Ultrafast electron transfer in riboflavin binding protein in macromolecular crowding of nano-sized micelle

In this contribution, we have studied the dynamics of electron transfer (ET) of a flavoprotein to the bound cofactor, an important metabolic process, in a model molecular/macromolecular crowding environments. Vitamin B₂ (riboflavin, Rf) and riboflavin binding protein (RBP) are used as model cofactor and flavoprotein, respectively. An anionic surfactant sodium dodecyl sulfate (SDS) is considered to be model crowding agent. A systematic study on the ET dynamics in various SDS concentration, ranging from below critical micellar concentration (CMC), where the surfactants remain as monomeric form to above CMC, where the surfactants self-assemble to form nanoscopic micelle, explores the dynamics of ET in the model molecular and macromolecular crowding environments. With energy selective excitation in picosecond-resolved studies, we have followed temporal quenching of the tryptophan residue of the protein and Rf in the RBP–Rf complex in various degrees of molecular/macromolecular crowding. The structural integrity of the protein (secondary and tertiary structures) and the vitamin binding capacity of RBP have been investigated using various techniques including UV–Vis, circular dichroism (CD) spectroscopy and dynamic light scattering (DLS) studies in the crowding environments. Our finding suggests that the effect of molecular/macromolecular crowding could have major implication in the intra-protein ET dynamics in cellular environments.     

Laboratory observations of benthic foraminiferal cysts

Long-term observations on living benthic foraminifera in the laboratory were performed to investigate their behaviour and life style. We noticed that the formation of cysts or sedimentary envelopes is a common feature within many groups of foraminifera (organic walled, agglutinated and calcareous) in the laboratory. Several kinds of cyst were observed. In most cases, the entire foraminiferal shell was canopied with detritus or particles, but some specimens covered only parts of their body, such as the aperture region or pseudopods. Cysts were found attached to the glass walls of culture vessels or free in and on the sediment. Foraminifera stayed within cysts for hours to weeks. After leaving sedimentary envelopes, some specimens immediately started to build new ones, others not. The function of cyst formation observed in the present study was not clear, except one case where reproduction took place. Some monitored structures seemed not to be sedimentary cysts but unilocular agglutinated foraminifera with probably allogromiid-like organization. The formation of sedimentary envelopes seems to be a very basic character of foraminifera, suggesting a mechanism for the evolution of shells.     

Extraction of extracellular polymeric substances from extreme acidic microbial biofilms

The efficiency of five extraction methods for extracellular polymeric substances (EPS) was compared on three benthic eukaryotic biofilms isolated from an extreme acidic river, Río Tinto (SW, Spain). Three chemical methods (MilliQ water, NaCl, and ethylenediamine tetraacetic acid [EDTA]) and two physical methods (Dowex 50.8 and Crown Ether cation exchange resins) were tested. The quality and quantity of the EPS extracted from acidic biofilms varied according to which EPS extraction protocol was used. Higher amounts were obtained when NaCl and Crown Ether resins were used as extractant agents, followed by EDTA, Dowex, and MilliQ. EPS amounts varied from approximately 155 to 478 mg g⁻¹ of dry weight depending on the extraction method and biofilm analyzed. EPS were primarily composed of carbohydrate, heavy metals, and humic acid, plus small quantities of proteins and DNA. Neutral hexose concentrations corresponded to more than 90% of the total EPS dry weight. The proportions of each metals in the EPS extracted with EDTA are similar to the proportions present in the water from each locality where the biofilms were collected except for Al, Cu, Zn, and Pb. In this study, the extracellular matrix heavy metal sorption efficiencies of five methods for extracting EPS from eukaryotic acidic biofilms were compared.     

Movement toward better environments and the evolution of rapid diffusion

We study a reaction-diffusion-advection model for two ecologically equivalent competitors with different dispersal strategies inhabiting a spatially heterogeneous environment. The competitors represent different phenotypes of the same species. One is assumed to disperse by simple diffusion, the other by diffusion together with directed movement toward more favorable environments. We show that under suitable conditions on the underlying spatial domain, the competitor that moves toward more favorable environments may have a competitive advantage even if it diffuses more rapidly than the other competitor. This is in contrast with the case in which both competitors disperse by pure diffusion, where the competitor that diffuses more slowly always has the advantage. We determine competitive advantage by examining the invasibility, i.e. stability or instability, of steady states with only one competitor present. The mathematical approach is a perturbation analysis of principal eigenvalues.     

Differential modulation of host plant delta13C and delta18O by native and nonnative arbuscular mycorrhizal fungi in a semiarid environment

Native, drought-adapted arbuscular mycorrhizal fungi (AMF) often improve host-plant performance to a greater extent than nonnative AMF in dry environments. However, little is known about the physiological basis for this differential plant response. Seedlings of Olea europaea and Rhamnus lycioides were inoculated with either a mixture of eight native Glomus species or with the nonnative Glomus claroideum before field transplanting in a semiarid area. Inoculation with native AMF produced the greatest improvement in nutrient and water status as well as in long-term growth for both Olea and Rhamnus. Foliar delta18O measurements indicated that native AMF enhanced stomatal conductance to a greater extent than nonnative AMF in Olea and Rhamnus.delta13C data showed that intrinsic water-use efficiency in Olea was differentially stimulated by native AMF compared with nonnative AMF. Our results suggest that modulation of leaf gas exchange by native, drought-adapted AMF is critical to the long-term performance of host plants in semiarid environments. delta18O can provide a time-integrated measure of the effect of mycorrhizal infection on host-plant water relations.     

Freeze tolerance of soil chytrids from temperate climates in Australia

Very little is known about the capacity of soil chytrids to withstand freezing in the field. Tolerance to freezing was tested in 21 chytrids isolated from cropping and undisturbed soils in temperate Australia. Samples of thalli grown on peptone–yeast–glucose (PYG) agar were incubated for seven days at −15 °C. Recovery of growth after thawing and transferring to fresh medium at 20 °C indicated survival. All isolates in the Blastocladiales and Spizellomycetales survived freezing in all tests. All isolates in the Chytridiales also survived freezing in some tests. None of the isolates in the Rhizophydiales survived freezing in any of the tests. However, some isolates in the Rhizophydiales recovered growth after freezing if they were grown on PYG agar supplemented with either 1 % sodium chloride or 1 % glycerol prior to freezing. After freezing, the morphology of the thalli of all isolates was observed under LM. In those isolates that recovered growth after transfer to fresh media, mature zoosporangia were observed in the monocentric isolates and resistant sporangia or resting spores in the polycentric isolates. Encysted zoospores in some monocentric isolates also survived freezing. In some of the experiments the freezing and thawing process caused visible structural damage to the thalli. The production of zoospores after freezing and thawing was also used as an indicator of freeze tolerance. The chytrids in this study responded differently to freezing. These data add significantly to our limited knowledge of freeze tolerance in chytrids but leave many questions unanswered.     

The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large‐effect alleles can allow range expansion

Range expansions are complex evolutionary and ecological processes. From an evolutionary standpoint, a populations' adaptive capacity can determine the success or failure of expansion. Using individual‐based simulations, we model range expansion over a two‐dimensional, approximately continuous landscape. We investigate the ability of populations to adapt across patchy environmental gradients and examine how the effect sizes of mutations influence the ability to adapt to novel environments during range expansion. We find that genetic architecture and landscape patchiness both have the ability to change the outcome of adaptation and expansion over the landscape. Adaptation to new environments succeeds via many mutations of small effect or few of large effect, but not via the intermediate between these cases. Higher genetic variance contributes to increased ability to adapt, but an alternative route of successful adaptation can proceed from low genetic variance scenarios with alleles of sufficiently large effect. Steeper environmental gradients can prevent adaptation and range expansion on both linear and patchy landscapes. When the landscape is partitioned into local patches with sharp changes in phenotypic optimum, the local magnitude of change between subsequent patches in the environment determines the success of adaptation to new patches during expansion.     

On the excited-state energy transfer between tryptophan residues in proteins: the case of penicillin acylase

The problem, whether excited-state energy transfer occurs between Trp residues in a multi-tryptophan proteins and if it does, what kind of changes it induces in different parameters of protein fluorescence, is currently under active investigation. In our previous paper [Biophys. Chem. 72 (1998) 265], the energy transfer was found and studied in detail for Na,K-ATPase. It was shown that this transfer influences all parameters of fluorescence emission, which is detected at site-selective conditions (red-edge of excitation, blue and red edges of emission). Present experiments were performed on unusually tryptophan-rich protein, bacterial penicillin acylase (28 Trp per dimer of 82 kDa) and were aimed to extend these observations. They demonstrate substantial heterogeneity in the environments of tryptophan residues within the protein structure. This suggests, that in the present case, if the energy transfer exists, it should be directed from short-wavelength-emitting to long-wavelength-emitting tryptophan residues and thus could be easily observed by a number of time-resolved and steady-state fluorescence techniques. Unexpectedly, no signature of inter-tryptophan energy transfer was found.     

The effect of habitat and human disturbance on the spatiotemporal activity of two urban carnivores: The results of an intensive camera trap study

With rising urbanization, the presence of urban wildlife is becoming more common, increasing the need for wildlife‐friendly spaces in urban planning. Despite this, understanding is limited to how wildlife exploits urban environments and interacts with human populations, and this is vital to our ability to manage and conserve wildlife in urban habitats. Here, we investigate how two urban mammal species, the red fox (Vulpes vulpes) and the European badger (Meles meles), exploit urban environments. Using intensive camera trap surveys, we assessed how habitat and human disturbance influenced the spatiotemporal activity of these species across south‐west London. Firstly, we found elevated activity levels of both species at boundaries and within built‐up areas, suggesting movement paths follow anthropogenic features. However, badgers were most active in woodland, indicating the importance of high cover habitats suitable for setts and foraging. Secondly, we found badger activity levels were negatively affected by human activity, whilst foxes were unaffected. Further investigation suggested foxes may adapt their activity patterns to avoid human disturbance, with badger activity patterns less plastic. Whilst the results of this study are useful for both the conservation and management of urban wildlife populations, these results also show potential factors which either facilitate or limit wildlife from fully exploiting urban environments.