Biology subjects

Dolezal, M.

Publications and source records attributed to Dolezal, M..

8 recordsLinked to original sources

bioRxiv2025

The inner dynamics of positive human-animal interactions: investigating the roles of oxytocin, opioids, dopamine, serotonin and the proteome

Research on the neuroendocrine basis of positive interactions has predominantly focused on oxytocin (OT), although dopamine (DA) and opioids also play crucial roles. Furthermore, these neurotransmitters are known to interact with each other but have seldom been studied concurrently. In this study, we quantified longitudinal changes in these neurotransmitters using a within-subject, 2 x 2 factorial design by varying human familiarity (familiar versus unfamiliar) and contact type (positive contacts versus ignoring) for 10 min human-pig interaction sessions. We repeatedly sampled cerebrospinal fluid from 10 pigs through a spinal catheter 65 and 5 min before the test and at 10, 30, 60, 120 and 240 min after the start of the test. Samples at various timepoints were analysed for OT, DA metabolites 3,4-dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA), serotonin metabolite 5-hydroxyindoleacetic acid (5-HIAA), {beta}-endorphin opioids concentrations, and using proteomics to explore novel protein candidates. The test condition (human familiarity x contact type) had a significant effect on the concentration of {beta}-endorphin (F1,118.59 = 4.45; P = 0.04) and 5-HIAA (F1,73.47 = 5.02; P = 0.03), and tended to affect the concentration of oxytocin (F1, 119.8 = 3.19; P = 0.08) and DOPAC (F1,70.57 = 3.31; P = 0.07), but pair-wise comparisons were not significant. There was only a minor effect on the pigs behaviour, which suggests that the test conditions may have had limited effect. Nevertheless, this approach provides a valuable method to study neurotransmitter changes over time and simultaneously. Highlights- Oxytocin was higher when pigs were ignored than when they had positive contacts - Oxytocin was highest in the novel condition of an unfamiliar human ignoring the pig - Human familiarity and contact type affected {beta}-endorphin and 5-HIAA concentrations - Dopamine metabolites and the proteome were not affected by the test conditions

animal behavior and cognition↗

bioRxiv2025

Tracking polygenic adaptation: phenotypic stasis after rapid adaptation in large populations of Drosophila

Most adaptive traits have a polygenic basis, and their evolution in response to environmental change results from the cumulative effect of many underlying loci. Theoretical studies predict two phases of phenotypic evolution: an initial directional phase, characterized by shifts in the mean of the trait towards a new optimum; and a subsequent stabilizing phase, in which the mean phenotype remains constant. However, there is limited empirical evidence to confirm these predictions. We exposed six replicate populations of Drosophila simulans, each with 100,000 individuals, to a new high-protein diet for 31 generations. Using time-series of high-order and molecular phenotypes, we characterized the phases of polygenic adaptation and inferred the transition between the directional and stabilizing selection phases empirically. The initial (directional) phase was characterized by a rapid phenotypic response, followed by a plateau after seven generations of adaptation, suggesting proximity to the new trait optimum (i.e. the stabilizing phase). The phenotypic responses were highly parallel among the replicate populations throughout the experiment. The contribution of pleiotropic loci to adaptive phenotypic evolution varied across the different phases of adaptation. Adaptation throughout the experiment was mainly facilitated by genes with low-to-intermediate pleiotropy, while highly pleiotropic genes played a significant role in the initial phase of adaptation. Parallel evolutionary responses across the replicate populations were also driven by genes with low-to-intermediate pleiotropy. Our findings support the predictions of theoretical models and provide empirical evidence for directional and stabilizing phases of polygenic adaptation.

evolutionary biology↗

bioRxiv2021

Genome-wide selection signatures reveal widespread synergistic effects of culture conditions and temperature stress in Drosophila melanogaster

Experimental evolution combined with whole-genome sequencing is a powerful approach to study the adaptive architecture of selected traits, in particular when replicated experimental populations evolving in opposite selective conditions (e.g. hot vs. cold temperature) are compared. Nevertheless, such comparisons could be affected by environmental effects shared between selective regimes (e.g. laboratory adaptation), which complicate the interpretation of selection signatures. Here, we used an experimental design, which takes advantage of the simplicity of selection signatures from founder populations with reduced variation, to study the fitness consequences of the laboratory environment (culture conditions) at two temperature regimes. After 20 generations of adaptation at 18{degrees}C and 29{degrees}C, strong genome-wide selection signatures were observed. About one third of the selection signatures can be either attributed to temperature effects, laboratory adaptation or the joint effects of both. The fitness consequences reflecting the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions, fitting the pattern of larger expression differences between founders at 29{degrees}C. We propose that evolve and resequence (E&R) with reduced genetic variation allows to study genome-wide fitness consequences driven by the interaction of multiple environmental factors.

evolutionary biology↗

bioRxiv2021

The mycobacterial guaB1 gene encodes a guanosine 5'-monophosphate reductase with a cystathione-β-synthase domain

Purine metabolism plays a pivotal role in bacterial life cycle, however, regulation of the de novo and purine salvage pathways have not been extensively detailed in mycobacteria. By gene knockout, biochemical and structural analyses, we identified Mycobacterium smegmatis (Msm) and Mycobacterium tuberculosis (Mtb) guaB1 gene product as a novel type of guanosine 5-monophosphate reductase (GMPR), which recycles guanosine monophosphate to inosine monophosphate within the purine salvage pathway and contains cystathione {beta}-synthase (CBS) domains with atypical orientation in the octamer. CBS domains share a much larger interacting area with a conserved catalytic domain in comparison with the only known CBS containing protozoan GMPR and closely related inosine monophosphate dehydrogenase structures. Our results revealed essential effect of pH on allosteric regulation of Msm GMPR activity and oligomerization with adenine and guanosine nucleotides binding to CBS domains.Bioinformatic analysis indicated the presence of GMPRs containing CBS domains across the entire Actinobacteria phylum.

biochemistry↗

bioRxiv2021

Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation

Many adaptive traits are polygenic and frequently more loci contributing to the phenotype than needed are segregating in populations to express a phenotypic optimum. Experimental evolution provides a powerful approach to study polygenic adaptation using replicated populations adapting to a new controlled environment. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequencing (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29{degrees}C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.

evolutionary biology↗

bioRxiv2021

Fine mapping without phenotyping: Identification of selection targets in secondary Evolve and Resequence experiments

Evolve and Resequence (E&R) studies investigate the genomic selection response of populations in an Experimental Evolution setup. Despite the popularity of E&R, empirical studies in sexually reproducing organisms typically suffer from an excess of candidate loci due to linkage disequilibrium, and single gene or SNP resolution is the exception rather than the rule. Recently, so-called "secondary E&R" has been suggested as promising experimental follow-up procedure to confirm putatively selected regions from a primary E&R study. Secondary E&R provides also the opportunity to increase mapping resolution by allowing for additional recombination events, which separate the selection target from neutral hitchhikers. Here, we use computer simulations to assess the effect of different crossing schemes, population size, experimental duration, and number of replicates on the power and resolution of secondary E&R. We find that the crossing scheme and population size are crucial factors determining power and resolution of secondary E&R: a simple crossing scheme with few founder lines consistently outcompetes crossing schemes where evolved populations from a primary E&R experiment are mixed with a complex ancestral founder population. Regardless of the experimental design tested, a population size of at least 4,800 individuals, which is roughly 5 times larger than population sizes in typical E&R studies, is required to achieve a power of at least 75%. Our study provides an important step towards improved experimental designs aiming to characterize causative SNPs in Experimental Evolution studies. SignificanceDespite the popularity of Evolve and Resequence (E&R) to investigate genomic selection responses, most studies that use sexually reproducing organisms have broad selection signatures and an excess of candidate loci due to linkage disequilibrium. In this study, we use computer simulations and statistical modelling to evaluate the effects of different experimental and population genetic parameters on the success of potential follow-up experiments (=secondary E&R) aiming to validate and fine-map selection signatures of primary studies. We found that a large population size in combination with a simple crossing scheme is key to the success of secondary E&R in Drosophila.

evolutionary biology↗

bioRxiv2019

Secondary evolve and re-sequencing: an experimental confirmation of putative selection targets without phenotyping

Evolve and re-sequencing (E&R) studies investigate the genomic responses of adaptation during experimental evolution. Because replicate populations evolve in the same controlled environment, consistent responses to selection across replicates are frequently used to identify reliable candidate regions that underlie adaptation to a new environment. However, recent work demonstrated that selection signatures can be restricted to one or a few replicate(s) only. These selection signatures frequently have a weak statistical support, and given the difficulties of functional validation, additional evidence is needed before considering them as candidates for functional analysis. Here, we introduce an experimental procedure to validate candidate loci with weak or replicate-specific selection signature(s). Crossing an evolved population from a primary E&R experiment to the ancestral founder population reduces the frequency of candidate alleles that have reached a high frequency. We hypothesize that genuine selection targets will experience a repeatable frequency increase after the mixing with the ancestral founders if they are exposed to the same environment (secondary E&R experiment). Using this approach, we successfully validate two overlapping selection targets, which showed a mutually exclusive selection signature in a primary E&R experiment of Drosophila simulans adapting to a novel temperature regime. We conclude that secondary E&R experiments provide a reliable confirmation of selection signatures that are either not replicated or show only a low statistical significance in a primary E&R experiment. Such experiments are particularly helpful to prioritize candidate loci for time-consuming functional follow-up investigations.

molecular biology↗

bioRxiv2018

Polygenic adaptation fuels genetic redundancy in Drosophila

The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic - i.e. result from selection on a large number of genetic loci - but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes across many contributing loci. To resolve this, we use laboratory natural selection, a framework that is powerful enough to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among adaptive alleles. We observed convergent phenotypic responses, e.g. fitness, metabolic rate and fat content, and a strong polygenic response (99 selected alleles; mean s=0.061). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses. The observed genetic redundancy potentiates this genotypic variation through multiple genetic pathways leading to phenotypic convergence. This key property of adaptive alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.

evolutionary biology↗