Biology subjects

Cech, M.

Publications and source records attributed to Cech, M..

4 recordsLinked to original sources

bioRxiv2024

Hungry catfish - effect of prey availability on movement dynamics of a top predator

O_LIThe availability and spatial distribution of prey determines the energetic costs of predators foraging and largely drives their space use, activity level and foraging timing. Consequently, predators in ecosystems with different prey availability and distribution should adjust their movement patterns to optimise their foraging success in order to maximise efficiency. C_LIO_LIThe aim of this study was to investigate the ability of a top predator, European catfish (Silurus glanis), to adapt its space use, temporal activity and diet patterns in environments with varying prey density and distribution, and to examine the consequences for the catfishs body growth. C_LIO_LICatfish activity, tracked with high-resolution acoustic telemetry positioning systems deployed in two oligotrophic lakes with limited fish prey and one eutrophic reservoir with abundant fish prey, showed clear differences in their spatial and foraging behaviour. In oligotrophic, prey-poor lakes, catfish showed larger space use, altered diurnal activity patterns, reduced use of the open water, increased variability in inter- and intra-individual space use and had a more diverse diet compared to their conspecifics in the eutrophic, prey-rich reservoir. However, despite these behavioural alterations the reduced food availability in prey-poor lakes ultimately led to a reduced catfish growth, as these behavioural changes could not fully compensate for the lower prey fish abundance. C_LIO_LIThe study showed that top predators can combine different behavioural mechanisms and individual strategies to adapt to different ecological contexts. The observed ability of catfish to optimize activity, space use and diet highlights the evolutionary need to maximise foraging efficiency and overall fitness in different habitats, giving catfish a significant competitive advantage. Such competitive abilities are prerequisites for the actual catfish success as an invasive species within a Europe. C_LI

ecology↗

bioRxiv2022

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. In order to streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemos implementation and describe its broad range of functionality for designing, testing and executing Galaxy tools, workflows and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers. Planemo is a mature project widely used within the Galaxy community which has been downloaded over 80,000 times.

bioinformatics↗

bioRxiv2021

Influence of internal seiche dynamics on vertical movement of fish

O_LIInternal seiches are common in stratified lakes, with significant effects on stratification patterns, hydrodynamics and vertical nutrient transport. In particular, seiche can change the vertical distribution of the thermocline and the cold hypolimnetic and warm epilimnetic water masses by several meters on a timescale of a few hours. The results are rapid and strong changes in temperature profiles and oxygen availability that can have profound effects on vagrant and sessile organisms. Internal seiche dynamics could therefore affect fish communities directly through physiological stress and elevated mortality, and indirectly through prey distribution. C_LIO_LIThe aim of this study was to analyze the effects of internal seiche dynamics on lacustrine fish behaviour, and to characterize fish reaction patterns, with the main focus on vertical movement of fish in the vicinity of a shifting thermocline, and avoidance of cold hypolimnetic water. C_LIO_LIThe analysis was based on acoustic telemetry data from Lake Milada, a post-mining lake in the Czech Republic, with a total of 55 tracked individuals of four species: northern pike (Esox lucius), wels catfish (Silurus glanis), tench (Tinca tinca) and rudd (Scardinius erythropthalmus). C_LIO_LIThe effects of seiche dynamics on the four species studied were weak but significant during the day, but only on rudd during the night. Upward seiche produced stronger reactions in fish than downward seiche, and the effects were manifested only during the strongest seiche events. C_LIO_LIThermocline shifting during seiche events may induce a transient reduction in habitat for seiche-reacting species, thus potentially affecting predation and other inter- and intra-specific interactions, and probably affecting fish community dynamics. C_LI Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

ecology↗

bioRxiv2017

Community-driven data analysis training for biology

The primary problem with the explosion of biomedical datasets is not the data itself, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web-browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences.

bioinformatics↗