Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding

Determining the host-parasitoid interactions and parasitism rates for invasive species entering novel environments is an important first step in assessing potential routes for biocontrol and integrated pest management. Conventional insect rearing techniques followed by taxonomic identification are widely used to obtain such data, but this can be time consuming and prone to biases. Here we present a Next Generation Sequencing approach for use in ecological studies which allows for individual level metadata tracking of large numbers of invertebrate samples through the use of hierarchically organised molecular identification tags. We demonstrate its utility using a sample data set examining both species identity and levels of parasitism in late larval stages of the Oak Processionary Moth (Thaumetopoea processionea - Linn. 1758), an invasive species recently established in the UK. Overall we find that there are two main species exploiting the late larval stages of Oak Processionary Moth in the UK with the main parasitoid (Carcelia iliaca - Ratzeburg, 1840) parasitising 45.7% of caterpillars, while a rare secondary parasitoid (Compsilura conccinata - Meigen, 1824) was also detected in 0.4% of caterpillars. Using this approach on all life stages of the Oak Processionary Moth may demonstrate additional parasitoid diversity. We discuss the wider potential of nested tagging DNA-metabarcoding for constructing large, highly-resolved species interaction networks

Foraminiferal biodiversity associated with cold-water coral carbonate mounds and open slope of SE Rockall Bank (Irish continental margin-NE Atlantic)

Cold-water coral (CWC) ecosystems are hotspots of macro- and microfaunal biodiversity and provide refuge for a wide variety of deep-sea species. We investigated how the abundance and biodiversity of 'live' (Rose Bengal stained) foraminifera varies with, and is related to, the occurrence of CWC on the Rockall Bank (NE Atlantic). Qualitative and quantitative analyses were performed on 21 replicate samples from 8 deep-sea stations, including 4 stations on CWC-covered carbonate mounds at depths of 567-657 m, and 4 stations on the adjacent slope at depths of 469-1958 m where CWC were absent. This sampling strategy enabled us to demonstrate that sediments surrounding the living CWC were characterised by higher foraminiferal abundance and biodiversity than open-slope sediments from the same area. A total of 163 foraminiferal species was identified. The dominant species in CWC sediments were: Spirillina vivipara, Allogromiid sp. 1. Globocassidulina subglobosa, Adercotryma wrighti, Eponides pusillus, Ehrenbergina carinata, Planulina ariminensis, Trochammina inflate and Paratrochammina challenged. Foraminifera were nearly absent in adjacent open slope areas subject to strong tidal currents and characterised by coarse grained deposits. We suggest that CWC create a heterogeneous three-dimensional substrate offering microhabitats to a diverse benthic foraminiferal community

Counterion adsorption on flexible polyelectrolytes: comparison of theories

Counterion adsorption on a flexible polyelectrolyte chain in a spherical cavity is considered by taking a "permuted" charge distribution on the chain so that the "adsorbed" counterions are allowed to move along the backbone. We compute the degree of ionization by using self-consistent field theory (SCFT) and compare with the previously developed variational theory. Analysis of various contributions to the free energy in both theories reveals that the equilibrium degree of ionization is attained mainly as an interplay of the adsorption energy of counterions on the backbone, the translational entropy of the small ions, and their correlated density fluctuations. Degree of ionization computed from SCFT is significantly lower than that from the variational formalism. The difference is entirely due to the density fluctuations of the small ions in the system, which are accounted for in the variational procedure. When these fluctuations are deliberately suppressed in the truncated variational procedure, there emerges a remarkable quantitative agreement in the various contributing factors to the equilibrium degree of ionization, in spite of the fundamental differences in the approximations and computational procedures used in these two schemes. Nevertheless, since the significant effects from density fluctuations of small ions are not captured by the SCFT, and due to the close agreement between SCFT and the other contributing factors in the more transparent variational procedure, the latter is a better computational tool for obtaining the degree of ionization

Alterações recentes nas razões isotópicas de Pb em sedimentos do Canhão Submarino de Cascais, Portugal

Temporal variations in lead concentrations and stable lead isotopic ratios in two sediment cores from the Cascais Canyon shows changes in sources of Pb during the last two centuries. The increase of total Pb contents wIth the evolution of Pb ratio recorded in both cores reveals the Increase of Pb from industrial sources. Nevertheless, this increase is lower in deeper core location (252-32) due to dilution and mixing with uncontaminated marine materials. An isotopic shift towards lower Pb/Pb in the shallower core (252-35) during the 1970s may reflect the increasing number of vehicles in the Lisboa area during that time

Equation of state for polymer liquid crystals: theory and experiment

The first part of this paper develops a theory for the free energy of lyotropic polymer nematic liquid crystals. We use a continuum model with macroscopic elastic moduli for a polymer nematic phase. By evaluating the partition function, considering only harmonic fluctuations, we derive an expression for the free energy of the system. We find that the configurational entropic part of the free energy enhances the effective repulsive interactions between the chains. This configurational contribution goes as the fourth root of the direct interactions. Enhancement originates from the coupling between bending fluctuations and the compressibility of the nematic array normal to the average director. In the second part of the paper we use osmotic stress to measure the equation of state for DNA liquid crystals in 0.1M to 1M NaCl solutions. These measurements cover 5 orders of magnitude in DNA osmotic pressure. At high osmotic pressures the equation of state, dominated by exponentially decaying hydration repulsion, is independent of the ionic strength. At lower pressures the equation of state is dominated by fluctuation enhanced electrostatic double layer repulsion. The measured equation of state for DNA fits well with our theory for all salt concentrations. We are able to extract the strength of the direct electrostatic double layer repulsion. This is a new and alternative way of measuring effective charge densities along semiflexible polyelectrolytes.Comment: text + 5 figures. Submitted to PR

The Whittard Canyon - A case study of submarine canyon processes

Submarine canyons are large geomorphological features that incise continental shelves and slopes around the world. They are often suggested to be biodiversity and biomass hotspots, although there is no consensus about this in the literature. Nevertheless, many canyons do host diverse faunal communities but owing to our lack of understanding of the processes shaping and driving this diversity, appropriate management strategies have yet to be developed. Here, we integrate all the current knowledge of one single system, the Whittard Canyon (Celtic Margin, NE Atlantic), including the latest research on its geology, sedimentology, geomorphology, oceanography, ecology, and biodiversity in order to address this issue. The Whittard Canyon is an active system in terms of sediment transport. The net suspended sediment transport is mainly up-canyon causing sedimentary overflow in some upper canyon areas. Occasionally sediment gravity flow events do occur, some possibly the result of anthropogenic activity. However, the role of these intermittent gravity flows in transferring labile organic matter to the deeper regions of the canyon appears to be limited. More likely, any labile organic matter flushed downslope in this way becomes strongly diluted with bulk material and is therefore of little food value for benthic fauna. Instead, the fresh organic matter found in the Whittard Channel mainly arrives through vertical deposition and lateral transport of phytoplankton blooms that occur in the area during spring and summer. The response of the Whittard Canyon fauna to these processes is different in different groups. Foraminiferal abundances are higher in the upper parts of the canyon and on the slope than in the lower canyon. Meiofaunal abundances in the upper and middle part of the canyon are higher than on adjacent slopes, but lower in the deepest part. Mega- and macrofauna abundances are higher in the canyon compared with the adjacent slope and are higher in the eastern than the western branch. These faunal patterns reflect the fact that the Whittard Canyon encompasses considerable environmental heterogeneity, related to a combination of organic matter trapping, current regimes (due to focused internal tides) and different substrates. We conclude that coordinated observations of processes driving faunal patterns are needed at a fine scale in order to understand the functioning of communities in this and other submarine canyons

Adsorption of mono- and multivalent cat- and anions on DNA molecules

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure

Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions

The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete charge pattern on the protein surface are explicitly incorporated. For parameters roughly corresponding to lysozyme, we find that $B_2$ first decreases with added salt concentration up to a threshold concentration, then increases to a maximum, and then decreases again upon further raising the ionic strength. Our studies demonstrate that the existence of a discrete charge pattern on the protein surface profoundly influences the effective interactions and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek (DLVO) theory fail for large ionic strength. The observed non-monotonicity of $B_2$ is compared to experiments. Implications for protein crystallization are discussed.Comment: 43 pages, including 17 figure

Qualitative Evaluation of Common Quantitative Metrics for Clinical Acceptance of Automatic Segmentation:a Case Study on Heart Contouring from CT Images by Deep Learning Algorithms

Organs-at-risk contouring is time consuming and labour intensive. Automation by deep learning algorithms would decrease the workload of radiotherapists and technicians considerably. However, the variety of metrics used for the evaluation of deep learning algorithms make the results of many papers difficult to interpret and compare. In this paper, a qualitative evaluation is done on five established metrics to assess whether their values correlate with clinical usability. A total of 377 CT volumes with heart delineations were randomly selected for training and evaluation. A deep learning algorithm was used to predict the contours of the heart. A total of 101 CT slices from the validation set with the predicted contours were shown to three experienced radiologists. They examined each slice independently whether they would accept or adjust the prediction and if there were (small) mistakes. For each slice, the scores of this qualitative evaluation were then compared with the Sørensen-Dice coefficient (DC), the Hausdorff distance (HD), pixel-wise accuracy, sensitivity and precision. The statistical analysis of the qualitative evaluation and metrics showed a significant correlation. Of the slices with a DC over 0.96 (N = 20) or a 95% HD under 5 voxels (N = 25), no slices were rejected by the readers. Contours with lower DC or higher HD were seen in both rejected and accepted contours. Qualitative evaluation shows that it is difficult to use common quantification metrics as indicator for use in clinic. We might need to change the reporting of quantitative metrics to better reflect clinical acceptance

Effective interaction between helical bio-molecules

The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple model for B-DNA incorporating explicitly its charge pattern as a double-helix structure. The effective force and the effective torque exerted onto the molecules depend on the central distance and on the relative orientation. The contributions of nonlinear screening by monovalent counterions to these forces and torques are analyzed and calculated for different salt concentrations. As a result, we find that the sign of the force depends sensitively on the relative orientation. For intermolecular distances smaller than $6\AA$ it can be both attractive and repulsive. Furthermore we report a nonmonotonic behaviour of the effective force for increasing salt concentration. Both features cannot be described within linear screening theories. For large distances, on the other hand, the results agree with linear screening theories provided the charge of the bio-molecules is suitably renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog