ultrabright immunoassays. Surprisingly, the use of low-power microwaves and silver nanostructures provides for localized heating, concentrating the effect to the particles themselves as compared to the generic heating of the high dielectric assay fluid. We have subsequently applied our microwave-accelerated MEF approach to the detection of myoglobin, where its rapid quantification is paramount for the clinical assessment of an acute myocardial infarction.     

Nucleosome deposition and DNA methylation may participate in the recognition of premature termination codon in nonsense-mediated mRNA decay

In non-mammalian eukaryotes, an abnormally long 3′ untranslated region (UTR) is generally thought to be the definitive signal in the recognition of a premature termination codon (PTC) in nonsense-mediated mRNA decay (NMD). However, because the lengths of 3′ UTRs in normal mRNAs are widely distributed, “abnormally long” is hard to define. Distinct peaks of nucleosome deposition and DNA methylation have recently been found at coding region boundaries. We propose that nucleosomes and DNA methylation just upstream of a normal stop codon are ideal indicators for the position of a normal stop codon and may thus serve as signals in PTC recognition.     

Interpretation of intramolecular stacking effect on the fluorescence intensity decay of 3-methylbenzimidazolyl(5′-5′)guanosine dinucleotides using a model of lifetime distribution

Time-resolved fluorescence of 3-methylbenzimidazole (m³B) was used to study stacking interaction between base moieties in di-, tri- and tetra-phosphate analogues of 3-methylbenzimidazolyl(5′-5′)guanosine (m³Bp _n G, n = 2, 3, 4), using 5′-triphosphate of 3-methylbenzimidazole riboside (m³BTP) as reference. Fluorescence intensity decays of all compounds cannot be satisfactory fitted with single-exponential function. Although an increase of a number of exponents led to better fits, interpretation of the individual exponential terms, i.e. pre-exponential amplitudes and fluorescence lifetimes, cannot be adequately characterized. We show that these fluorescence decays are best fitted by power-like function derived from physically justified distribution of the fluorescence lifetimes, and characterized by the mean value of the excited-state lifetime and relative variance of lifetime fluctuations around the mean value. The latter led to the parameter of heterogeneity and number of decay paths, which depend on the factors responsible for non-radiative decay of the excited state, including base–base stacking interaction. This was studied by means of changes of temperature and the number of phosphate groups in dinucleotides. It was shown that the strongest effect of stacking interactions, characterized by lowest values of both fluorescence mean decay time and relative variance, occurs in the case of m³Bp₃G containing the same number of phosphates as natural mRNA cap. The possible importance of these results for interpretation of the mechanism of function of the mRNA cap structure is discussed.