Identification of the PcrA DNA helicase reaction pathway by applying advanced targeted molecular dynamic simulations

PcrA DNA helicase uses the free energy of hydrolysis and binding of ATP to unwind double-stranded DNA (ds-DNA). There are two states of PcrA, termed the substrate and product complexes and, through the conformational changes between these two states, PcrA moves along ds-DNA and separates the two strands. In this study, two different methods, namely chain minimisation (CM, less reliable method) and auto targeted molecular dynamic (TMD) simulation (more reliable), were performed to generate two different initial reaction pathways between these two states, and then fixed root mean square distance (RMSD) TMD simulation was performed to optimise these two initial pathways. In general, the two optimised pathways share very similar major conformational changes, but are different in the minor motions. The potential energy profiles of the two improved pathways are generally similar, but the one generated by the improved TMD path is slightly lower. Considering the poor reliability of the initial path generated by CM and insignificant improvements of the auto-TMD path, our study suggests that fixed RMSD TMD simulation can generate reliable reaction pathways, but the different initial paths still have some influence on the detailed conformational analysis.     

Particle size influences decay rates of environmental DNA in aquatic systems

Environmental DNA (eDNA) analysis is a powerful tool for remote detection of target organisms. However, obtaining quantitative and longitudinal information from eDNA data is challenging, requiring a deep understanding of eDNA ecology. Notably, if the various size components of eDNA decay at different rates, and we can separate them within a sample, their changing proportions could be used to obtain longitudinal dynamics information on targets. To test this possibility, we conducted an aquatic mesocosm experiment in which we separated fish-derived eDNA components using sequential filtration to evaluate the decay rate and changing proportion of various eDNA particle sizes over time. We then fit four alternative mathematical decay models to the data, building towards a predictive framework to interpret eDNA data from various particle sizes. We found that medium-sized particles (1–10 μm) decayed more slowly than other size classes (i.e., <1 and > 10 μm), and thus made up an increasing proportion of eDNA particles over time. We also observed distinct eDNA particle size distribution (PSD) between our Common carp and Rainbow trout samples, suggesting that target-specific assays are required to determine starting eDNA PSDs. Additionally, we found evidence that different sizes of eDNA particles do not decay independently, with particle size conversion replenishing smaller particles over time. Nonetheless, a parsimonious mathematical model where particle sizes decay independently best explained the data. Given these results, we suggest a framework to discern target distance and abundance with eDNA data by applying sequential filtration, which theoretically has both metabarcoding and single-target applications.     

Concentric photothermal coagulation with basket‐integrated optical device for treatment of tracheal stenosis

A basket‐integrated optical device is developed to consistently treat tubular tissue by centering an optical diffuser in the lumen. Four nitinol arms in conjunction with the optical diffusing applicator are deployed to induce homogeneous circumferential light emission and concentric photothermal coagulation on tracheal tissue. A 1470‐nm laser light is employed for the tissue testing at various irradiation conditions and evaluated in terms of thermal gradient and temperature evolution. Preliminary experiments on liver tissue demonstrate the concentric development of the radial thermal coagulation in the tissue (eccentric ratio = ~5.5%). The interstitial tissue temperature increases with the total amount of energy delivery (around 65°C). Ex vivo trachea testing yields up to 16.5% tissue shrinkage due to dehydration as well as uniform ablation of the cilia and goblet cells in a mucosa layer under 7‐W irradiation for 10 s. The proposed optical device may be a feasible therapeutic method to entail the circumferential coagulation in the tubular tissues in a reliable manner.      

Real‐time functional optical‐resolution photoacoustic microscopy using high‐speed alternating illumination at 532 and 1064 nm

Optical‐resolution photoacoustic microscopy (OR‐PAM), which has been widely used and studied as a noninvasive and in vivo imaging technique, can yield high‐resolution and absorption contrast images. Recently, metallic nanoparticles and dyes, such as gold nanoparticles, methylene blue, and indocyanine green, have been used as contrast agents of OR‐PAM. This study demonstrates real‐time functional OR‐PAM images with high‐speed alternating illumination at 2 wavelengths. To generate 2 wavelengths, second harmonic generation at 532 nm with an LBO crystal and a pump wavelength of 1064 nm is applied at a pulse repetition rate of 300 kHz. For alternating illumination, an electro‐optical modulator is used as an optical switch. Therefore, the A‐line rate for the functional image is 150 kHz, which is half of the laser repetition rate. To enable fast signal processing and real‐time displays, parallel signal processing using a graphics processing unit (GPU) is performed. OR‐PAM images of the distribution of blood vessels and gold nanorods in a BALB/c‐nude mouse's ear can be simultaneously obtained with 500 × 500 pixels and real‐time display at 0.49 fps.      

Geographic range determinants of two commercially important marine molluscs

Aim We modelled the spatial abundance patterns of two abalone species (Haliotis rubra Donovan 1808 and H. laevigata Leach 1814) inhabiting inshore rocky reefs to better understand the importance of current sea surface temperature (SST) (among other predictors) and, ultimately, the effect of future climate change, on marine molluscs. Location Southern Australia. Methods We used an ensemble species distribution modelling approach that combined likelihood‐based generalized linear models and boosted regression trees. For each modelling technique, a two‐step procedure was used to predict: (1) the current probability of presence, followed by (2) current abundance conditional on presence. The resulting models were validated using an independent, spatially explicit dataset of abalone abundance patterns in Victoria. Results For both species, the presence of reef was the main driver of abalone occurrence, while SST was the main driver of spatial abundance patterns. Predictive maps at c. 1‐km resolution showed maximal abundance on shallow coastal reefs characterized by mild winter SSTs for both species. Main conclusions Sea surface temperature was a major driver of abundance patterns for both abalone species, and the resulting ensemble models were used to build fine‐resolution predictive range maps (c. 1 km) that incorporate measures of habitat suitability and quality in support of resource management. By integrating this output with structured spatial population models, a more robust understanding of the potential impacts of threatening human processes such as climate change can be established.     

Some aspects of forest soil and litter ecology in the Dawyck Cryptogamic Sanctuary with a particular reference to fungi

Here we report on ecology and biodiversity of fungi in a unique mycological sanctuary in Britain, where data on species composition have been collected since 1994. To complement the biodiversity data by the information on the fungal ecological interactions and their role in the overall ecosystem functioning, soil properties and the composition of forest litter and field layer, bacterial population numbers and fungal biomass (in terms of ergosterol) were measured in 8 plots covered with different vegetations (beech, birch, birch-oak-beech, grass) over a May–Aug. period, and the results were analysed by correlation analysis and stepwise regression modelling together with data on protozoa and nematodes available from parallel research. The results highlighted the complexity of factors influencing temporal dynamics and spatial variability of fungal biomass in soil and forest litter. Most of the registered interactions appeared to be transient, and this should be taken into account while interpreting environmental observations. Interpretation of the specific relationships is given and implications for further research and overall ecosystem functioning are discussed.     

Mathematical modelling of primary production in Green Bay (Lake Michigan,USA), a phosphorus-and light-limited system

Application of mathematical models in the design and evaluation of lake restoration programmes must include due consideration of three basic concepts of model development; 1) that the model framework is appropriately matched to the intended management use, 2) that selection of the proper degree of model complexity is fundamental to the achievement of model credibility and 3) that field and laboratory studies must be designed and interpreted with the aid of the model to insure development of a comprehensive, integrated tool.These concepts are demonstrated for the case of lake restoration efforts in Green Bay (Lake Michigan, USA). Striking gradients in water quality (transparency, algal standing crop, hypolimnetic oxygen depletion) and trophic state occur along the major axis of the bay in response to phosphorus loaded from the Fox River. A simple model for gross primary production is developed to permit calculation of the relative importance of internal carbon production to the total organic carbon budget of the bay. Primary production varies from high rates over a limited photic depth in the turbid, phosphorus-rich waters of the eutrophic portions of the bay to low rates over an extensive photic depth in the transparent, phosphoruspoor reaches of the oligotrophic regions. Internal production accounts for approximately 90% of the total organic carbon loaded to the system over the summer growing season. Water quality management strategies must address the stimulation of primary production by phosphorus loaded from the Fox River in any attempt to lower the standing crop of nuisance algae, improve water clarity, and reduce rates of hypolimnetic oxygen depletion in Green Bay.     

Spatially modelling native vegetation condition

Summary   The assessment of vegetation condition is seen as an increasingly important requirement for effective biodiversity conservation in Australia. Condition assessments that operate at the scale of the site are well established. However, there is a need for mapped representations of vegetation condition at regional scales to: (i) assist with regional planning and target setting; (ii) provide regional context for site-based assessment; and (iii) monitor the change in vegetation condition at multiple scales. This paper describes a methodology for converting site condition data collected in plots into maps of vegetation condition across entire regions using a predictive statistical modelling framework (Generalized Additive Modelling) combined with a GIS. The research demonstrates how explanatory variables including topographic position, terrain roughness, landscape connectivity and remote sensing derived indices can be used to map the condition of native vegetation at the scale of a subcatchment. The inclusion of indices derived from remotely sensed imagery (SPOT4) as explanatory variables in the modelling is a novel component of this research. Although the methodology generates statistically and ecologically plausible models of vegetation condition, there are nevertheless limitations associated with the way plot data were collected and some of the explanatory variables, which impacts upon model utility. We discuss how these problems can be minimized when embarking upon studies of this type. We demonstrate how maps produced from exercises such as this could be used for conservation planning and discuss the limitations of these data for monitoring.     

Spatial segregation of specialists and generalists in bird communities

Each species generally has a close relationship with one or more habitats and can therefore be classified as either specialist or generalist. We studied whether specialist and generalist species are spatially distributed independently of each other. Repeating the analysis for 100 of the most frequent terrestrial bird species recorded over the 10 000 sampled sites of the French Breeding Bird survey, we found that specialists were more abundant if the rest of the community was specialized, and that the inverse was also true. This pattern was far subtler than just a simple dichotomy: most species actually presented a maximum abundance at a value of community specialization similar to their own level of specialization. Bird communities appear very well defined along a specialist–generalist gradient. We believe this pattern becomes more apparent with habitat degradation. The consequences on both ecological services and community resilience may well be considerable.