Transition to Piscivory Seen Through Brain Transcriptomics in a Juvenile Percid Fish: Complex Interplay of Differential Gene Transcription, Alternative Splicing, and ncRNA Activity.

Pikeperch (Sander Lucioperca) belongs to main predatory fish species in freshwater bodies throughout Europe playing the key role by reducing planktivorous fish abundance. Two size classes of the young-of-the-year (YOY) pikeperch are known in Europe and North America. Our long-term fish survey elucidates late-summer size distribution of YOY pikeperch in the Lipno Reservoir (Czechia) and recognizes two distinct subcohorts: smaller pelagic planktivores heavily outnumber larger demersal piscivores.

Long-lines for research monitoring and efficient population regulation of an invasive apex predator, European catfish ().

European catfish is a large-bodied apex predator, a key species in native areas, but invasive in others where it negatively impacts local aquatic fauna necessitates catfish regulation. However, traditional ichthyological methods face challenges in capturing it. The study presents a detailed description of the efficient long-line method, refined through 48 sampling campaigns across twelve European water bodies.

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.

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.

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.

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 (C, N) 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).

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.

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, Římov and Lipno).

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.

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.

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.

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

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 PAO1 () to traverse a solid-liquid interface. Using time-lapse fluorescence microscopy and image analysis, we analyzed the motion of that were challenged with steps ranging in height from 0.

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.

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.

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.

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.

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.

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.

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.

Tuned-aperture computed tomography versus parallax analog and digital radiographic images in detecting second mesiobuccal canals in maxillary first molars.

Objective: We sought to evaluate the detectability of second mesiobuccal (MB2) canals in the MB root of maxillary first molar teeth by comparing (1) parallax with pairs of conventional direct-exposure film intraoral radiographs (both D-speed and F-speed), (2) parallax with pairs of charge-coupled device-based digital images acquired through the use of Trophy RVG-ui, and (3) charge-coupled device-based images acquired through the use of a Trophy RVG-ui sensor and tomosynthetically reconstructed by TACT (tuned-aperture computed tomography) Workbench Software.

Study Design: Maxillary first molars were mounted in simulated bone. Pairs of images were generated by conventional D-speed and F-speed radiography and digital radiography with a charge-coupled device-based sensor, the RVG-ui.