Data-driven modelling makes quantitative predictions regarding bacteria surface motility.

In this work, we quantitatively compare computer simulations and existing cell tracking data of P. aeruginosa surface motility in order to analyse the underlying motility mechanism. We present a three dimensional twitching motility model, that simulates the extension, retraction and surface association of individual Type IV Pili (TFP), and is informed by recent experimental observations of TFP. Sensitivity analysis is implemented to minimise the number of model parameters, and quantitative estimates for the remaining parameters are inferred from tracking data by approximate Bayesian computation. We argue that the motility mechanism is highly sensitive to experimental conditions. We predict a TFP retraction speed for the tracking data we study that is in a good agreement with experimental results obtained under very similar conditions. Furthermore, we examine whether estimates for biologically important parameters, whose direct experimental determination is challenging, can be inferred directly from tracking data. One example is the width of the distribution of TFP on the bacteria body. We predict that the TFP are broadly distributed over the bacteria pole in both walking and crawling motility types. Moreover, we identified specific configurations of TFP that lead to transitions between walking and crawling states.

A non-lethal stable isotope analysis of valued freshwater predatory fish using blood and fin tissues as alternatives to muscle tissue.

Stable isotope analysis (SIA) is widely used to study trophic ecology and food webs in aquatic ecosystems. In the case of fish, muscle tissue is generally preferred for SIA, and the method is lethal in most cases. We tested whether blood and fin clips can be used as non-lethal alternatives to muscle tissue for examining the isotopic composition of two freshwater predatory fish, European catfish (Silurus glanis) and Northern pike (Esox lucius), species of high value for many freshwater systems as well as invasive species in many others. Blood samples from the caudal vein, anal fin clips, and dorsal muscle obtained by biopsy punch were collected from four catfish and pike populations (14-18 individuals per population). Subsequently, these samples were analyzed for δ13C and δ15N. The effects of alternative tissues, study site, and fish body mass on the isotopic offset were investigated. Both species showed a correlation between the isotopic offset and the tissue type, as well as the study site, but no significant relationship with the body mass. The isotopic offsets between tissues were used to calculate the conversion equations. The results demonstrated that both blood and fin clips are suitable and less invasive alternative to muscle in SIA studies focused on European catfish and Northern pike. Blood provided better correspondence to muscle isotope values. However, our results clearly demonstrated that isotopic offsets between tissues vary significantly among populations of the same species. Therefore, obtaining a muscle biopsy from several individuals in any population is advisable to gain initial insights and establish a possible population-specific inter-tissue conversion.

Development of a Multi-technique Characterization Portfolio for Stainless Steels Exposed to Magnox Reprocessing Liquors.

AISI Type 304 stainless steel coupons have been exposed to a simulant aqueous environment representative of the Magnox Reprocessing Plant (MRP) at Sellafield, UK. The experiments were performed for extended time periods (up to 420 days) at elevated temperatures to develop a comprehensive understanding of the extent, nature, and depth of contamination for pipework and vessels in Magnox spent nuclear fuel reprocessing environments. This will inform upcoming decommissioning work which represents a major post-operational challenge. Previous relevant literature has focused on developing fundamental understanding of contamination mechanisms of stainless steels in simplistic, single-element systems, which lack elements of industrial relevance. Contamination behavior is expected to be drastically different in these more complex environments. A characterization portfolio has been developed to enable detailed assessment of corrosion and contamination behavior in acidic reprocessing environments. Solution, surface, and depth analysis determined that uptake was dominated by the elements present in highest concentrations within the environment, namely, Mg, Nd, and Cs. Most contaminants were incorporated into a relatively thin surface oxide layer (<100 nm) in metal oxide form, although there were some exceptions (Cs and Sr). Grain boundary etching was present despite very low corrosion rates (3 µm year-1). As a result of this lack of corrosion, diffusion of contaminants beyond the immediate surface (10-20 nm) did not occur, evidenced through depth profiling. As a result of these findings, surface-based decontamination techniques minimizing excess secondary waste generation can be further developed in order to reduce the environmental and economic burden associated with decommissioning activities.

Trophic Position of the Species and Site Trophic State Affect Diet Niche and Individual Specialization: From Apex Predator to Herbivore.

Intra-species variability in isotopic niches, specifically isotopic total niche width (ITNW), isotopic individual niche width (IINW), and isotopic individual specialization (IIS), was studied using an innovative approach without sacrificing the vertebrates. Stable isotopes (δ13C, δ15N) in four body tissues differing in isotopic half-life were analyzed from four freshwater fish species representing different trophic positions. ITNW was widest for the apex predator (European catfish) and narrowest for the obligate predator (Northern pike). IINW exhibited a polynomial trend for the European catfish, Northern pike, and Eurasian perch (mesopredator), decreasing with body mass and increasing again after exceeding a certain species-dependent body mass threshold. Thus, for ectotherms, apex predator status is linked rather to its size than to the species. In herbivores (rudd), IINW increased with body mass. The IIS of predators negatively correlated with site trophic state. Therefore, eutrophication can significantly change the foraging behavior of certain species. We assume that the observed trends will occur in other species at similar trophic positions in either aquatic or terrestrial systems. For confirmation, we recommend conducting a similar study on other species in different habitats.

Diverse environmental cues drive the size of reproductive aggregation in a rheophilic fish.

BACKGROUND: Animal migrations are periodic and relatively predictable events, and their precise timing is essential to the reproductive success. Despite large scientific effort in monitoring animal reproductive phenology, identification of complex environmental cues that determine the timing of reproductive migrations and temporal changes in the size of reproductive aggregations in relation to environmental variables is relatively rare in the current scientific literature. METHODS: We tagged and tracked 1702 individuals of asp (Leuciscus aspius), a large minnow species, and monitored with a resolution of one hour the size of their reproductive aggregations (counts of sexes present at the breeding grounds standardized by the sum of individuals in the season) over seven breeding seasons using passive integrated transponder tag systems. We examined the size of reproductive aggregations in relation to environmental cues of day number within a reproductive season (intra-year seasonality), water temperature, discharge, hour in a day (intra-day pattern), temperature difference between water and air, precipitation, atmospheric pressure, wind speed and lunar phase. A generalized additive model integrating evidence from seven breeding seasons and providing typical dynamics of reproductive aggregations was constructed. RESULTS: We demonstrated that all environmental cues considered contributed to the changes in the size of reproductive aggregations during breeding season, and that some effects varied during breeding season. Our model explained approximately 50% of the variability in the data and the effects were sex-dependent (models of the same structure were fitted to each sex separately, so that we effectively stratified on sex). The size of reproductive aggregations increased unimodally in response to day in season, correlated positively with water temperature and wind speed, was highest before and after the full moon, and highest at night (interacting with day in a season). Males responded negatively and females positively to increase in atmospheric pressure. CONCLUSION: The data demonstrate complex utilization of available environmental cues to time reproductive aggregations in freshwater fish and their interactions during the reproductive season. The study highlights the need to acquire diverse data sets consisting of many environmental cues to achieve high accuracy of interpretation of reproductive timing.

Different hosts in different lakes: prevalence and population genetic structure of plerocercoids of Ligula intestinalis (Cestoda) in Czech water bodies.

Ligula intestinalis (Linnaeus, 1758) is a tapeworm parasite with a worldwide distribution that uses a wide variety of fish species as its second intermediate host. In the present study, we investigated the prevalence and population genetic structure of plerocercoids of L. intestinalis in five common cyprinoid species, roach Rutilus rutilus (Linnaeus), freshwater bream Abramis brama (Linnaeus), white bream Blicca bjoerkna (Linnaeus), bleak Alburnus alburnus (Linnaeus), and rudd Scardinius erythrophthalmus (Linnaeus), collected in six water bodies of the Czech Republic (Milada, Most, Medard, Jordán, Rímov and Lipno). Of the six study sites, the highest frequency of parasitism was recorded in Lake Medard (15%). The overall prevalence rate among the species was as follows: roach > rudd ≥ freshwater bream > bleak > white bream. Two mitochondrial genes (cytb and COI) were used to compare the population genetic structure of parasite populations using selected samples from the five fish species. The results of the phylogenetic analysis indicated that all populations of L. intestinalis were placed in Clade A, previously identified as the most common in Europe. At a finer scale, haplotype network and PCoA analyses indicated the possible emergence of host specificity of several mtDNA haplotypes to the freshwater bream. Moreover, pairwise Fixation indices (FST) revealed a significant genetic structure between the parasite population in freshwater bream and other host species. Parasite populations in roach not only showed the highest rate of prevalence but also depicted a maximum number of shared haplotypes with populations from bleak and rudd. Our results suggest that recent ecological differentiation might have influenced tapeworm populations at a fine evolutionary scale. Thus, the differences in prevalence between fish host species in different lakes might be influenced not only by the parasite's ecology, but also by its genetic diversity.

Hydropeaking causes spatial shifts in a reproducing rheophilic fish.

The hydropeaking regime below hydropower facilities represents a serious threat to riverine fauna and may cause declines in populations living under its influence. However, the knowledge on direct fish responses to the threat of hydropeaking is limited. Here, we aimed to test whether the hydropeaking generated 12 km upstream may have a negative effect on the position of actively spawning rheophilic fish, asp, Leuciscus aspius. Two passive telemetry antenna arrays were used to record fish position on the spawning ground. We monitored the position of spawning fish (545, 764 and 852 individuals) in three one-month long spawning seasons in 2017-2019 and related the changes in detection probability on the two antenna arrays to flow conditions, temperature, time of a day and individual fish ID. The fish detection on the spawning ground was negatively affected by the flow change (both increase and decrease) in time. Moreover, the probability of fish detection was also influenced by water temperature, the time of the day and, as seen from the magnitude of individual random effect variability, the detection probability was rather individual-specific. Hydropeaking resulted in the change of spawning behaviour and likely caused interruption of spawning or shifting spawning outside the optimal area for egg development. We therefore advise to reduce the hydropeaking regime during the rheophilic fish spawning season under fisheries or conservation interests.

Alignment of Biological Sequences with Jalview.

In this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments. A workflow is described based on Jalview's core functions: from data import to figure generation, including import of alignment reliability scores from T-Coffee and use of Jalview from the command line. The accompanying notes provide background information on the underlying methods and discuss additional options for working with Jalview to perform multiple sequence alignment, functional site analysis, and publication of alignments on the web.

Impacts of the COVID-19 pandemic on field instruction and remote teaching alternatives: Results from a survey of instructors.

Education in ecology and evolution often utilizes field instruction to teach key learning outcomes. Remote teaching of learning outcomes that have been traditionally taught in the field, necessitated by the COVID-19 pandemic, presents unique challenges for students, instructors, and institutions. A survey of 117 faculty conducted during spring 2020 revealed substantial reduction of learning outcomes typically taught in the field, and frequent substitutions of less active and more instructor-centered remote activities for field activities. The survey revealed generally negative instructor views on many remote teaching substitutions, yet also showed several approaches that instructors regarded as more effective, despite potential challenges with equitably teaching them. I suggest several models of remote substitutions for traditional field teaching of identification, field techniques, data collection, and study design in the context of the results of this survey.

Negative feedback concept in tagging: Ghost tags imperil the long-term monitoring of fishes.

Wildlife monitoring using passive telemetry has become a robust method for investigating animal migration. With increased use, this method progressively pollutes the environment with technological waste represented by so called ghost tags (PIT tags ending in the environment due to reproductive expulsions, shedding or animal mortality). However, their presence in the environment may lead to failed detections of living individuals. We used tagging data from studies of the asp Leuciscus aspius and the bleak Alburnus alburnus collected from 2014 to 2018 and located ghost tag positions on the monitored spawning site using portable backpack reader for their detection. We modelled virtual river-wide flat-bed antennas (widths 0.2, 0.4, 0.6 and 0.8 m) representing monitoring effort and estimated the probability of the presence of ghost tags within the antenna field. Of 3724 PIT tags used in the study, we detected on the spawning ground 173 ghost tags originating from long-term monitoring. The ghost tags accumulated in the environment in time, suggesting insufficient degradation rate or shift downstream from the research site. Number of ghost tags present on the spawning ground led to high probability of disabled readings of tagged fish passing through the antenna electro-magnetic field. We demonstrate how accumulated ghost tags may cause detection failures for focal species and incomplete data acquisition. We infer that intensive long-term monitoring using PIT tag technology may encumber future data acquisition or entail additional costs for clean-up.

Testing the applicability of tagging the Great crested newt (Triturus cristatus) using passive integrated transponders.

Tracking individual animals with small-sized passive integrated transponder tags (PIT tags) has become a popular and widespread method, one which can be used for investigating life history traits, including dispersal patterns of small protected animals such as newts. In this study, we tested the applicability of PIT tag usage for individual marking with the Great crested newt (Triturus cristatus) as a model amphibian species, and to test the detection of the newts in nature using a passive telemetry system. Clove oil was used as an anaesthetic before surgery. We implanted PIT tags under the skin of 140 newts. The survival rate of newts was 98.57%. X-ray images were taken to check the exact positions of the PIT tags. Since approximately 15.71% of the newts were capable of expelling the tag from their bodies, tag loss has to be accounted for in future behavioural studies dealing with newts and other amphibians potentially capable of frequent tag expulsion. Lastly, we detected by passive telemetry 97 individuals out of 100 released into a natural breeding pond. Males had higher activity (13 detected males vs 7 females per hour) than females, thus males could be detected if present with more certainty. The result of the movement behaviour showed that e.g. the male of T. cristatus in a breeding pond can travel up to 20 m in 78 seconds. In summary, this promising method could allow the automatic data collection of marked newts in aquatic as well as in terrestrial biotopes, providing data on their dispersal, diurnal activity and movement behaviour.

The pros and cons of the invasive freshwater apex predator, European catfish Silurus glanis, and powerful angling technique for its population control.

Catfish have spread across Europe and several countries out of this region within the last decades. Basic knowledge of this apex predator has revealed concerns of invasive behaviour and questions regarding its utilization as a biomanipulation species. However, a method enabling its regulation to a required level has not yet been developed. We simulated the impact of angling on the catfish population by method of hook-lines in two post-mining lakes with a monitored population consisting of tagged individuals and in two reservoirs as reference sites. Further, the efficiency of hook-lines as a reducing device was examined and the economic aspects were determined. Catfish population in localities where the species is unwanted or invasive may be efficiently reduced to a harmless level by hook-lines and angling (depending on the approach of anglers). The most efficient time of the year seems to be spring to early summer with catch efficiency of 5.4 individuals per 10 baits in one day. The catch efficiency markedly decreased during the second part of the year and did not exceed 2.8 individuals per 10 baits in one day. Mean size of catfish had negative impact whereas catfish biomass had positive impact on the catch efficiency. Trophic status and number of catfish in the locality had no impact on the catch efficiency. According to model, 11-18 bait-days per 1 ha per season is efficient to decrease catfish population to 10% of the original size. Both angling and hook-lines are very simple, they are financially and time bearable mechanisms of catfish regulation in any condition. However, catfish play an important role as a biomanipulative species in many localities. In this case where catfish is beneficial, angling presents a real threat of population collapse and loss of the biomanipulative effect.

Effect of Topographical Steps on the Surface Motility of the Bacterium Pseudomonas aeruginosa.

Bacteria traverse surfaces as part of colonizing solids, and it is of interest to hinder this motion to potentially thwart infections in humans. Here, we demonstrate that topographical steps hinder the ability of Pseudomonas aeruginosa PAO1 (P. aeruginosa) to traverse a solid-liquid interface. Using time-lapse fluorescence microscopy and image analysis, we analyzed the motion of P. aeruginosa that were challenged with steps ranging in height from 0.4 to 9.0 µm. Bacterial trajectories are sensitive to the height of the step, the curvature of the step face, and the direction of their motion relative to gravity. When the step height is ≥0.9 µm, which is similar to the cell diameter, there is a reduced probability of the cell crossing the step. For those bacteria that do cross a step, there is a time penalty for crossing steps of height 2-3 µm; this height is similar to the length of the bacterium. For higher steps, the bacteria reorient their cell body while traversing the step riser. Our findings elucidate how topography influences the motion of bacteria and informs strategies for hindering bacterial motion at surfaces.

Nocturnal spawning as a way to avoid egg exposure to diurnal predators.

Animals that do not provide parental care have to secure the survival of their offspring by ensuring a safe reproductive environment or smart timing tactics. Nocturnal spawning behaviour of many fish species is an example of the latter behaviour in the animal kingdom and is hypothesized to provide a survival advantage to the eggs spawned during the night. In order to test the efficiency of the smart timing tactics in a freshwater fish, a study was carried out of the interaction of the rheophilic spawner (asp Leuciscus aspius) and the predator of its drifting eggs (bleak Alburnus alburnus) using passive telemetry. According to a model based on acquired data, asp laid 63% of its eggs at night, while vision-oriented bleak was present in 92% of the time during the day. This study gives support to the predator avoidance hypothesis, which expects animals to reproduce in a period when the probability of offspring predation is at its lowest.

Invasive round goby Neogobius melanostomus has sex-dependent locomotor activity and is under-represented in catches from passive fishing gear compared with seine catches.

The higher proportion of males of the invasive round goby Neogobius melanostomus in samples from two activity selective passive fishing gears compared with one activity non-selective fishing gear in three Dutch lakes is related to higher male locomotory activity and is a sex-dependent trait. This difference in activity reflects the different ecology of male and female N. melanostomus.

JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure.

Summary: JABAWS 2.2 is a computational framework that simplifies the deployment of web services for Bioinformatics. In addition to the five multiple sequence alignment (MSA) algorithms in JABAWS 1.0, JABAWS 2.2 includes three additional MSA programs (Clustal Omega, MSAprobs, GLprobs), four protein disorder prediction methods (DisEMBL, IUPred, Ronn, GlobPlot), 18 measures of protein conservation as implemented in AACon, and RNA secondary structure prediction by the RNAalifold program. JABAWS 2.2 can be deployed on a variety of in-house or hosted systems. JABAWS 2.2 web services may be accessed from the Jalview multiple sequence analysis workbench (Version 2.8 and later), as well as directly via the JABAWS command line interface (CLI) client. JABAWS 2.2 can be deployed on a local virtual server as a Virtual Appliance (VA) or simply as a Web Application Archive (WAR) for private use. Improvements in JABAWS 2.2 also include simplified installation and a range of utility tools for usage statistics collection, and web services querying and monitoring. The JABAWS CLI client has been updated to support all the new services and allow integration of JABAWS 2.2 services into conventional scripts. A public JABAWS 2 server has been in production since December 2011 and served over 800 000 analyses for users worldwide. Availability and implementation: JABAWS 2.2 is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws. Contact: g.j.barton@dundee.ac.uk.

Early life-history predator-prey reversal in two cyprinid fishes.

Predator-prey relationships are often perceived simply as a situation in which a predator enhances its own fitness while reducing the fitness of its prey. However, this relationship may become reversed when the prey feeds on the juvenile predator stages. We investigated this phenomenon in a model asp (Leuciscus aspius; predator)-bleak (Alburnus alburnus; prey) relationship. The adhesive asp eggs are available for bleak predation after a spawning event for only tens of seconds before they adhere to the stones, where bleak do not forage. Gut content analysis demonstrated that eggs were utilized in high quantities, especially in the spawning peak of the asp reproductive season. Furthermore, using underwater video, we recorded the bleak feeding efficiency on naturally drifting asp eggs as the percentage of eggs eaten. Within the 40 cm egg trajectory captured by our cameras, total egg mortality was 21.2 ± 2.2% on average. The highest survival chances occurred among eggs drifting in aggregations, since the short drifting distance together with their aggregated distribution satiated bleak and part of the egg aggregation could attach to the spawning ground. This study emphasizes the potential efficiency of predator egg utilization by prey, which may have further consequences in predator-prey dynamics.

Active Vertex Model for cell-resolution description of epithelial tissue mechanics.

We introduce an Active Vertex Model (AVM) for cell-resolution studies of the mechanics of confluent epithelial tissues consisting of tens of thousands of cells, with a level of detail inaccessible to similar methods. The AVM combines the Vertex Model for confluent epithelial tissues with active matter dynamics. This introduces a natural description of the cell motion and accounts for motion patterns observed on multiple scales. Furthermore, cell contacts are generated dynamically from positions of cell centres. This not only enables efficient numerical implementation, but provides a natural description of the T1 transition events responsible for local tissue rearrangements. The AVM also includes cell alignment, cell-specific mechanical properties, cell growth, division and apoptosis. In addition, the AVM introduces a flexible, dynamically changing boundary of the epithelial sheet allowing for studies of phenomena such as the fingering instability or wound healing. We illustrate these capabilities with a number of case studies.

Growth rate variation among passerine species in tropical and temperate sites: an antagonistic interaction between parental food provisioning and nest predation risk.

Causes of interspecific variation in growth rates within and among geographic regions remain poorly understood. Passerine birds represent an intriguing case because differing theories yield the possibility of an antagonistic interaction between nest predation risk and food delivery rates on evolution of growth rates. We test this possibility among 64 Passerine species studied on three continents, including tropical and north and south temperate latitudes. Growth rates increased strongly with nestling predation rates within, but not between, sites. The importance of nest predation was further emphasized by revealing hidden allometric scaling effects. Nestling predation risk also was associated with reduced total feeding rates and per-nestling feeding rates within each site. Consequently, faster growth rates were associated with decreased per-nestling food delivery rates across species, both within and among regions. These relationships suggest that Passerines can evolve growth strategies in response to predation risk whereby food resources are not the primary limit on growth rate differences among species. In contrast, reaction norms of growth rate relative to brood size suggest that food may limit growth rates within species in temperate, but not tropical, regions. Results here provide new insight into evolution of growth strategies relative to predation risk and food within and among species.